I am a Professor of Marine Biology at UTS, and Executive Director of the Climate Change Cluster (C3) in the Faculty of Science. I am also founder of the Deep Green Biotech Hub, member of the IOC-UNESCO Blue Carbon International Scientific Working Group and former leader of the CSIRO Marine and Coastal Carbon Biogeochemistry Cluster. Within C3, I lead two research programs: Algae Biosystems and Biotechnology, and Seagrass Health.
I have made significant advances in the understanding of photosynthetic processes in seagrass, coral, plankton, and algae growing at their environmental extremes. Currently, I am applying my knowledge of bio-optics and photosynthesis to develop new sensors, diagnostics and cultivation systems to develop the algae-biotechnology sector, as well as mitigate the impact of dredging on seagrasses. My research partners include international collaborators within the education, research and industry sectors.
Scientific Advisory Board of GzechGlobe Research Institute
Australia21 Algae Round Table Think Tank
National Greenhouse Accounts Wetlands Advisory Panel, Federal Department of Environment
Invited member of the Conservation International, IUCN, IOC?UNESCO International Blue Carbon Scientific Working Group
Member of the IMOS Bio-optical Working Group
ARC Selection Advisory Committee for Future Fellows
Member, Scientific Advisory Committee for the Sydney Institute of Marine Science (SIMS)
Review editor, Marine Ecology-Progress Series
Can supervise: YES
Algae-based bioproducts including the production of food, energy, green chemistry and bio-products using microalgae.
Mass scale agal cultivation to overcome commercialisation barriers in the algae-based biotechnology sector.
Photosynthetic efficient algae cultivation systems for the production of speciality chemicals, toxins, cosmetic components, valuable oils, foods for consumption, feeds for agriculture, nutraceuticals, biologics, vaccines and small molecules.
Dredging impact mitigation using optics, photobiology and molecular physiology to provide managers with the next generation of decision making tools.
Blue Carbon derived from seagrass and saltmarsh, and recognition of seagrasses and saltmarsh in carbon accounting.
Seagrass-bacteria interactome and understanding of the diversity of microorganisms associated with seagrass and the metabolic activity of this collective community of organisms, which is essential to coastal biogeochemical cycles.
Molecular physiology of seagrasses to understand the complex responses and adaptations of seagrasses to the marine environment, using advanced technologies (isotopic imaging, metabolomics and transcriptomics)
Marine Primary Producers and Climate Change
Coastal and Marine Ecosystems
Tropical Reef Ecosystems
GIS and Resource Assessments
Mapping and Remote Sensing
Biology and Ecology for Engineers
© Springer International Publishing AG, part of Springer Nature 2018. All rights reserved. This book takes the place of "Biology of Seagrasses: A Treatise on the Biology of Seagrasses with Special Reference to the Australian Region", co-edited by A.W.D. Larkum, A.J. MaCComb and S.A. Shepherd and published by Elsevier in 1989. The first book has been influential, but it is now 25 years since it was published and seagrass studies have progressed and developed considerably since then. The design of the current book follows in the steps of the first book. There are chapters on taxonomy, floral biology, biogeography and regional studies. The regional studies emphasize the importance of Australia having over half of the world's 62 species, including some ten species published for Australia since the previous book. There are a number of chapters on ecology and biogeography; fish biology and fisheries and dugong biology are prominent chapters. Physiological aspects again play an important part, including new knowledge on the role of hydrogen sulphide in sediments and on photosynthetic processes. Climate change, pollution and environmental degradation this time gain an even more important part of the book. Decline of seagrasses around Australia are also discussed in detail in several chapters. Since the first book was published two new areas have received special attention: blue carbon and genomic studies. Seagrasses are now known to be a very important player in the formation of blue carbon, i.e. carbon that has a long turnover time in soils and sediments. Alongside salt marshes and mangroves, seagrasses are now recognized as playing a very important role in the formation of blue carbon. And because Australia has such an abundance and variety of seagrasses, their role in blue carbon production and turnover is of great importance. The first whole genomes of seagrasses are now available and Australia has played an important role here. It appears that seagrasses have severa...
This book describes the latest advances in systems biology in four plant-based marine ecosystems: seaweeds, seagrasses, microalgae, and corals. Marine organisms that inhabit the oceanic environment experience a diverse range of environmental fluctuations, anthropogenic stress, and threats from invasive species and pathogens. System biology integrates physiology, genomics, transcriptomics, proteomics, and metabolomics into numerical models and is emerging as an important approach to elucidate the functional adaptations of marine organisms to adverse environmental conditions. This book focuses on how ecophysiology, omics platforms, their integration (a systems biology perspective), and next generation sequencing tools are being used to address the stress response of marine seaweeds, seagrasses, corals, marine microbe diversity, and micro-and macroalgae/corals-bacterial interactions to global climate change and anthropogenic activities. The contents of the book are of special interest to graduate and postgraduate marine biology students and marine biology researchers, particularly those interested in marine ecology, stress physiology of marine macrophytes/corals/phytoplankton, and environmental microbiology. This book would also be of interest to marine engineers engaged in the management and conservation of our valuable marine resources.
Sutherland, DL, Park, J, Heubeck, S, Ralph, PJ & Craggs, RJ 2020, 'Size matters – Microalgae production and nutrient removal in wastewater treatment high rate algal ponds of three different sizes', Algal Research, vol. 45.View/Download from: UTS OPUS or Publisher's site
© 2019 Elsevier B.V. High rate algal ponds for coupled wastewater treatment and resource recovery have been the focus of much international research over the last 15 years. Microalgal biomass productivity reported in full-scale studies (1-ha or greater) have often been substantially lower than that reported from smaller scale ponds in similar climates, regardless of the season or the dominant microalgal species used. The disconnect between smaller-scale and full-scale productivity is unclear and uncertainty remains regarding the applicability of smaller scale studies to full-scale systems. In order to better understand the differences in reported productivity, the performance of three different size wastewater treatment high rate algal ponds (5 m2, 330 m2 and 1-ha) were assessed with respect to nutrient removal and microalgal productivity over three seasons. Both daily areal nutrient removal and biomass production were affected by the size of the pond. NH4-N removal via nitrification/denitrification decreased with increasing pond size, with the highest removal rate in the 5 m2 pond and the lowest in the 1-ha. Microalgal areal productivity was maximal in the 330 m2 pond, suggesting that a combination of mixing frequency and higher photosynthetic potential under low light conditions were the main drivers of enhanced productivity in this pond compared to the 5 m2 (mesocosm) and 1-ha (full-scale) ponds. The lowest daily nutrient removal and biomass production occurred in the 1-ha (full-scale) pond. Our results suggest that, based on the current design and operation of high rate algal ponds, the optimum size for maximum productivity is considerably smaller than the current full-scale systems. This has implications for commercial scale systems, with respect to capital and operational costs.
Hughes, DJ, Crosswell, JR, Doblin, MA, Oxborough, K, Ralph, PJ, Varkey, D & Suggett, DJ 2020, 'Dynamic variability of the phytoplankton electron requirement for carbon fixation in eastern Australian waters', JOURNAL OF MARINE SYSTEMS, vol. 202.View/Download from: UTS OPUS or Publisher's site
Nguyen, LN, Commault, AS, Kahlke, T, Ralph, PJ, Semblante, GU, Johir, MAH & Nghiem, LD 2020, 'Genome sequencing as a new window into the microbial community of membrane bioreactors - A critical review', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 704.View/Download from: UTS OPUS or Publisher's site
Jaramillo-Madrid, AC, Ashworth, J, Fabris, M & Ralph, PJ 2019, 'Phytosterol biosynthesis and production by diatoms (Bacillariophyceae).', Phytochemistry, vol. 163, pp. 46-57.View/Download from: UTS OPUS or Publisher's site
Diatoms are abundant unicellular marine photosynthetic algae that have genetically diversified their physiology and metabolism while adapting to numerous environments. The metabolic repertoire of diatoms presents opportunities to characterise the biosynthesis and production of new and potentially valuable microalgal compounds, including sterols. Sterols of plant origin, known as phytosterols, have been studied for health benefits including demonstrated cholesterol-lowering properties. In this review we summarise sterol diversity, the unique metabolic features of sterol biosynthesis in diatoms, and prospects for the extraction of diatom phytosterols in comparison to existing sources. We also review biotechnological efforts to manipulate diatom biosynthesis, including culture conditions and avenues for the rational engineering of metabolism and cellular regulation.
Serrano, O, Lovelock, CE, B Atwood, T, Macreadie, PI, Canto, R, Phinn, S, Arias-Ortiz, A, Bai, L, Baldock, J, Bedulli, C, Carnell, P, Connolly, RM, Donaldson, P, Esteban, A, Ewers Lewis, CJ, Eyre, BD, Hayes, MA, Horwitz, P, Hutley, LB, Kavazos, CRJ, Kelleway, JJ, Kendrick, GA, Kilminster, K, Lafratta, A, Lee, S, Lavery, PS, Maher, DT, Marbà, N, Masque, P, Mateo, MA, Mount, R, Ralph, PJ, Roelfsema, C, Rozaimi, M, Ruhon, R, Salinas, C, Samper-Villarreal, J, Sanderman, J, J Sanders, C, Santos, I, Sharples, C, Steven, ADL, Cannard, T, Trevathan-Tackett, SM & Duarte, CM 2019, 'Australian vegetated coastal ecosystems as global hotspots for climate change mitigation.', Nature communications, vol. 10, no. 1.View/Download from: UTS OPUS or Publisher's site
Policies aiming to preserve vegetated coastal ecosystems (VCE; tidal marshes, mangroves and seagrasses) to mitigate greenhouse gas emissions require national assessments of blue carbon resources. Here, we present organic carbon (C) storage in VCE across Australian climate regions and estimate potential annual CO2 emission benefits of VCE conservation and restoration. Australia contributes 5-11% of the C stored in VCE globally (70-185 Tg C in aboveground biomass, and 1,055-1,540 Tg C in the upper 1 m of soils). Potential CO2 emissions from current VCE losses are estimated at 2.1-3.1 Tg CO2-e yr-1, increasing annual CO2 emissions from land use change in Australia by 12-21%. This assessment, the most comprehensive for any nation to-date, demonstrates the potential of conservation and restoration of VCE to underpin national policy development for reducing greenhouse gas emissions.
Emerging contaminants (ECs) are primarily synthetic organic chemicals that have a focus of increasing attention due to either increased awareness of their potential risks to humans and aquatic biota, or only recently been detected in the aquatic environment or drinking water supplies, through improved analytical techniques. . Many ECs have no regulatory standards due to the lack of information on the effects of chronic exposure. Pharmaceuticals, personal care products, pesticides and flame retardants are some of the most frequently detected ECs in aquatic environments, with over 200 individual compounds identified, to date. Current wastewater treatment is ineffective at removing ECs and there is a vital need for the development of efficient, cost-effective EC treatment systems that can be applied to a range of scales and wastewater types. Microalgae have demonstrated potential for detoxifying organic and inorganic pollutants, with a number of large-scale wastewater treatment microalgal technologies already developed. There are three main pathways that microalgae can bioremediate ECs; bioadsorption, bio-uptake and biodegradation. Microalgal bioadsorption occurs when ECs are either adsorbed to cell wall components, or onto organic substances excreted by the cells, while bio-uptake involves the active transport of the contaminant into the cell, where it binds to intracellular proteins and other compounds. Microalgal biodegradation of ECs involves the transformation of complex compounds into simpler breakdown molecules through catalytic metabolic degradation. Biodegradation provides one of the most promising technologies for the remediation of contaminants of concern as it can transform the contaminant to less toxic compounds rather than act as a biofilter. Further research is needed to exploit microalgal species for EC bioremediation properties, such as increased bioadsorption, enhanced biodegrading enzymes and optimised growth conditions. When coupled with nutrient...
Thomson, A, Trevathan-Tackett, S, Ralph, P, Macreadie, P & Maher, D 2019, 'Bioturbator-stimulated loss of seagrass sediment carbon stocks', Limnology and Oceanography, vol. 64, pp. 342-356.View/Download from: UTS OPUS or Publisher's site
Seagrass ecosystems are highly productive, and are sites of significant carbon sequestration. Sediment‐held carbon stocks can be many thousands of years old, and persist largely due to sediment anoxia and because microbial activity is decreasing with depth. However, the carbon sequestered in seagrass ecosystems may be susceptible to remineralization via the activity of bioturbating fauna. Microbial priming is a process whereby remineralization of sediment carbon (recalcitrant organic matter) is stimulated by disturbance, i.e., burial of a labile source of organic matter (seagrass). We investigated the hypothesis that bioturbation could mediate remineralization of sediment carbon stocks through burial of seagrass leaf detritus. We carried out a 2‐month laboratory study to compare the remineralization (measured as CO2 release) of buried seagrass leaves (Zostera muelleri) to the total rate of sediment organic matter remineralization in sediment with and without the common Australian bioturbating shrimp Trypaea australiensis (Decapoda: Axiidea). In control sediment containing seagrass but no bioturbators, we observed a negative microbial priming effect, whereby seagrass remineralization was favored over sediment remineralization (and thus preserving sediment stocks). Bioturbation treatments led to a two‐ to five‐fold increase in total CO2 release compared to controls. The estimated bioturbator‐stimulated microbial priming effect was equivalent to 15% of the total daily sediment‐derived CO2 releases. We propose that these results indicate that bioturbation is a potential mechanism that converts these sediments from carbon sinks to sources through stimulation of priming‐enhanced sediment carbon remineralization. We further hypothesized that significant changes to seagrass faunal communities may influence seagrass sediment carbon stocks.
Verma, A, Kohli, GS, Harwood, DT, Ralph, PJ & Murray, SA 2019, 'Transcriptomic investigation into polyketide toxin synthesis in Ostreopsis (Dinophyceae) species', ENVIRONMENTAL MICROBIOLOGY, vol. 21, no. 11, pp. 4196-4211.View/Download from: Publisher's site
Hurtado-McCormick, V, Kahlke, T, Petrou, K, Jeffries, T, Ralph, PJ & Seymour, JR 2019, 'Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome.', Frontiers in Microbiology, vol. 10.View/Download from: UTS OPUS or Publisher's site
Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify "core microbiome" members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with "core" taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, across geographically discrete sampling...
Kim, M, Pernice, M, Watson-Lazowski, A, Guagliardo, P, Kilburn, MR, Larkum, AWD, Raven, JA & Ralph, PJ 2019, 'Effect of reduced irradiance on 13C uptake, gene expression and protein activity of the seagrass Zostera muelleri.', Marine environmental research, vol. 149, pp. 80-89.View/Download from: UTS OPUS or Publisher's site
Photosynthesis in the seagrass Zostera muelleri remains poorly understood. We investigated the effect of reduced irradiance on the incorporation of 13C, gene expression of photosynthetic, photorespiratory and intermediates recycling genes as well as the enzymatic content and activity of Rubisco and PEPC within Z. muelleri. Following 48 h of reduced irradiance, we found that i) there was a ∼7 fold reduction in 13C incorporation in above ground tissue, ii) a significant down regulation of photosynthetic, photorespiratory and intermediates recycling genes and iii) no significant difference in enzyme activity and content. We propose that Z. muelleri is able to alter its physiology in order to reduce the amount of C lost through photorespiration to compensate for the reduced carbon assimilation as a result of reduced irradiance. In addition, the first estimated rate constant (Kcat) and maximum rates of carboxylation (Vcmax) of Rubisco is reported for the first time for Z. muelleri.
Bates, H, Zavafer, A, Szabo, M & Ralph, PJ 2019, 'A guide to Open-JIP, a low-cost open-source chlorophyll fluorometer', PHOTOSYNTHESIS RESEARCH, vol. 142, no. 3, pp. 361-368.View/Download from: Publisher's site
Buapet, P, Mohammadi, NS, Pernice, M, Kumar, M, Kuzhiumparambil, U & Ralph, PJ 2019, 'Excess copper promotes photoinhibition and modulates the expression of antioxidant-related genes in Zostera muelleri', AQUATIC TOXICOLOGY, vol. 207, pp. 91-100.View/Download from: UTS OPUS or Publisher's site
Commault, AS, Fabris, M, Kuzhiumparambil, U, Adriaans, J, Pernice, M & Ralph, PJ 2019, 'Methyl jasmonate treatment affects the regulation of the 2-C-methyl-D-erythritol 4-phosphate pathway and early steps of the triterpenoid biosynthesis in Chlamydomonas reinhardtii', Algal Research, vol. 39.View/Download from: UTS OPUS or Publisher's site
© 2019 Elsevier B.V. Terpenoids are a large and diverse class of naturally occurring metabolites serving many industrial applications and natural roles. Economically important terpenoids are often produced in low abundance from their natural sources, making their industrial-scale production challenging or uneconomical, therefore engineered microorganisms are frequently used as heterologous production platforms. Photosynthetic microorganisms, such as the green alga Chlamydomonas reinhardtii, represent promising systems to produce terpenoids in a cost-effective and sustainable manner, but knowledge about the regulation of their terpenoid metabolism remains limited. Here we report on the investigation of the phytohormone methyl jasmonate (MeJA) as elicitor of algal terpenoid synthesis. We treated C. reinhardtii cells in mid-exponential growth phase with three different concentrations of MeJA (0.05, 0.5 and 1 mM). The highest concentration of MeJA affected the photosynthetic activity of the cells, arrested the growth and up-regulated key genes of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, leading to a significant increase in intermediates of this pathway, squalene and (S)-2,3-epoxysqualene, while the abundance of cycloartenol, and two main sterols (ergosterol and 7-dehydroporiferasterol) decreased. These data suggest the redirection of the carbon flux towards the synthesis of yet uncharacterised triterpenoid secondary metabolites upon MeJA treatment. Our results offer important new insights into the regulation of the triterpenoid metabolism in C. reinhardtii and raise important questions on hormonal signalling in microalgae. Phytohormone treatment is tested for the first time in algae, where it holds great potential for identifying key transcriptional regulators of the MEP pathway as targets for future metabolic engineering studies for improve production of high-value triterpenoids.
Ramarajan, M, Fabris, M, Abbriano, RM, Pernice, M & Ralph, PJ 2019, 'Novel endogenous promoters for genetic engineering of the marine microalga Nannochloropsis gaditana CCMP526', Algal Research, vol. 44.View/Download from: UTS OPUS or Publisher's site
© 2019 Elsevier B.V. Nannochloropsis is a marine microalga from the Eustigmatophyceae stramenopile lineage that has been studied extensively due to a broad range of industrial applications, mostly related to their oil and pigment production. However, tools to genetically engineer members of this group, and therefore further understand and maximise their industrial potential are still limited. In order to expand the potential industrial uses of this organism, several molecular tools, including gene promoters of different strength, are needed. A comprehensive and diverse set of well-characterized promoters is key to a number of genetic engineering and synthetic biology applications, such as the assembly of complex biological functions or entire metabolic pathways. In this study, we measured the promoter activity of three endogenous constitutive promoters from N. gaditana genes EPPSII (Nga02101); HSP90 (Nga00934); ATPase (Nga06354.1) in driving the expression of a Sh ble- mVenus fluorescent reporter fusion protein. Through a combined approach that includes flow cytometry, RT-qPCR and immunoblotting, we profiled the activity of these promoters at both the transcript and protein level. Two promoters HSP90 (Nga00934) and EPPSII (Nga02101) outperformed the widely used β-tubulin promoter, exhibiting 4.5 and 3.1-fold higher mVenus fluorescence, respectively. A third promoter ATPase (Nga06354.1) was also able to drive the expression of transgenes, albeit at lower levels. We show that the new promoters identified in this study are valuable tools, which can be used for genetic engineering and functional genetics studies in N. gaditana.
Shah Mohammadi, N, Buapet, P, Pernice, M, Signal, B, Kahlke, T, Hardke, L & Ralph, PJ 2019, 'Transcriptome profiling analysis of the seagrass, Zostera muelleri under copper stress.', Marine pollution bulletin, vol. 149.View/Download from: UTS OPUS or Publisher's site
Copper (Cu) in an essential trace metal but it can also contaminate coastal waters at high concentrations mainly from agricultural run-off and mining activities which are detrimental to marine organisms including seagrasses. The molecular mechanisms driving Cu toxicity in seagrasses are not clearly understood yet. Here, we investigated the molecular responses of the Australian seagrass, Z. muelleri at the whole transcriptomic level after 7 days of exposure to 250 μg Cu L-1 and 500 μg Cu L-1. The leaf-specific whole transcriptome results showed a concentration-dependent disturbance in chloroplast function, regulatory stress responses and defense mechanisms. This study provided new insights into the responses of seagrasses to trace metal stress and reports possible candidate genes which can be considered as biomarkers to improve conservation and management of seagrass meadows.
Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunensse, T, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave', Coral Reefs, vol. 38, no. 4, pp. 815-830.View/Download from: UTS OPUS or Publisher's site
© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. High-latitude coral communities are distinct from their tropical counterparts, and how they respond to recent heat wave events that have decimated tropical reefs remains unknown. In Australia, the 2016 El Niño resulted in the largest global mass coral bleaching event to date, reaching as far south as Sydney Harbour (~ 34°S). Coral bleaching was observed for the first time (affecting ca., 60% of all corals) as sea surface temperatures in Sydney Harbour remained > 2 °C above the long-term mean summer maxima, enabling us to examine whether high-latitude corals bleached in a manner described for tropical corals. Responses of the geographically cosmopolitan Plesiastrea versipora and southerly restricted Coscinaraea mcneilli were contrasted across two harbour sites, both in situ and among samples-maintained ex situ in aquaria continually supplied with Sydney Harbour seawater. While both coral taxa hosted the same species of microalgal endosymbiont (Breviolum spp; formerly clade B), only P. versipora bleached both in situ and ex situ via pronounced losses of endosymbiont cells. Both species displayed very different metabolic responses (growth, photosynthesis, respiration and calcification) and bleaching susceptibilities under elevated temperatures. Bacterial microbiome profiling, however, revealed a convergence of bacterial community composition across coral species throughout the bleaching. Corals species found in temperate regions, including the generalist P. versipora, will therefore likely be highly susceptible to future change as heat waves grow in frequency and severity unless their thermal thresholds increase. Our observations provide further evidence that high-latitude systems are susceptible to community reorganisation under climate change.
Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunesse, TC, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015-2016 heatwave (vol 38, pg 815, 2019)', CORAL REEFS, vol. 38, no. 4, pp. 877-877.View/Download from: Publisher's site
Kahlke, T & Ralph, PJ 2019, 'BASTA – Taxonomic classification of sequences and sequence bins using last common ancestor estimations', Methods in Ecology and Evolution, vol. 10, no. 1, pp. 100-103.View/Download from: UTS OPUS or Publisher's site
1. Identification of the taxonomic origin of a DNA sequence is crucial for many sequencing projects, e.g. metagenomics studies, identification of contaminations in whole genome sequencing projects and filtering of organisms of interest in marker‐gene based community analyses.
2. Last common ancestor algorithms are powerful approaches to estimate the taxonomy of a given sequence and have been widely used for classification of next‐generation sequencing (NGS) reads, also known as 2nd generation sequencing reads.
3. Here, we present BASTA (https://github.com/timkahlke/BASTA), a basic sequence taxonomy annotator, which extends last common ancestor estimations from sequencing reads to any kind of nucleotide or amino acid sequence utilizing NCBI taxonomies of user‐defined best hits.
4. BASTA can be configured to use the output of many common sequence comparison tools, e.g. BLAST and Diamond, in conjunction with either provided or user‐defined target sequence databases.
Nguyen, LN, Labeeuw, L, Commault, AS, Emmerton, B, Ralph, PJ, Johir, MAH, Guo, W, Ngo, HH & Nghiem, LD 2019, 'Validation of a cationic polyacrylamide flocculant for the harvesting fresh and seawater microalgal biomass', Environmental Technology and Innovation, vol. 16.View/Download from: UTS OPUS or Publisher's site
© 2019 Elsevier B.V. A simple, efficient, and fast settling flocculation technique to harvest microalgal biomass was demonstrated using a proprietary cationic polyacrylamide flocculant for a freshwater (Chlorella vulgaris) and a marine (Phaeodactylum tricornutum) microalgal culture at their mid-stationary growth phase. The optimal flocculant doses were 18.9 and 13.7 mg/g of dry algal biomass for C. vulgaris and P. tricornutum, respectively (equivalent to 7 g per m3 of algal culture for both species). The obtained optimal dose was well corroborated with changes in cell surface charge, and culture solution optical density and turbidity. At the optimal dose, charge neutralization of 64 and 86% was observed for C. vulgaris and P. tricornutum algal cells, respectively. Algae recovery was independent of the culture solution pH in the range of pH 6 to 9. Algal biomass recovery was achieved of 100 and 90% for C vulgaris and P. tricornutum respectively, and over 98% medium recovery was achievable by simple decanting.
Baker, KG, Radford, DT, Evenhuis, C, Kuzhiumparam, U, Ralph, PJ & Doblin, MA 2018, 'Thermal niche evolution of functional traits in a tropical marine phototroph.', Journal of phycology, vol. 54, no. 6, pp. 799-810.View/Download from: UTS OPUS or Publisher's site
Land-based plants and ocean-dwelling microbial phototrophs known as phytoplankton, are together responsible for almost all global primary production. Habitat warming associated with anthropogenic climate change has detrimentally impacted marine primary production, with the effects observed on regional and global scales. In contrast to slower-growing higher plants, there is considerable potential for phytoplankton to evolve rapidly with changing environmental conditions. The energetic constraints associated with adaptation in phytoplankton are not yet understood, but are central to forecasting how global biogeochemical cycles respond to contemporary ocean change. Here, we demonstrate a number of potential trade-offs associated with high-temperature adaptation in a tropical microbial eukaryote, Amphidinium massartii (dinoflagellate). Most notably, the population became high-temperature specialized (higher fitness within a narrower thermal envelope and higher thermal optimum), and had a greater nutrient requirement for carbon, nitrogen and phosphorus. Evidently, the energetic constraints associated with living at elevated temperature alter competiveness along other environmental gradients. While high-temperature adaptation led to an irreversible change in biochemical composition (i.e., an increase in fatty acid saturation), the mechanisms underpinning thermal evolution in phytoplankton remain unclear, and will be crucial to understanding whether the trade-offs observed here are species-specific or are representative of the evolutionary constraints in all phytoplankton.
Tamburic, B, Evenhuis, CR, Crosswell, JR & Ralph, PJ 2018, 'An empirical process model to predict microalgal carbon fixation rates in photobioreactors', Algal Research, vol. 31, pp. 334-346.View/Download from: UTS OPUS or Publisher's site
© 2018 Elsevier B.V. An empirical process model was developed to infer the instantaneous net photosynthesis and carbon fixation rates from continuous pH and dissolved oxygen measurements during microalgal cultivation in photobioreactors. The model is based on the physical and chemical processes that govern the relationship between inorganic carbon supplied to a microalgal culture and the organic carbon fixed into microalgal biomass, with a particular focus on carbonate chemistry and mass transfer. Bayesian statistics were used to estimate the uncertainty in state variables, such as pH, net photosynthesis rate, and bicarbonate ion concentration, based on the constraints imposed by prior knowledge about these variables. The model was verified by batch-culturing the chlorophyte microalga Chlorella vulgaris in a photobioreactor under both bicarbonate-replete and bicarbonate-limiting conditions in order to test its predictive ability under different operational settings. The replicate photobioreactors were set up to simulate a scaled-down vertical cross-section of a typical raceway pond. This model could be used to test the activity and efficiency of carbon concentrating mechanisms in different microalgal species. It also provides a detailed understanding of how the rate of photosynthesis depends on dissolved inorganic carbon concentration, which could lead to better management of carbon supply in large-scale microalgal cultivation facilities.
Trevathan‐Tackett, SM, Caitlin Wessel, Just Cebrián, Peter J. Ralph, Pere Masqué & Peter I. Macreadie 2018, 'Effects of small‐scale, shading‐induced seagrass loss on blue carbon storage: Implications for management of degraded seagrass ecosystems', The Journal of Applied Ecology, vol. 55, no. 3, pp. 1351-1359.View/Download from: UTS OPUS or Publisher's site
Seagrass meadows are important global blue carbon sinks. Despite a 30% loss of seagrasses globally during the last century, there is limited empirical research investigating the effects of disturbance and loss of seagrass on blue carbon stocks. In this study, we hypothesised that seagrass loss would reduce blue carbon stocks. Using shading cloth, we simulated small‐scale die‐offs of two subtropical seagrass species, Halodule wrightii and Thalassia testudinum, in a dynamic northern Gulf of Mexico lagoon. The change in quantity and quality of sediment organic matter (OM) and organic carbon was compared among die‐off, control and bare plots before the die‐off treatment, shortly after the die‐off treatment and 11 months after the die‐off treatment. ²¹⁰Pb age dating was performed on bare and Thalassia plots at 11 months to evaluate the impact of sediment erosion in the absence of vegetation. The small‐scale die‐off led to a 50%–65% OM loss in the sediment in the top 8 cm of Halodule plots. Thalassia plots lost significant portions of OM (50%) and organic carbon (Cₒᵣg; 21%–47%) in only the top 1 cm of sediment. The ²¹⁰Pb profiles indicated Thalassia die‐off reduced the Cₒᵣg sequestration rate by 10%, in addition to a loss of c. 1 year's worth of Cₒᵣg stocks (c. 22 g/m²). Furthermore, analyses on OM/Cₒᵣg quality indicated a loss of labile OM/Cₒᵣg and enhanced remineralisation by microbes. Synthesis and applications. This study provides empirical evidence that small‐scale shading‐induced seagrass die‐offs can reduce seagrass carbon sequestration capacity and trigger losses of blue carbon stocks. While the losses recorded here are modest, these losses in blue carbon storage capacity are notable due to the proximity of shading structures (e.g. boat docks) to seagrass habitats. Thus, policies to avoid or protect seagrass habitats from common small‐scale, shading disturbances are important for optimising both carbon sequestration capacity and coastline development and manage...
Trevathan-Tackett, SM, Thomson, ACG, Ralph, PJ & Macreadie, PI 2018, 'Fresh carbon inputs to seagrass sediments induce variable microbial priming responses.', Science of the Total Environment, vol. 621, pp. 663-669.View/Download from: UTS OPUS or Publisher's site
Microbes are the 'gatekeepers' of the marine carbon cycle, yet the mechanisms for how microbial metabolism drives carbon sequestration in coastal ecosystems are still being defined. The proximity of coastal habitats to runoff and disturbance creates ideal conditions for microbial priming, i.e., the enhanced remineralisation of stored carbon in response to fresh substrate availability and oxygen introduction. Microbial priming, therefore, poses a risk for enhanced CO2 release in these carbon sequestration hotspots. Here we quantified the existence of priming in seagrass sediments and showed that the addition of fresh carbon stimulated a 1.7- to 2.7-fold increase in CO2 release from recent and accumulated carbon deposits. We propose that priming taking place at the sediment surface is a natural occurrence and can be minimised by the recalcitrant components of the fresh inputs (i.e., lignocellulose) and by reduced metabolism in low oxygen and high burial rate conditions. Conversely, priming of deep sediments after the reintroduction to the water column through physical disturbances (e.g., dredging, boat scars) would cause rapid remineralisation of previously preserved carbon. Microbial priming is identified as a process that weakens sediment carbon storage capacity and is a pathway to CO2 release in disturbed or degraded seagrass ecosystems; however, increased management and restoration practices can reduce these anthropogenic disturbances and enhance carbon sequestration capacity.
Schrameyer, V, York, PH, Chartrand, K, Ralph, PJ, Kühl, M, Brodersen, KE & Rasheed, MA 2018, 'Contrasting impacts of light reduction on sediment biogeochemistry in deep- and shallow-water tropical seagrass assemblages (Green Island, Great Barrier Reef).', Marine environmental research, vol. 136, pp. 38-47.View/Download from: UTS OPUS or Publisher's site
Seagrass meadows increasingly face reduced light availability as a consequence of coastal development, eutrophication, and climate-driven increases in rainfall leading to turbidity plumes. We examined the impact of reduced light on above-ground seagrass biomass and sediment biogeochemistry in tropical shallow- (∼2 m) and deep-water (∼17 m) seagrass meadows (Green Island, Australia). Artificial shading (transmitting ∼10-25% of incident solar irradiance) was applied to the shallow- and deep-water sites for up to two weeks. While above-ground biomass was unchanged, higher diffusive O2 uptake (DOU) rates, lower O2 penetration depths, and higher volume-specific O2 consumption (R) rates were found in seagrass-vegetated sediments as compared to adjacent bare sand (control) areas at the shallow-water sites. In contrast, deep-water sediment characteristics did not differ between bare sand and vegetated sites. At the vegetated shallow-water site, shading resulted in significantly lower hydrogen sulphide (H2S) levels in the sediment. No shading effects were found on sediment biogeochemistry at the deep-water site. Overall, our results show that the sediment biogeochemistry of shallow-water (Halodule uninervis, Syringodium isoetifolium, Cymodocea rotundata and C. serrulata) and deep-water (Halophila decipiens) seagrass meadows with different species differ in response to reduced light. The light-driven dynamics of the sediment biogeochemistry at the shallow-water site could suggest the presence of a microbial consortium, which might be stimulated by photosynthetically produced exudates from the seagrass, which becomes limited due to lower seagrass photosynthesis under shaded conditions.
Kim, M, Brodersen, KE, Szabó, M, Larkum, AWD, Raven, JA, Ralph, PJ & Pernice, M 2018, 'Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri.', Photosynthesis Research, vol. 136, no. 2, pp. 147-160.View/Download from: UTS OPUS or Publisher's site
Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C4 metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C3 mechanism of carbon assimilation, and (ii) decreased the expression levels of phosphoenolpyruvate carboxylase and carbonic anhydrase. These molecular-physiological results suggest that regulation of the photophysiology of Z. muelleri might involve a close integration between the C3 and C4, or other CO2 concentrating mechanisms metabolic pathways. Overall, this study highlights that the photophysiological response of Z. muelleri to changing oxygen in water is capable of rapid acclimation and the dynamic modulation of pathways should be considered when assessing seagrass primary production.
Sablok, G, Hayward, RJ, Davey, PA, Santos, RP, Schliep, M, Larkum, A, Pernice, M, Dolferus, R & Ralph, PJ 2018, 'SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants', SCIENTIFIC REPORTS, vol. 8.View/Download from: UTS OPUS or Publisher's site
Zavřel, T, Szabó, M, Tamburic, B, Evenhuis, C, Kuzhiumparambil, U, Literáková, P, Larkum, AWD, Raven, JA, Červený, J & Ralph, PJ 2018, 'Effect of carbon limitation on photosynthetic electron transport in Nannochloropsis oculata.', Journal of photochemistry and photobiology. B, Biology, vol. 181, pp. 31-43.View/Download from: UTS OPUS or Publisher's site
This study describes the impacts of inorganic carbon limitation on the photosynthetic efficiency and operation of photosynthetic electron transport pathways in the biofuel-candidate microalga Nannochloropsis oculata. Using a combination of highly-controlled cultivation setup (photobioreactor), variable chlorophyll a fluorescence and transient spectroscopy methods (electrochromic shift (ECS) and P700 redox kinetics), we showed that net photosynthesis and effective quantum yield of Photosystem II (PSII) decreased in N. oculata under carbon limitation. This was accompanied by a transient increase in total proton motive force and energy-dependent non-photochemical quenching as well as slightly elevated respiration. On the other hand, under carbon limitation the rapid increase in proton motive force (PMF, estimated from the total ECS signal) was also accompanied by reduced conductivity of ATP synthase to protons (estimated from the rate of ECS decay in dark after actinic illumination). This indicates that the slow operation of ATP synthase results in the transient build-up of PMF, which leads to the activation of fast energy dissipation mechanisms such as energy-dependent non-photochemical quenching. N. oculata also increased content of lipids under carbon limitation, which compensated for reduced NAPDH consumption during decreased CO2 fixation. The integrated knowledge of the underlying energetic regulation of photosynthetic processes attained with a combination of biophysical methods may be used to identify photo-physiological signatures of the onset of carbon limitation in microalgal cultivation systems, as well as to potentially identify microalgal strains that can better acclimate to carbon limitation.
Chartrand, KM, Szabó, M, Sinutok, S, Rasheed, MA & Ralph, PJ 2018, 'Living at the margins - The response of deep-water seagrasses to light and temperature renders them susceptible to acute impacts.', Marine environmental research, vol. 136, pp. 126-138.View/Download from: UTS OPUS or Publisher's site
Seagrasses inhabit environments where light varies at different timescales, nonetheless are acutely sensitive to reductions in light beyond some conditional bounds. Two tropical deep-water seagrasses, Halophila decipiens and Halophila spinulosa, from the Great Barrier Reef were tested for their response to defined light and temperature regimes to identify their growth requirements and potential thresholds of mortality. Species were exposed to two light intensities, saturating (75 μmol photons m-2 s-1) and limiting (25 μmol photons m-2 s-1) light and two temperature treatments (26 °C and 30 °C) over a four-week period. Wavelength-specific parameters of PSII photochemistry were evaluated for seagrass leaves, as well as shoot density, gas exchange, and pigment content. Both species were sustained under saturating light levels (3.2 mol photons m-2 d-1) while limiting light led to decreased shoot density for H. decipiens and H. spinulosa after two and four weeks, respectively. Wavelength-specific photochemistry was also affected under light-limiting treatments for both species while the functional absorption cross section was highly conserved. Photoacclimation and physiological adjustments by either species was not adequate to compensate for reduced irradiance suggesting these plants reside at the margins of their functional limits. As such, relatively short periods of light attenuating events, like dredging or flood plumes, may be detrimental to deep-water seagrass populations.
Davey, PA, Pernice, M, Ashworth, J, Kuzhiumparambil, U, Szabó, M, Dolferus, R & Ralph, PJ 2018, 'A new mechanistic understanding of light-limitation in the seagrass Zostera muelleri.', Marine Environmental Research, vol. 134, pp. 55-67.View/Download from: UTS OPUS or Publisher's site
In this study we investigated the effect of light-limitation (∼20 μmol photons m-2 s-1) on the southern hemisphere seagrass, Zostera muelleri. RNA sequencing, chlorophyll fluorometry and HPLC techniques were used to investigate how the leaf-specific transcriptome drives changes in photosynthesis and photo-pigments in Z. muelleri over 6 days. 1593 (7.51%) genes were differentially expressed on day 2 and 1481 (6.98%) genes were differentially expressed on day 6 of the experiment. Differential gene expression correlated with significant decreases in rETRMax, Ik, an increase in Yi (initial photosynthetic quantum yield of photosystem II), and significant changes in pigment composition. Regulation of carbohydrate metabolism was observed along with evidence that abscisic acid may serve a role in the low-light response of this seagrass. This study provides a novel understanding of how Z. muelleri responds to light-limitation in the marine water column and provides potential molecular markers for future conservation monitoring efforts.
Fujise, L, Nitschke, MR, Frommlet, JC, Serôdio, J, Woodcock, S, Ralph, PJ & Suggett, DJ 2018, 'Cell Cycle Dynamics of Cultured Coral Endosymbiotic Microalgae (Symbiodinium) Across Different Types (Species) Under Alternate Light and Temperature Conditions', Journal of Eukaryotic Microbiology, vol. 65, pp. 505-517.View/Download from: UTS OPUS or Publisher's site
Hughes, DJ, Campbell, DA, Doblin, MA, Kromkamp, JC, Lawrenz, E, Moore, CM, Oxborough, K, Prášil, O, Ralph, PJ, Alvarez, MF & Suggett, DJ 2018, 'Roadmaps and Detours: Active Chlorophyll- a Assessments of Primary Productivity Across Marine and Freshwater Systems.', Environmental science & technology, vol. 52, pp. 12039-12054.View/Download from: UTS OPUS or Publisher's site
Assessing phytoplankton productivity over space and time remains a core goal for oceanographers and limnologists. Fast Repetition Rate fluorometry (FRRf) provides a potential means to realize this goal with unprecedented resolution and scale yet has not become the "go-to" method despite high expectations. A major obstacle is difficulty converting electron transfer rates to equivalent rates of C-fixation most relevant for studies of biogeochemical C-fluxes. Such difficulty stems from methodological inconsistencies and our limited understanding of how the electron requirement for C-fixation (Φe,C) is influenced by the environment and by differences in the composition and physiology of phytoplankton assemblages. We outline a "roadmap" for limiting methodological bias and to develop a more mechanistic understanding of the ecophysiology underlying Φe,C. We 1) re-evaluate core physiological processes governing how microalgae invest photosynthetic electron transport-derived energy and reductant into stored carbon versus alternative sinks. Then, we 2) outline steps to facilitate broader uptake and exploitation of FRRf, which could transform our knowledge of aquatic primary productivity. We argue it is time to 3) revise our historic methodological focus on carbon as the currency of choice, to 4) better appreciate that electron transport fundamentally drives ecosystem biogeochemistry, modulates cell-to-cell interactions, and ultimately modifies community biomass and structure.
Hughes, DJ, Varkey, D, Doblin, MA, Ingleton, T, Mcinnes, A, Ralph, PJ, van Dongen-Vogels, V & Suggett, DJ 2018, 'Impact of nitrogen availability upon the electron requirement for carbon fixation in Australian coastal phytoplankton communities', Limnology and Oceanography, vol. 63, no. 5, pp. 1891-1910.View/Download from: UTS OPUS or Publisher's site
© 2018 Association for the Sciences of Limnology and Oceanography Nitrogen (N) availability affects phytoplankton photosynthetic performance and regulates marine primary production (MPP) across the global coast and oceans. Bio-optical tools including Fast Repetition Rate fluorometry (FRRf) are particularly well suited to examine MPP variability in coastal regions subjected to dynamic spatio-temporal fluctuations in nutrient availability. FRRf determines photosynthesis as an electron transport rate through Photosystem II (ETRPSII), requiring knowledge of an additional parameter, the electron requirement for carbon fixation (KC), to retrieve rates of CO2-fixation. KC strongly depends upon environmental conditions regulating photosynthesis, yet the importance of N-availability to this parameter has not been examined. Here, we use nutrient bioassays to isolate how N (relative to other macronutrients P, Si) regulates KC of phytoplankton communities from the Australian coast during summer, when N-availability is often highly variable. KC consistently responded to N-amendment, exhibiting up to a threefold reduction and hence an apparent increase in the efficiency with which electrons were used to drive C-fixation. However, the process driving this consistent reduction was dependent upon initial conditions. When diatoms dominated assemblages and N was undetectable (e.g., post bloom), KC decreased predominantly via a physiological adjustment of the existing community to N-amendment. Conversely, for mixed assemblages, N-addition achieved a similar reduction in KC through a change in community structure toward diatom domination. We generate new understanding and parameterization of KC that is particularly critical to advance how FRRf can be applied to examine C-uptake throughout the global ocean where nitrogen availability is highly variable and thus frequently limits primary productivity.
Nitschke, MR, Gardner, SG, Goyen, S, Fujise, L, Camp, EF, Ralph, PJ & Suggett, DJ 2018, 'Utility of photochemical traits as diagnostics of thermal tolerance amongst great barrier reef corals', Frontiers in Marine Science, vol. 5, no. FEB.View/Download from: UTS OPUS or Publisher's site
© 2018 Nitschke, Gardner, Goyen, Fujise, Camp, Ralph and Suggett. Light availability is considered a key factor regulating the thermal sensitivity of reef building corals, where excessive excitation of photosystem II (PSII) further exacerbates pressure on photochemical pathways already compromised by heat stress. Coral symbionts acclimate to changes in light availability (photoacclimation) by continually fine-tuning the photochemical operating efficiency of PSII. However, how this process adjusts throughout the warmest months in naturally heat-tolerant or sensitive species is unknown, and whether this influences the capacity to tolerate transient heat stress is untested. We therefore examined the PSII photophysiology of 10 coral species (with known thermal tolerances) from shallow reef environments at Heron Island (Great Barrier Reef, Australia), in spring (October-November, 2015) vs. summer (February-March, 2016). Corals were maintained in flow-through aquaria and rapid light curve (RLC) protocols using pulse amplitude modulated (PAM) fluorometry captured changes in the PSII photoacclimation strategy, characterized as the minimum saturating irradiance (Ek), and the extent of photochemical ([1-C], operating efficiency) vs. non-photochemical ([1-Q]) energy dissipation. Values of Ekacross species were > 2-fold higher in all coral species in spring, consistent with a climate of higher overall light exposure (i.e., higher PAR from lower cloud cover, rainfall and wind speed) compared with summer. Summer decreases in Ekwere combined with a shift toward preferential photochemical quenching in all species. All coral species were subsequently subjected to thermal stress assays. An equivalent temperature-ramping profile of 1°C increase per day and then maintenance at 32°C was applied in each season. Despite the significant seasonal photoacclimation, the species hierarchy of thermal tolerance [maximum quantum yields of PSII (Fv/Fm), monitored at dawn and dusk] did not shift...
Vuppaladadiyam, AK, Yao, JG, Florin, N, George, A, Wang, X, Labeeuw, L, Jiang, Y, Davis, RW, Abbas, A, Ralph, P, Fennell, PS & Zhao, M 2018, 'Impact of Flue Gas Compounds on Microalgae and Mechanisms for Carbon Assimilation and Utilization.', ChemSusChem, vol. 11, no. 2, pp. 334-355.View/Download from: UTS OPUS or Publisher's site
To shift the world to a more sustainable future, it is necessary to phase out the use of fossil fuels and focus on the development of low-carbon alternatives. However, this transition has been slow, so there is still a large dependence on fossil-derived power, and therefore, carbon dioxide is released continuously. Owing to the potential for assimilating and utilizing carbon dioxide to generate carbon-neutral products, such as biodiesel, the application of microalgae technology to capture CO2 from flue gases has gained significant attention over the past decade. Microalgae offer a more sustainable source of biomass, which can be converted into energy, over conventional fuel crops because they grow more quickly and do not adversely affect the food supply. This review focuses on the technical feasibility of combined carbon fixation and microalgae cultivation for carbon reuse. A range of different carbon metabolisms and the impact of flue gas compounds on microalgae are appraised. Fixation of flue gas carbon dioxide is dependent on the selected microalgae strain and on flue gas compounds/concentrations. Additionally, current pilot-scale demonstrations of microalgae technology for carbon dioxide capture are assessed and its future prospects are discussed. Practical implementation of this technology at an industrial scale still requires significant research, which necessitates multidisciplinary research and development to demonstrate its viability for carbon dioxide capture from flue gases at the commercial level.
Brodersen, KE, Siboni, N, Nielsen, DA, Pernice, M, Ralph, PJ, Seymour, J & Kühl, M 2018, 'Seagrass rhizosphere microenvironment alters plant-associated microbial community composition.', Environmental microbiology, vol. 20, no. 8, pp. 2854-2864.View/Download from: UTS OPUS or Publisher's site
The seagrass rhizosphere harbors dynamic microenvironments, where plant-driven gradients of O2 and dissolved organic carbon form microhabitats that select for distinct microbial communities. To examine how seagrass-mediated alterations of rhizosphere geochemistry affect microbial communities at the microscale level, we applied 16S rRNA amplicon sequencing of artificial sediments surrounding the meristematic tissues of the seagrass Zostera muelleri together with microsensor measurements of the chemical conditions at the basal leaf meristem (BLM). Radial O2 loss (ROL) from the BLM led to ∼ 300 µm thick oxic microzones, wherein pronounced decreases in H2 S and pH occurred. Significantly higher relative abundances of sulphate-reducing bacteria were observed around the meristematic tissues compared to the bulk sediment, especially around the root apical meristems (RAM; ∼ 57% of sequences). Within oxic microniches, elevated abundances of sulphide-oxidizing bacteria were observed compared to the bulk sediment and around the RAM. However, sulphide oxidisers within the oxic microzone did not enhance sediment detoxification, as rates of H2 S re-oxidation here were similar to those observed in a pre-sterilized root/rhizome environment. Our results provide novel insights into how chemical and microbiological processes in the seagrass rhizosphere modulate plant-microbe interactions potentially affecting seagrass health.
Kelleway, JJ, Saintilan, N, Macreadie, PI, Baldock, JA & Ralph, PJ 2017, 'Sediment and carbon deposition vary among vegetation assemblages in a coastal salt marsh', Biogeosciences, vol. 14, no. 16, pp. 3763-3779.View/Download from: UTS OPUS or Publisher's site
Coastal salt marshes are dynamic, intertidal ecosystems that are increasingly being recognised for their contributions to ecosystem services, including carbon (C) accumulation and storage. The survival of salt marshes and their capacity to store C under rising sea levels, however, is partially reliant upon sedimentation rates and influenced by a combination of physical and biological factors. In this study, we use several complementary methods to assess short-term (days) deposition and medium-term (months) accretion dynamics within a single marsh that contains three salt marsh vegetation types common throughout southeastern (SE) Australia. br br We found that surface accretion varies among vegetation assemblages, with medium-term (19 months) bulk accretion rates in the upper marsh rush (Juncus) assemblage (1.74g ±g 0.13g mmg yrg '1) consistently in excess of estimated local sea-level rise (1.15g mmg yrg '1). Accretion rates were lower and less consistent in both the succulent (Sarcocornia, 0.78g ±g 0.18g mmg yrg '1) and grass (Sporobolus, 0.88g ±g 0.22g mmg yrg '1) assemblages located lower in the tidal frame. Short-term (6 days) experiments showed deposition within Juncus plots to be dominated by autochthonous organic inputs with C deposition rates ranging from 1.14g ±g 0.41g mgg Cg cmg '2g dg '1 (neap tidal period) to 2.37g ±g 0.44g mgg Cg cmg '2g dg '1 (spring tidal period), while minerogenic inputs and lower C deposition dominated Sarcocornia (0.10g ±g 0.02 to 0.62g ±g 0.08g mgg Cg cmg '2g dg '1) and Sporobolus (0.17g ±g 0.04 to 0.40g ±g 0.07g mgg Cg cmg '2g dg '1) assemblages. br br Elemental (Cg :g N), isotopic (?13C), mid-infrared (MIR) and 13C nuclear magnetic resonance (NMR) analyses revealed little difference in either the source or character of materials being deposited among neap versus spring tidal periods. Instead, these analyses point to substantial redistribution of materials within the Sarcocornia and Sporobolus assemblages, compared to high rete...
Kelleway, JJ, Saintilan, N, Macreadie, PI, Baldock, JA, Heijnis, H, Zawadzki, A, Gadd, P, Jacobsen, G & Ralph, PJ 2017, 'Geochemical analyses reveal the importance of environmental history for blue carbon sequestration', Journal of Geophysical Research: Biogeosciences, vol. 122, no. 7, pp. 1789-1805.View/Download from: UTS OPUS or Publisher's site
©2017. American Geophysical Union. All Rights Reserved. Coastal habitats including saltmarshes and mangrove forests can accumulate and store significant blue carbon stocks, which may persist for millennia. Despite this implied stability, the distribution and structure of intertidal-supratidal wetlands are known to respond to changes imposed by geomorphic evolution, climatic, sea level, and anthropogenic influences. In this study, we reconstruct environmental histories and biogeochemical conditions in four wetlands of similar contemporary vegetation in SE Australia. The objective is to assess the importance of historic factors to contemporary organic carbon (C) stocks and accumulation rates. Results from the four cores—two collected from marine-influenced saltmarshes (Wapengo marine site (WAP-M) and Port Stephens marine site (POR-M)) and two from fluvial influenced saltmarshes (Wapengo fluvial site (WAP-F) and Port Stephens fluvial site (POR-F))—highlight different environmental histories and preservation conditions. High C stocks are associated with the presence of a mangrove phase below the contemporary saltmarsh sediments in the POR-M and POR-F cores. 13 C nuclear magnetic resonance analyses show this historic mangrove root C to be remarkably stable in its molecular composition despite its age, consistent with its position in deep sediments. WAP-M and WAP-F cores did not contain mangrove root C; however, significant preservation of char C (up to 46% of C in some depths) in WAP-F reveals the importance of historic catchment processes to this site. Together, these results highlight the importance of integrating historic ecosystem and catchment factors into attempts to upscale C accounting to broader spatial scales.
Robinson, CM, Cherukuru, N, Hardman-Mountford, NJ, Everett, JD, McLaughlin, MJ, Davies, KP, van Dongen-Vogels, V, Ralph, PJ & Doblin, MA 2017, 'Phytoplankton absorption predicts patterns in primary productivity in Australian coastal shelf waters', Estuarine, Coastal and Shelf Science, vol. 192, pp. 1-16.View/Download from: UTS OPUS or Publisher's site
© 2017 Elsevier Ltd The phytoplankton absorption coefficient (a PHY ) has been suggested as a suitable alternate first order predictor of net primary productivity (NPP). We compiled a dataset of surface bio-optical properties and phytoplankton NPP measurements in coastal waters around Australia to examine the utility of an in-situ absorption model to estimate NPP. The magnitude of surface NPP (0.20–19.3 mmol C m −3 d −1 ) across sites was largely driven by phytoplankton biomass, with higher rates being attributed to the microplankton ( > 20 μm) size class. The phytoplankton absorption coefficient a PHY for PAR (photosynthetically active radiation; ā PHY )) ranged from 0.003 to 0.073 m -1 , influenced by changes in phytoplankton community composition, physiology and environmental conditions. The a PHY coefficient also reflected changes in NPP and the absorption model-derived NPP could explain 73% of the variability in measured surface NPP (n = 41; RMSE = 2.49). The absorption model was applied to two contrasting coastal locations to examine NPP dynamics: a high chlorophyll-high variation (HCHV; Port Hacking National Reference Station) and moderate chlorophyll-low variation (MCLV; Yongala National Reference Station) location in eastern Australia using the GIOP-DC satellite a PHY product. Mean daily NPP rates between 2003 and 2015 were higher at the HCHV site (1.71 ± 0.03 mmol C m −3 d −1 ) with the annual maximum NPP occurring during the austral winter. In contrast, the MCLV site annual NPP peak occurred during the austral wet season and had lower mean daily NPP (1.43 ± 0.03 mmol C m −3 d −1 ) across the time-series. An absorption-based model to estimate NPP is a promising approach for exploring the spatio-temporal dynamics in phytoplankton NPP around the Australian continental shelf.
Trevathan-Tackett, SM, Macreadie, PI, Sanderman, J, Baldock, J, Howes, JM & Ralph, PJ 2017, 'A Global Assessment of the Chemical Recalcitrance of Seagrass Tissues: Implications for Long-Term Carbon Sequestration', FRONTIERS IN PLANT SCIENCE, vol. 8.View/Download from: UTS OPUS or Publisher's site
Wilkinson, AD, Collier, CJ, Flores, F, Langlois, L, Ralph, PJ & Negri, AP 2017, 'Combined effects of temperature and the herbicide diuron on Photosystem II activity of the tropical seagrass Halophila ovalis.', Scientific Reports, vol. 7, pp. 1-11.View/Download from: UTS OPUS or Publisher's site
Tropical seagrasses are at their highest risk of exposure to photosystem II (PSII) herbicides when elevated rainfall and runoff from farms transports these toxicants into coastal habitats during summer, coinciding with periods of elevated temperature. PSII herbicides, such as diuron, can increase the sensitivity of corals to thermal stress, but little is known of the potential for herbicides to impact the thermal optima of tropical seagrass. Here we employed a well-plate approach to experimentally assess the effects of diuron on the photosynthetic performance of Halophila ovalis leaves across a 25 °C temperature range (36 combinations of these stressors across 15-40 °C). The thermal optimum for photosynthetic efficiency (▵) in H. ovalis was 31 °C while lower and higher temperatures reduced ▵ as did all elevated concentrations of diuron. There were significant interactions between the effects of temperature and diuron, with a majority of the combined stresses causing sub-additive (antagonistic) effects. However, both stressors caused negative responses and the sum of the responses was greater than that caused by temperature or diuron alone. These results indicate that improving water quality (reducing herbicide in runoff) is likely to maximise seagrass health during extreme temperature events that will become more common as the climate changes.
Commault, AS, Laczka, O, Siboni, N, Tamburic, B, Crosswell, JR, Seymour, JR & Ralph, PJ 2017, 'Electricity and biomass production in a bacteria-Chlorella based microbial fuel cell treating wastewater', Journal of Power Sources, vol. 356, pp. 299-309.View/Download from: UTS OPUS or Publisher's site
© 2017 Elsevier B.V. The chlorophyte microalga Chlorella vulgaris has been exploited within bioindustrial settings to treat wastewater and produce oxygen at the cathode of microbial fuel cells (MFCs), thereby accumulating algal biomass and producing electricity. We aimed to couple these capacities by growing C. vulgaris at the cathode of MFCs in wastewater previously treated by anodic bacteria. The bioelectrochemical performance of the MFCs was investigated with different catholytes including phosphate buffer and anode effluent, either in the presence or absence of C. vulgaris. The power output fluctuated diurnally in the presence of the alga. The maximum power when C. vulgaris was present reached 34.2 ± 10.0 mW m −2 , double that observed without the alga (15.6 ± 9.7 mW m −2 ), with a relaxation of 0.19 gL −1 d −1 chemical oxygen demand and 5 mg L −1 d −1 ammonium also removed. The microbial community associated with the algal biofilm included nitrogen-fixing (Rhizobiaceae), denitrifying (Pseudomonas stutzeri and Thauera sp., from Pseudomonadales and Rhodocyclales orders, respectively), and nitrate-reducing bacteria (Rheinheimera sp. from the Alteromonadales), all of which likely contributed to nitrogen cycling processes at the cathode. This paper highlights the importance of coupling microbial community screening to electrochemical and chemical analyses to better understand the processes involved in photo-cathode MFCs.
Tout, J, Astudillo-García, C, Taylor, MW, Tyson, GW, Stocker, R, Ralph, PJ, Seymour, JR & Webster, NS 2017, 'Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds.', Environmental Microbiology Reports, vol. 9, no. 6, pp. 750-755.View/Download from: UTS OPUS or Publisher's site
Marine sponges host stable and species-specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile. Flow cytometry analysis revealed significant levels of microbial chemotaxis towards R. odorabile extracts and 16S rRNA gene amplicon sequencing showed enrichment of 'sponge-specific' microbial phylotypes, including a cluster within the Gemmatimonadetes and another within the Actinobacteria. These findings infer a potential mechanism for how sponges can acquire bacterial symbionts from the surrounding environment and suggest an active role of the symbionts in finding their host.
Brodersen, KE, Hammer, KJ, Schrameyer, V, Floytrup, A, Rasheed, MA, Ralph, PJ, Kühl, M & Pedersen, O 2017, 'Sediment Resuspension and Deposition on Seagrass Leaves Impedes Internal Plant Aeration and Promotes Phytotoxic H2S Intrusion.', Frontiers in Plant Science, vol. 8, pp. 1-13.View/Download from: UTS OPUS or Publisher's site
HIGHLIGHTS: Sedimentation of fine sediment particles onto seagrass leaves severely hampers the plants' performance in both light and darkness, due to inadequate internal plant aeration and intrusion of phytotoxic H2S. Anthropogenic activities leading to sediment re-suspension can have adverse effects on adjacent seagrass meadows, owing to reduced light availability and the settling of suspended particles onto seagrass leaves potentially impeding gas exchange with the surrounding water. We used microsensors to determine O2 fluxes and diffusive boundary layer (DBL) thickness on leaves of the seagrass Zostera muelleri with and without fine sediment particles, and combined these laboratory measurements with in situ microsensor measurements of tissue O2 and H2S concentrations. Net photosynthesis rates in leaves with fine sediment particles were down to ~20% of controls without particles, and the compensation photon irradiance increased from a span of 20-53 to 109-145 μmol photons m-2 s-1. An ~2.5-fold thicker DBL around leaves with fine sediment particles impeded O2 influx into the leaves during darkness. In situ leaf meristematic O2 concentrations of plants exposed to fine sediment particles were lower than in control plants and exhibited long time periods of complete meristematic anoxia during night-time. Insufficient internal aeration resulted in H2S intrusion into the leaf meristematic tissues when exposed to sediment resuspension even at relatively high night-time water-column O2 concentrations. Fine sediment particles that settle on seagrass leaves thus negatively affect internal tissue aeration and thereby the plants' resilience against H2S intrusion.
Brodersen, KE, Koren, K, Moßhammer, M, Ralph, PJ, Kühl, M & Santner, J 2017, 'Seagrass-Mediated Phosphorus and Iron Solubilization in Tropical Sediments.', Environmental Science and Technology, vol. 51, no. 24, pp. 14155-14163.View/Download from: UTS OPUS or Publisher's site
Tropical seagrasses are nutrient-limited owing to the strong phosphorus fixation capacity of carbonate-rich sediments, yet they form densely vegetated, multispecies meadows in oligotrophic tropical waters. Using a novel combination of high-resolution, two-dimensional chemical imaging of O2, pH, iron, sulfide, calcium, and phosphorus, we found that tropical seagrasses are able to mobilize the essential nutrients iron and phosphorus in their rhizosphere via multiple biogeochemical pathways. We show that tropical seagrasses mobilize phosphorus and iron within their rhizosphere via plant-induced local acidification, leading to dissolution of carbonates and release of phosphate, and via local stimulation of microbial sulfide production, causing reduction of insoluble Fe(III) oxyhydroxides to dissolved Fe(II) with concomitant phosphate release into the rhizosphere porewater. These nutrient mobilization mechanisms have a direct link to seagrass-derived radial O2 loss and secretion of dissolved organic carbon from the below-ground tissue into the rhizosphere. Our demonstration of seagrass-derived rhizospheric phosphorus and iron mobilization explains why seagrasses are widely distributed in oligotrophic tropical waters.
Wangpraseurt, D, Holm, JB, Larkum, AWD, Pernice, M, Ralph, PJ, Suggett, DJ & Kühl, M 2017, 'In vivo Microscale Measurements of Light and Photosynthesis during Coral Bleaching: Evidence for the Optical Feedback Loop?', Frontiers in Microbiology, vol. 8, pp. 1-12.View/Download from: UTS OPUS or Publisher's site
Climate change-related coral bleaching, i.e., the visible loss of zooxanthellae from the coral host, is increasing in frequency and extent and presents a major threat to coral reefs globally. Coral bleaching has been proposed to involve accelerating light stress of their microalgal endosymbionts via a positive feedback loop of photodamage, symbiont expulsion and excess in vivo light exposure. To test this hypothesis, we used light and O2 microsensors to characterize in vivo light exposure and photosynthesis of Symbiodinium during a thermal stress experiment. We created tissue areas with different densities of Symbiodinium cells in order to understand the optical properties and light microenvironment of corals during bleaching. Our results showed that in bleached Pocillopora damicornis corals, Symbiodinium light exposure was up to fivefold enhanced relative to healthy corals, and the relationship between symbiont loss and light enhancement was well-described by a power-law function. Cell-specific rates of Symbiodinium gross photosynthesis and light respiration were enhanced in bleached P. damicornis compared to healthy corals, while areal rates of net photosynthesis decreased. Symbiodinium light exposure in Favites sp. revealed the presence of low light microniches in bleached coral tissues, suggesting that light scattering in thick coral tissues can enable photoprotection of cryptic symbionts. Our study provides evidence for the acceleration of in vivo light exposure during coral bleaching but this optical feedback mechanism differs between coral hosts. Enhanced photosynthesis in relation to accelerating light exposure shows that coral microscale optics exerts a key role on coral photophysiology and the subsequent degree of radiative stress during coral bleaching.
Larkum, AWD, Davey, PA, Kuo, J, Ralph, PJ & Raven, JA 2017, 'Carbon-concentrating mechanisms in seagrasses.', Journal of Experimental Botany, vol. 68, no. 14, pp. 3773-3784.View/Download from: UTS OPUS or Publisher's site
Seagrasses are unique angiosperms that carry out growth and reproduction submerged in seawater. They occur in at least three families of the Alismatales. All have chloroplasts mainly in the cells of the epidermis. Living in seawater, the supply of inorganic carbon (Ci) to the chloroplasts is diffusion limited, especially under unstirred conditions. Therefore, the supply of CO2 and bicarbonate across the diffusive boundary layer on the outer side of the epidermis is often a limiting factor. Here we discuss the evidence for mechanisms that enhance the uptake of Ci into the epidermal cells. Since bicarbonate is plentiful in seawater, a bicarbonate pump might be expected; however, the evidence for such a pump is not strongly supported. There is evidence for a carbonic anhydrase outside the outer plasmalemma. This, together with evidence for an outward proton pump, suggests the possibility that local acidification leads to enhanced concentrations of CO2 adjacent to the outer tangential epidermal walls, which enhances the uptake of CO2, and this could be followed by a carbon-concentrating mechanism (CCM) in the cytoplasm and/or chloroplasts. The lines of evidence for such an epidermal CCM are discussed, including evidence for special 'transfer cells' in some but not all seagrass leaves in the tangential inner walls of the epidermal cells. It is concluded that seagrasses have a CCM but that the case for concentration of CO2 at the site of Rubisco carboxylation is not proven.
Szabó, M, Larkum, AWD, Suggett, DJ, Vass, I, Sass, L, Osmond, B, Zavafer, A, Ralph, PJ & Chow, WS 2017, 'Non-intrusive assessment of photosystem II and photosystem I in whole coral tissues', Frontiers in Marine Science, vol. 4, pp. 1-12.View/Download from: UTS OPUS or Publisher's site
© 2017 Szabó, Larkum, Suggett, Vass, Sass, Osmond, Zavafer, Ralph and Chow. Reef building corals (phylum Cnidaria) harbor endosymbiotic dinoflagellate algae (genus Symbiodinium) that generate photosynthetic products to fuel their host's metabolism. Non-invasive techniques such as chlorophyll (Chl) fluorescence analyses of Photosystem II (PSII) have been widely used to estimate the photosynthetic performance of Symbiodinium in hospite. However, since the spatial origin of PSII chlorophyll fluorescence in coral tissues is uncertain, such signals give limited information on depth-integrated photosynthetic performance of the whole tissue. In contrast, detection of absorbance changes in the near infrared (NIR) region integrates signals from deeper tissue layers due to weak absorption and multiple scattering of NIR light. While extensively utilized in higher plants, NIR bio-optical techniques are seldom applied to corals. We have developed a non-intrusive measurement method to examine photochemistry of intact corals, based on redox kinetics of the primary electron donor in Photosystem I (P700) and chlorophyll fluorescence kinetics (Fast-Repetition Rate fluorometry, FRRf). Since the redox state of P700 depends on the operation of both PSI and PSII, important information can be obtained on the PSII-PSI intersystem electron transfer kinetics. Under moderate, sub-lethal heat stress treatments (33 ◦ C for~20 min), the coral Pavona decussata exhibited down-regulation of PSII electron transfer kinetics, indicated by slower rates of electron transport from Q A to plastoquinone (PQ) pool, and smaller relative size of oxidized PQ with concomitant decrease of a specifically-defined P700 kinetics area, which represents the active pool of PSII. The maximum quantum efficiency of PSII (F v /F m ) and functional absorption cross-section of PSII (σ PSII ) remained unchanged. Based on the coordinated response of P700 parameters and PSII-PSI electron transport properties, we propose that...
Goyen, S, Pernice, M, Szabó, M, Warner, ME, Ralph, PJ & Suggett, DJ 2017, 'A molecular physiology basis for functional diversity of hydrogen peroxide production amongst Symbiodinium spp. (Dinophyceae)', Marine Biology: international journal on life in oceans and coastal waters, vol. 164, no. 3.View/Download from: UTS OPUS or Publisher's site
Gardner, SG, Raina, J-B, Ralph, PJ & Petrou, K 2017, 'Reactive oxygen species (ROS) and dimethylated sulphur compounds in coral explants under acute thermal stress.', Journal of Experimental Biology, vol. 220, no. Pt 10, pp. 1787-1791.View/Download from: UTS OPUS or Publisher's site
Coral bleaching is intensifying with global climate change. Although the causes for these catastrophic events are well understood, the cellular mechanism that triggers bleaching is not well established. Our understanding of coral bleaching processes is hindered by the lack of robust methods for studying interactions between host and symbiont at the single-cell level. Here, we exposed coral explants to acute thermal stress and measured oxidative stress, more specifically, reactive oxygen species (ROS), in individual symbiont cells. Furthermore, we measured concentrations of dimethylsulphoniopropionate (DMSP) and dimethylsulphoxide (DMSO) to elucidate the role of these compounds in coral antioxidant function. This work demonstrates the application of coral explants for investigating coral physiology and biochemistry under thermal stress and delivers a new approach to study host-symbiont interactions at the microscale, allowing us to directly link intracellular ROS with DMSP and DMSO dynamics.
Wilkinson, SJ, Stoller, P, Ralph, P, Hamdorf, B, Navarro Catana, L & Santana Kuzava, G 2017, 'Exploring the feasibility of algae building technology in NSW', Procedia Engineering, vol. 180, pp. 1121-1130.View/Download from: UTS OPUS or Publisher's site
For some time, Biochemists have been exploring the potential to produce biofuels as an alternative to fossil fuel energy. Biofuels can be derived from crops such as corn, soybean and sugarcane however these crops can contribute to water scarcity and deforestation. Furthermore, large areas of land are used that could otherwise be used for food production. Another possibility is to use microalgae, which does not have the disadvantages associated with crop-based biofuels. Depending on conditions, microalgae can produce bio compounds that are converted into biofuels.
The built environment is responsible for around 40 to 50% of total greenhouse gas emissions through fossil fuel consumption. Not only is it necessary to design and to retrofit our built environment to be more energy efficient, but it is also necessary to consider alternative fuel sources. To date, this has mostly focused on solar, wind and geothermal sources, however one residential building in Hamburg Germany has adopted algae building technology in the form of façade panels which act as a source of energy for heating the apartments and for hot water. The climate in northern Germany is very different to Australia, and the question arises; what is the feasibility to adopt algae building technology in New South Wales? There are issues around the physical and technical aspects of the technology, the social and environmental aspects, the regulatory and planning aspects, as well as the economic considerations. This paper reports on a study with key stakeholders in New South Wales to explore barriers and drivers associated with the adoption of algae building technology.
Gardner, SG, Raina, J-B, Nitschke, MR, Nielsen, DA, Stat, M, Motti, CA, Ralph, PJ & Petrou, K 2017, 'A multi-trait systems approach reveals a response cascade to bleaching in corals', BMC BIOLOGY, vol. 15.View/Download from: UTS OPUS or Publisher's site
Macreadie, PI, Nielsen, DA, Kelleway, JJ, Atwood, TB, Seymour, JR, Petrou, K, Connolly, RM, Thomson, ACG, Trevathan-Tackett, SM & Ralph, PJ 2017, 'Can we manage coastal ecosystems to sequester more blue carbon?', Frontiers in Ecology and the Environment, vol. 15, no. 4, pp. 206-213.View/Download from: UTS OPUS or Publisher's site
© The Ecological Society of America To promote the sequestration of blue carbon, resource managers rely on best-management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment-level approaches. Drawing upon knowledge from a broad range of environmental variables that influence blue carbon sequestration, including warming, carbon dioxide levels, water depth, nutrients, runoff, bioturbation, physical disturbances, and tidal exchange, we discuss three potential management strategies that hold promise for optimizing coastal blue carbon sequestration: (1) reducing anthropogenic nutrient inputs, (2) reinstating top-down control of bioturbator populations, and (3) restoring hydrology. By means of case studies, we explore how these three strategies can minimize blue carbon losses and maximize gains. A key research priority is to more accurately quantify the impacts of these strategies on atmospheric greenhouse-gas emissions in different settings at landscape scales.
Petrou, K, Ralph, PJ & Nielsen, DA 2017, 'A novel mechanism for host-mediated photoprotection in endosymbiotic foraminifera.', ISME Journal, vol. 11, no. 2, pp. 453-462.View/Download from: Publisher's site
Light underpins the health and function of coral reef ecosystems, where symbiotic partnerships with photosynthetic algae constitute the life support system of the reef. Decades of research have given us detailed knowledge of the photoprotective capacity of phototrophic organisms, yet little is known about the role of the host in providing photoprotection in symbiotic systems. Here we show that the intracellular symbionts within the large photosymbiotic foraminifera Marginopora vertebralis exhibit phototactic behaviour, and that the phototactic movement of the symbionts is accomplished by the host, through rapid actin-mediated relocation of the symbionts deeper into the cavities within the calcium carbonate test. Using a photosynthetic inhibitor, we identified that the infochemical signalling for host regulation is photosynthetically derived, highlighting the presence of an intimate communication between the symbiont and the host. Our results emphasise the central importance of the host in photosymbiotic photoprotection via a new mechanism in foraminifera that can serve as a platform for exploring host-symbiont communication in other photosymbiotic organisms.
Trevathan-Tackett, SM, Seymour, JR, Nielsen, DA, Macreadie, PI, Jeffries, TC, Sanderman, J, Baldock, J, Howes, JM, Steven, ADL & Ralph, PJ 2017, 'Sediment anoxia limits microbial-driven seagrass carbon remineralization under warming conditions.', FEMS Microbiology Ecology, vol. 93, no. 6.View/Download from: UTS OPUS or Publisher's site
Seagrass ecosystems are significant carbon sinks, and their resident microbial communities ultimately determine the quantity and quality of carbon sequestered. However, environmental perturbations have been predicted to affect microbial-driven seagrass decomposition and subsequent carbon sequestration. Utilizing techniques including 16S-rDNA sequencing, solid-state NMR and microsensor profiling, we tested the hypothesis that elevated seawater temperatures and eutrophication enhance the microbial decomposition of seagrass leaf detritus and rhizome/root tissues. Nutrient additions had a negligible effect on seagrass decomposition, indicating an absence of nutrient limitation. Elevated temperatures caused a 19% higher biomass loss for aerobically decaying leaf detritus, coinciding with changes in bacterial community structure and enhanced lignocellulose degradation. Although, community shifts and lignocellulose degradation were also observed for rhizome/root decomposition, anaerobic decay was unaffected by temperature. These observations suggest that oxygen availability constrains the stimulatory effects of temperature increases on bacterial carbon remineralization, possibly through differential temperature effects on bacterial functional groups, including putative aerobic heterotrophs (e.g. Erythrobacteraceae, Hyphomicrobiaceae) and sulfate reducers (e.g. Desulfobacteraceae). Consequently, under elevated seawater temperatures, carbon accumulation rates may diminish due to higher remineralization rates at the sediment surface. Nonetheless, the anoxic conditions ubiquitous to seagrass sediments can provide a degree of carbon protection under warming seawater temperatures.
Jiang, Z, Kumar, M, Padula, MP, Pernice, M, Kahlke, T, Kim, M & Ralph, PJ 2017, 'Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis.', Frontiers in Plant Science, vol. 8, pp. 1-14.View/Download from: UTS OPUS or Publisher's site
The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis. All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis. However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2% PVPP and protease inhibitors. Further, the extracted proteins were solubilized in 0.5% of zwitterionic detergent (C7BzO) instead of 4% CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoenolpyruvate carboxylase (PEPC-a key enzyme for carbon metabolism). ...
Kumar, M, Padula, MP, Davey, P, Pernice, M, Jiang, Z, Sablok, G, Contreras-Porcia, L & Ralph, PJ 2017, 'Proteome Analysis Reveals Extensive Light Stress-Response Reprogramming in the Seagrass Zostera muelleri (Alismatales, Zosteraceae) Metabolism.', Frontiers in Plant Science, vol. 7, pp. 1-19.View/Download from: UTS OPUS or Publisher's site
Seagrasses are marine ecosystem engineers that are currently declining in abundance at an alarming rate due to both natural and anthropogenic disturbances in ecological niches. Despite reports on the morphological and physiological adaptations of seagrasses to extreme environments, little is known of the molecular mechanisms underlying photo-acclimation, and/or tolerance in these marine plants. This study applies the two-dimensional isoelectric focusing (2D-IEF) proteomics approach to identify photo-acclimation/tolerance proteins in the marine seagrass Zostera muelleri. For this, Z. muelleri was exposed for 10 days in laboratory mesocosms to saturating (control, 200 μmol photons m-2 s-1), super-saturating (SSL, 600 μmol photons m-2 s-1), and limited light (LL, 20 μmol photons m-2 s-1) irradiance conditions. Using LC-MS/MS analysis, 93 and 40 protein spots were differentially regulated under SSL and LL conditions, respectively, when compared to the control. In contrast to the LL condition, Z. muelleri robustly tolerated super-saturation light than control conditions, evidenced by their higher relative maximum electron transport rate and minimum saturating irradiance values. Proteomic analyses revealed up-regulation and/or appearances of proteins belonging to the Calvin-Benson and Krebs cycle, glycolysis, the glycine cleavage system of photorespiration, and the antioxidant system. These proteins, together with those from the inter-connected glutamate-proline-GABA pathway, shaped Z. muelleri photosynthesis and growth under SSL conditions. In contrast, the LL condition negatively impacted the metabolic activities of Z. muelleri by down-regulating key metabolic enzymes for photosynthesis and the metabolism of carbohydrates and amino acids, which is consistent with the observation with lower photosynthetic performance under LL condition. This study provides novel insights into the underlying molecular photo-acclimation mechanisms in Z. muelleri, in addition to identify...
Baird, ME, Adams, MP, Babcock, RC, Oubelkheir, K, Mongin, M, Wild-Allen, KA, Skerratt, J, Robson, BJ, Petrou, K, Ralph, PJ, O'Brien, KR, Carter, AB, Jarvis, JC & Rasheed, MA 2016, 'A biophysical representation of seagrass growth for application in a complex shallow-water biogeochemical model', ECOLOGICAL MODELLING, vol. 325, pp. 13-27.View/Download from: Publisher's site
Baird, ME, Cherukuru, N, Jones, E, Margvelashvili, N, Mongin, M, Oubelkheir, K, Ralph, PJ, Rizwi, F, Robson, BJ, Schroeder, T, Skerratt, J, Steven, ADL & Wild-Allen, KA 2016, 'Remote-sensing reflectance and true colour produced by a coupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: Comparison with satellite data', ENVIRONMENTAL MODELLING & SOFTWARE, vol. 78, pp. 79-96.View/Download from: Publisher's site
Chartrand, KM, Bryant, CV, Carter, AB, Ralph, PJ & Rasheed, MA 2016, 'Light thresholds to prevent dredging impacts on the great barrier reef seagrass, Zostera muelleri ssp. capricorni', Frontiers in Marine Science, vol. 3, pp. 1-17.View/Download from: UTS OPUS or Publisher's site
© 2016 Chartrand, Bryant, Carter, Ralph and Rasheed. Coastal seagrass habitats are at risk from a range of anthropogenic activities that modify the natural light environment, including dredging activities associated with coastal and port developments. On Australia's east coast, the tropical seagrass Zostera muelleri ssp. capricorni dominates intertidal mudbanks in sheltered embayments which are also preferred locations for harbors and port facilities. Dredging to establish and maintain shipping channels in these areas can degrade water quality and diminish light conditions that are required for seagrass growth. Based on this potential conflict, we simulated in-situ light attenuation events to measure effects on Z. muelleri ssp. capricorni condition. Semi-annual in situ shading studies conducted over 3 years were used to quantify the impact of prolonged light reduction on seagrass morphometrics (biomass, percent cover, and shoot density). Experimental manipulations were complimented with an assessment of 46 months of light history and concurrent natural seagrass change at the study site in Gladstone Harbour. There was a clear light-dependent effect on seagrass morphometrics during seagrass growing seasons, but no effect during senescent periods. Significant seagrass declines occurred between 4 and 8 weeks after shading during the growing seasons with light maintained in the range of 4-5 mol photons m -2 d -1 . Sensitivity to shading declined when applied in 2-week intervals (fortnightly) rather than continuous over the same period. Field observations were correlated to manipulative experiments to derive an applied threshold of 6 mol photons m -2 d -1 which formed the basis of a reactive light-based management strategy which has been successfully implemented to ensure positive ecological outcomes for seagrass during a large-scale dredging program.
Kelleway, JJ, Saintilan, N, Macreadie, PI & Ralph, PJ 2016, 'Sedimentary Factors are Key Predictors of Carbon Storage in SE Australian Saltmarshes', ECOSYSTEMS, vol. 19, no. 5, pp. 865-880.View/Download from: Publisher's site
Kelleway, JJ, Saintilan, N, Macreadie, PI, Skilbeck, CG, Zawadzki, A & Ralph, PJ 2016, 'Seventy years of continuous encroachment substantially increases "blue carbon' capacity as mangroves replace intertidal salt marshes', GLOBAL CHANGE BIOLOGY, vol. 22, no. 3, pp. 1097-1109.View/Download from: Publisher's site
Mongin, M, Baird, ME, Tilbrook, B, Matear, RJ, Lenton, A, Herzfeld, M, Wild-Allen, K, Skerratt, J, Margvelashvili, N, Robson, BJ, Duarte, CM, Gustafsson, MS, Ralph, PJ & Steven, AD 2016, 'The exposure of the Great Barrier Reef to ocean acidification.', Nature Communications, vol. 7, pp. 1-8.View/Download from: UTS OPUS or Publisher's site
The Great Barrier Reef (GBR) is founded on reef-building corals. Corals build their exoskeleton with aragonite, but ocean acidification is lowering the aragonite saturation state of seawater (Ωa). The downscaling of ocean acidification projections from global to GBR scales requires the set of regional drivers controlling Ωa to be resolved. Here we use a regional coupled circulation-biogeochemical model and observations to estimate the Ωa experienced by the 3,581 reefs of the GBR, and to apportion the contributions of the hydrological cycle, regional hydrodynamics and metabolism on Ωa variability. We find more detail, and a greater range (1.43), than previously compiled coarse maps of Ωa of the region (0.4), or in observations (1.0). Most of the variability in Ωa is due to processes upstream of the reef in question. As a result, future decline in Ωa is likely to be steeper on the GBR than currently projected by the IPCC assessment report.
Petrou, K, Kranz, SA, Trimborn, S, Hassler, CS, Ameijeiras, SB, Sackett, O, Ralph, PJ & Davidson, AT 2016, 'Southern Ocean phytoplankton physiology in a changing climate', JOURNAL OF PLANT PHYSIOLOGY, vol. 203, pp. 135-150.View/Download from: UTS OPUS or Publisher's site
Sablok, G, Mudunuri, SB, Edwards, D & Ralph, PJ 2016, 'Chloroplast genomics: Expanding resources for an evolutionary conserved miniature molecule with enigmatic applications', Current Plant Biology, vol. 7-8, pp. 34-38.View/Download from: UTS OPUS or Publisher's site
© 2016 The Authors Chloroplast, methylation depreived uniparental organelle genome is the most studied organelle genome from the perspective of evolution and functional omics. Recent advances in organelle genome sequencing both in terms of genome or transcriptome sequencing has opened a wide range of opportunities to understand the transcriptional and translational role of the genes mainly involved in the light harvesting apparatus and the evolution of the inverted repeats across the lineage. However, as compared to the nuclear genome, limited resources are available in case of organelle genome. In this review, we discuss the recent advances in the chloroplast genomics and the resources that have been developed for understanding the evolution, repeat patterns, functional genomics of this miniature molecule with enigmatic applications.
Sablok, G, Pérez-Pulido, AJ, Do, T, Seong, TY, Casimiro-Soriguer, CS, La Porta, N, Ralph, PJ, Squartini, A, Muñoz-Merida, A & Harikrishna, JA 2016, 'PlantFuncSSR: Integrating first and next generation transcriptomics for mining of SSR-functional domains markers', Frontiers in Plant Science, vol. 7, pp. 1-9.View/Download from: UTS OPUS or Publisher's site
© 2016 Sablok, Pérez-Pulido, Do, Seong, Casimiro-Soriguer, La Porta, Ralph, Squartini, Muñoz-Merida and Harikrishna. Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intrageneric differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www. bioinfocabd.upo.es/plantssr.
Sackett, O, Petrou, K, Reedy, B, Hill, R, Doblin, M, Beardall, J, Ralph, P & Heraud, P 2016, 'Snapshot prediction of carbon productivity, carbon and protein content in a Southern Ocean diatom using FTIR spectroscopy.', The ISME journal, vol. 10, pp. 416-426.View/Download from: UTS OPUS or Publisher's site
Diatoms, an important group of phytoplankton, bloom annually in the Southern Ocean, covering thousands of square kilometers and dominating the region's phytoplankton communities. In their role as the major food source to marine grazers, diatoms supply carbon, nutrients and energy to the Southern Ocean food web. Prevailing environmental conditions influence diatom phenotypic traits (for example, photophysiology, macromolecular composition and morphology), which in turn affect the transfer of energy, carbon and nutrients to grazers and higher trophic levels, as well as oceanic biogeochemical cycles. The paucity of phenotypic data on Southern Ocean phytoplankton limits our understanding of the ecosystem and how it may respond to future environmental change. Here we used a novel approach to create a 'snapshot' of cell phenotype. Using mass spectrometry, we measured nitrogen (a proxy for protein), total carbon and carbon-13 enrichment (carbon productivity), then used this data to build spectroscopy-based predictive models. The models were used to provide phenotypic data for samples from a third sample set. Importantly, this approach enabled the first ever rate determination of carbon productivity from a single time point, circumventing the need for time-series measurements. This study showed that Chaetoceros simplex was less productive and had lower protein and carbon content during short-term periods of high salinity. Applying this new phenomics approach to natural phytoplankton samples could provide valuable insight into understanding phytoplankton productivity and function in the marine system.The ISME Journal advance online publication, 31 July 2015; doi:10.1038/ismej.2015.123.
Doblin, MA, Petrou, K, Sinutok, S, Seymour, JR, Messer, LF, Brown, MV, Norman, L, Everett, JD, McInnes, AS, Ralph, PJ, Thompson, PA & Hassler, CS 2016, 'Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current', PEERJ, vol. 4.View/Download from: UTS OPUS or Publisher's site
Jeffries, TC, Curlevski, NJ, Brown, MV, Harrison, DP, Doblin, MA, Petrou, K, Ralph, PJ & Seymour, JR 2016, 'Partitioning of fungal assemblages across different marine habitats', ENVIRONMENTAL MICROBIOLOGY REPORTS, vol. 8, no. 2, pp. 235-238.View/Download from: UTS OPUS or Publisher's site
Jeffries, TC, Schmitz Fontes, ML, Harrison, DP, Van-Dongen-Vogels, V, Eyre, BD, Ralph, PJ & Seymour, JR 2016, 'Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary.', Frontiers in Microbiology, vol. 6, pp. 1-17.View/Download from: UTS OPUS or Publisher's site
The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide insights into the simultaneous influence of natural and anthropogenic drivers on the structure and...
Murray, SA, Suggett, DJ, Seymour, JR, Doblin, M, Kohli, GS, Fabris, M & Ralph, PJ 2016, 'Unravelling the functional genetics of dinoflagellates: a review of approaches and opportunities', Perspectives in Phycology, vol. 3, no. 1, pp. 37-52.View/Download from: UTS OPUS or Publisher's site
Dinoflagellates occupy an extraordinarily diverse array of ecological niches. Their success stems from a suite of functional and ecological strategies, including the production of secondary metabolites with anti-predator or allelopathic impacts, nutritional flexibility, and the ability to form symbiotic relationships. Despite their ecological importance, we currently have a poor understanding of the genetic basis for many of these strategies, due to the complex genomes of dinoflagellates. Genomics and transcriptomic sequencing approaches are now providing the first insights into the genetic basis of some dinoflagellate functional traits, providing the opportunity for novel ecological experiments, novel methods for monitoring of harmful biotoxins, and allowing us to investigate the production of ecologically and economically important compounds such as the long chain polyunsaturated fatty acid, docosahexanoic acid and the climatically important metabolite, dimethylsulfoniopropionate. Despite these advances, we still generally lack the ability to genetically manipulate species, which would enable the confirmation of biosynthetic pathways and the development of novel bio-engineering applications. Here, we describe advances in understanding the genetic basis of dinoflagellate ecology, and propose biotechnological approaches that could be applied to further transform our understanding of this unique group of eukaryotes.
Davey, PA, Pernice, M, Sablok, G, Larkum, A, Lee, HT, Golicz, A, Edwards, D, Dolferus, R & Ralph, P 2016, 'The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses.', Functional & Integrative Genomics, vol. 16, no. 5, pp. 465-480.View/Download from: UTS OPUS or Publisher's site
Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.
Lee, H, Golicz, AA, Bayer, PE, Jiao, Y, Tang, H, Paterson, AH, Sablok, G, Krishnaraj, RR, Chan, C-KK, Batley, J, Kendrick, GA, Larkum, AWD, Ralph, PJ & Edwards, D 2016, 'The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri)', PLANT PHYSIOLOGY, vol. 172, no. 1, pp. 272-283.View/Download from: Publisher's site
Rehman, AU, Szabó, M, Deák, Z, Sass, L, Larkum, A, Ralph, P & Vass, I 2016, 'Symbiodinium sp. cells produce light-induced intra- and extracellular singlet oxygen, which mediates photodamage of the photosynthetic apparatus and has the potential to interact with the animal host in coral symbiosis.', The New phytologist, vol. 212, pp. 472-484.View/Download from: Publisher's site
Coral bleaching is an important environmental phenomenon, whose mechanism has not yet been clarified. The involvement of reactive oxygen species (ROS) has been implicated, but direct evidence of what species are involved, their location and their mechanisms of production remains unknown. Histidine-mediated chemical trapping and singlet oxygen sensor green (SOSG) were used to detect intra- and extracellular singlet oxygen ((1) O2 ) in Symbiodinium cultures. Inhibition of the Calvin-Benson cycle by thermal stress or high light promotes intracellular (1) O2 formation. Histidine addition, which decreases the amount of intracellular (1) O2 , provides partial protection against photosystem II photoinactivation and chlorophyll (Chl) bleaching. (1) O2 production also occurs in cell-free medium of Symbiodinium cultures, an effect that is enhanced under heat and light stress and can be attributed to the excretion of (1) O2 -sensitizing metabolites from the cells. Confocal microscopy imaging using SOSG showed most extracellular (1) O2 around the cell surface, but it is also produced across the medium distant from the cells. We demonstrate, for the first time, both intra- and extracellular (1) O2 production in Symbiodinium cultures. Intracellular (1) O2 is associated with photosystem II photodamage and pigment bleaching, whereas extracellular (1) O2 has the potential to mediate the breakdown of symbiotic interaction between zooxanthellae and their animal host during coral bleaching.
Schrameyer, V, Kraemer, W, Hill, R, Jeans, J, Larkum, AWD, Bischof, K, Campbell, DA & Ralph, PJ 2016, 'Under high light stress two Indo-Pacific coral species display differential photodamage and photorepair dynamics', MARINE BIOLOGY, vol. 163, no. 8.View/Download from: Publisher's site
Slavov, C, Schrameyer, V, Reus, M, Ralph, PJ, Hill, R, Buechel, C, Larkum, AWD & Holzwarth, AR 2016, '"Super-quenching" state protects Symbiodinium from thermal stress - Implications for coral bleaching', BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1857, no. 6, pp. 840-847.View/Download from: Publisher's site
Kumar, M, Kuzhiumparambil, U, Pernice, M, Jiang, Z & Ralph, PJ 2016, 'Metabolomics: an emerging frontier of systems biology in marine macrophytes', ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, vol. 16, pp. 76-92.View/Download from: UTS OPUS or Publisher's site
Pernice, M, Sinutok, S, Sablok, G, Commault, A, Schliep, M, Macreadie, P, Rasheed, M & Ralph, P 2016, 'Molecular physiology reveals ammonium uptake and related gene expression in the seagrass Zostera muelleri', Marine Environmental Research.View/Download from: UTS OPUS or Publisher's site
Gardner, SG, Nielsen, DA, Laczka, O, Shimmon, R, Beltran, VH, Ralph, PJ & Petrou, K 2016, 'Dimethylsulfoniopropionate, superoxide dismutase and glutathione as stress response indicators in three corals under short-term hyposalinity stress', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 283, no. 1824.View/Download from: UTS OPUS or Publisher's site
Tran, N-AT, Padula, MP, Evenhuis, CR, Commault, AS, Ralph, PJ & Tamburic, B 2016, 'Proteomic and biophysical analyses reveal a metabolic shift in nitrogen deprived Nannochloropsis oculata', ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, vol. 19, pp. 1-11.View/Download from: UTS OPUS or Publisher's site
Hill, R, Bellgrove, A, Macreadie, PI, Petrou, K, Beardall, J, Steven, A & Ralph, PJ 2015, 'Can macroalgae contribute to blue carbon? An Australian perspective', LIMNOLOGY AND OCEANOGRAPHY, vol. 60, no. 5, pp. 1689-1706.View/Download from: Publisher's site
Hong, Y, Burford, MA, Ralph, PJ & Doblin, MA 2015, 'Subtropical zooplankton assemblage promotes the harmful cyanobacterium Cylindrospermopsis raciborskii in a mesocosm experiment', JOURNAL OF PLANKTON RESEARCH, vol. 37, no. 1, pp. 90-101.View/Download from: UTS OPUS or Publisher's site
Kumar, M, Reddy, CRK & Ralph, PJ 2015, 'Polyamines in morphogenesis and development: a promising research area in seaweeds.', Frontiers in plant science, vol. 6, pp. 27-27.View/Download from: UTS OPUS or Publisher's site
Malik, A, Lenzen, M, Ralph, PJ & Tamburic, B 2015, 'Hybrid life-cycle assessment of algal biofuel production', BIORESOURCE TECHNOLOGY, vol. 184, pp. 436-443.View/Download from: UTS OPUS or Publisher's site
Sablok, G, Raju, GVP, Mudunuri, SB, Prabha, R, Singh, DP, Baev, V, Yahubyan, G, Ralph, PJ & La Porta, N 2015, 'ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection', DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.View/Download from: UTS OPUS or Publisher's site
Sablok, G, Srivastva, AK, Suprasanna, P, Baev, V & Ralph, PJ 2015, 'isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology.', Frontiers in plant science, vol. 6, pp. 949-949.View/Download from: UTS OPUS or Publisher's site
Trevathan-Tackett, SM, Kelleway, J, Macreadie, PI, Beardall, J, Ralph, P & Bellgrove, A 2015, 'Comparison of marine macrophytes for their contributions to blue carbon sequestration', ECOLOGY, vol. 96, no. 11, pp. 3043-3057.View/Download from: Publisher's site
Wilkinson, AD, Collier, CJ, Flores, F, Mercurio, P, O'Brien, J, Ralph, PJ & Negri, AP 2015, 'A Miniature Bioassay for Testing the Acute Phytotoxicity of Photosystem II Herbicides on Seagrass', PLOS ONE, vol. 10, no. 2.View/Download from: UTS OPUS or Publisher's site
Woodcock, S, Manojlovic, B, Baird, ME & Ralph, PJ 2015, 'A Poisson-Pareto Model of chlorophyll-A Fluorescence Signals in Marine Environments', Australia and New Zealand Industrial and Applied Mathematics (ANZIAM) Journal, vol. 56, no. 4, pp. 373-370.View/Download from: UTS OPUS or Publisher's site
Tout, J, Siboni, N, Messer, LF, Garren, M, Stocker, R, Webster, NS, Ralph, PJ & Seymour, JR 2015, 'Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis', Frontiers in Microbiology, vol. 6, pp. 1-12.View/Download from: UTS OPUS or Publisher's site
Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.
Tout, J, Siboni, N, Messer, LF, Garren, M, Stocker, R, Webster, NS, Ralph, PJ & Seymour, JR 2015, 'Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis.', Frontiers in Microbiology, vol. 6, pp. 432-432.View/Download from: UTS OPUS or Publisher's site
Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2-3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2-3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.
Golicz, AA, Schliep, M, Lee, HT, Larkum, AWD, Dolferus, R, Batley, J, Chan, C-KK, Sablok, G, Ralph, PJ & Edwards, D 2015, 'Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network', JOURNAL OF EXPERIMENTAL BOTANY, vol. 66, no. 5, pp. 1489-1498.View/Download from: UTS OPUS or Publisher's site
Tamburic, B, Evenhuis, CR, Suggett, DJ, Larkum, AWD, Raven, JA & Ralph, PJ 2015, 'Gas Transfer Controls Carbon Limitation During Biomass Production by Marine Microalgae', CHEMSUSCHEM, vol. 8, no. 16, pp. 2727-2736.View/Download from: UTS OPUS or Publisher's site
Radford, D, Szabo, M, Raven, J & Ralph, PJ 2015, 'SATISFYING THE NUTRIENT TANK OF NANNOCHLOROPSIS OCULATA; CO-LIMITATION REDUCES FILLING EFFICIENCY', EUROPEAN JOURNAL OF PHYCOLOGY, vol. 50, pp. 138-139.
Suggett, DJ, Goyen, S, Evenhuis, C, Szabo, M, Pettay, DT, Warner, ME & Ralph, PJ 2015, 'Functional diversity of photobiological traits within the genus Symbiodinium appears to be governed by the interaction of cell size with cladal designation', New Phytologist, vol. 208, no. 2, pp. 370-381.View/Download from: UTS OPUS or Publisher's site
© 2015 New Phytologist Trust. Dinoflagellates of the genus Symbiodinium express broad diversity in both genetic identity (phylogeny) and photosynthetic function to presumably optimize ecological success across extreme light environments; however, whether differences in the primary photobiological characteristics that govern photosynthetic optimization are ultimately a function of phylogeny is entirely unresolved. We applied a novel fast repetition rate fluorometry approach to screen genetically distinct Symbiodinium types (n = 18) spanning five clades (A-D, F) for potential phylogenetic trends in factors modulating light absorption (effective cross-section, reaction center content) and utilization (photochemical vs dynamic nonphotochemical quenching; [1 - C] vs [1 - Q]) by photosystem II (PSII). The variability of PSII light absorption was independent of phylogenetic designation, but closely correlated with cell size across types, whereas PSII light utilization intriguingly followed one of three characteristic patterns: (1) similar reliance on [1 - C] and [1 - Q] or (2) preferential reliance on [1 - C] (mostly A, B types) vs (3) preferential reliance on [1 - Q] (mostly C, D, F types), and thus generally consistent with cladal designation. Our functional trait-based approach shows, for the first time, how Symbiodinium photosynthetic function is governed by the interplay between phylogenetically dependent and independent traits, and is potentially a means to reconcile complex biogeographic patterns of Symbiodinium phylogenetic diversity in nature.
Schliep, M, Pernice, M, Sinutok, S, Bryant, CV, York, PH, Rasheed, MA & Ralph, PJ 2015, 'Evaluation of Reference Genes for RT-qPCR Studies in the Seagrass Zostera muelleri Exposed to Light Limitation', SCIENTIFIC REPORTS, vol. 5.View/Download from: UTS OPUS or Publisher's site
Raven, J & Ralph, PJ 2015, 'Enhanced biofuel production using optimality, pathway modification and waste minimization', Journal of Applied Phycology, vol. 27, pp. 1-31.View/Download from: UTS OPUS or Publisher's site
In response to their environment, algae in the wild may use an approximation to optimality of resource allocation in cellular structures, photosynthetic pigments, enzymes, transporters in membranes and RNAs and in their genetic material. However, under controlled conditions, when algae are grown for biofuel (lipid) production for example, some of these processes can be altered to increase the efficiency of photosynthesis and therefore, lipid yield. This suggests that there is scope for selecting mutations and for genetic engineering at various levels in the photosynthetic apparatus with the aim of increasing efficiency of photon use and the rate of transformation of resources per unit biomass to improve biofuel yields. More specifically, the wavelength range covered by photosynthetic pigments and photochemical reaction centres could be increased, the number of protons transported from the thylakoid lumen to the stroma per unit ATP synthesised by the ATP synthetase could be decreased, the fluctuating light effect could be utilised and photosynthetic pathways changed, e.g. replacing part or all of the current machinery for autotrophic fixation of inorganic carbon. There are also possibilities for decreasing carbon loss by decreasing `wasteful aspects of dark respiration and of dissolved organic carbon loss. Provided that the environmental fluctuations to which algal growth conditions are constrained, there are possibilities for decreasing the resource costs of protection from ROS, and by down-regulating photoprotective mechanisms, as well as limiting the capacity to repair processes related to photoinhibition. Decreased protein turnover is also a potential energetic saving. These interventions apply to individual processes; however, this may not be immediately incorporated into the optimal allocation of resources by the alga, and further intervention using a system biology approach may be required.
Brodersen, KE, Nielsen, DA, Ralph, PJ & Kuhl, M 2015, 'Oxic microshield and local pH enhancement protects Zostera muelleri from sediment derived hydrogen sulphide', NEW PHYTOLOGIST, vol. 205, no. 3, pp. 1264-1276.View/Download from: UTS OPUS or Publisher's site
Gardner, SG, Nielsen, DA, Petrou, K, Larkum, AWD & Ralph, PJ 2015, 'Characterisation of coral explants: a model organism for cnidarian-dinoflagellate studies', CORAL REEFS, vol. 34, no. 1, pp. 133-142.View/Download from: UTS OPUS or Publisher's site
Nielsen, DA, Pernice, M, Schliep, M, Sablok, G, Jeffries, TC, Kuehl, M, Wangpraseurt, D, Ralph, PJ & Larkum, AWD 2015, 'Microenvironment and phylogenetic diversity of Prochloron inhabiting the surface of crustose didemnid ascidians', ENVIRONMENTAL MICROBIOLOGY, vol. 17, no. 10, pp. 4121-4132.View/Download from: UTS OPUS or Publisher's site
Gustafsson, MSM, Baird, ME & Ralph, PJ 2014, 'Modeling photoinhibition-driven bleaching in Scleractinian coral as a function of light, temperature, and heterotrophy', LIMNOLOGY AND OCEANOGRAPHY, vol. 59, no. 2, pp. 603-622.View/Download from: UTS OPUS or Publisher's site
Hassler, CS, Ridgway, K, Bowie, AR, Butler, EC, Clementson, L, Doblin, MA, Davies, DM, Law, C, Ralph, PJ, van der Merwe, P, Watson, R & Ellwood, M 2014, 'Primary productivity induced by iron and nitrogen in the Tasman Sea - An overview of the PINTS expedition', Marine and Freshwater Research, vol. 65, no. 6, pp. 517-537.View/Download from: UTS OPUS or Publisher's site
The Tasman Sea and the adjacent Sub-Antarctic zone (SAZ) are economically important regions, where the parameters controlling the phytoplankton community composition and carbon fixation are not yet fully resolved. Contrasting nutrient distributions as well as phytoplankton biomass, biodiversity and productivity we observed between the North Tasman Sea and the SAZ. In-situ FV/FM, dissolved and particulate nutrients, iron biological uptake, and nitrogen and carbon fixation were used to determine the factor limiting phytoplankton growth and productivity in the North Tasman Sea and the SAZ. Highly productive cyanobacteria dominated the North Tasman Sea. High atmospheric nitrogen fixation and low nitrate dissolved concentrations indicated that non-diazotroph phytoplankton are nitrogen limited. Deck-board incubations also suggested that, at depth, iron could limit eukaryotes, but not cyanobacteria in that region. In the SAZ, the phytoplankton community was dominated by a bloom of haptophytes. The low productivity in the SAZ was mainly explained by light limitation, but nitrogen, silicic acid as well as iron were all depleted to the extent that they could become co-limiting. This study illustrates the challenge associated with identification of the limiting nutrient as it varied between phytoplankton groups, depths and sites.
Macreadie, PI, Schliep, MT, Rasheed, M, Chartrand, KM & Ralph, PJ 2014, 'Molecular indicators of chronic seagrass stress: A new era in the management of seagrass ecosystems?', Ecological Indicators, vol. 38, pp. 279-281.View/Download from: UTS OPUS or Publisher's site
Petrou, K, Trimborn, S, Rost, B, Ralph, PJ & Hassler, CS 2014, 'The impact of iron limitation on the physiology of the Antarctic diatom Chaetoceros simplex', Marine Biology, vol. 161, pp. 925-937.View/Download from: UTS OPUS or Publisher's site
Iron availability strongly governs the growth of Southern Ocean phytoplankton. To investigate how iron limitation affects photosynthesis as well as the uptake of carbon and iron in the Antarctic diatom Chaetoceros simplex, a combination of chlorophyll a fluorescence measurements and radiotracer incubations in the presence and absence of chemical inhibitors was conducted. Iron limitation in C. simplex led to a decline in growth rates, photochemical efficiency and structural changes in photosystem II (PSII), including a reorganisation of photosynthetic units in PSII and an increase in size of the functional absorption cross section of PSII. Iron-limited cells further exhibited a reduced plastoquinone pool and decreased photosynthetic electron transport rate, while non-photochemical quenching and relative xanthophyll pigment content were strongly increased, suggesting a photoprotective response. Additionally, iron limitation resulted in a strong decline in carbon fixation and thus the particulate organic carbon quotas. Inhibitor studies demonstrated that, independent of the iron supply, carbon fixation was dependent on internal, but not on extracellular carbonic anhydrase activity. Orthovanadate more strongly inhibited iron uptake in iron-limited cells, indicating that P-type ATPase transporters are involved in iron uptake. The stronger reduction in iron uptake by ascorbate in iron-limited cells suggests that the re-oxidation of iron is required before it can be taken up and further supports the presence of a high-affinity iron transport pathway. The measured changes to photosystem architecture and shifts in carbon and iron uptake strategies in C. simplex as a result of iron limitation provide evidence for a complex interaction of these processes to balance the iron requirements for photosynthesis and carbon demand for sustained growth in iron-limited waters.
Sackett, O, Armand, L, Beardall, J, Hill, R, Doblin, M, Connelly, C, Howes, J, Stuart, B, Ralph, P & Heraud, P 2014, 'Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy', Biogeosciences Discussions, vol. 11, no. 20, pp. 5795-5808.View/Download from: UTS OPUS or Publisher's site
Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value – furthermore, data on taxon-specific responses are almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate/silicic acid and carbohydrates. In contrast to some previous studies, silicate/silicic acid levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community mea...
Tout, JA, Jeffries, TC, Webster, NS, Stocker, R, Ralph, PJ & Seymour, JR 2014, 'Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef', Microbial Ecology, vol. 67, pp. 540-552.View/Download from: UTS OPUS or Publisher's site
To explore how microbial community composition and function varies within a coral reef ecosystem, we performedmetagenomic sequencing of seawater fromfour niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.
Trevathan-Tackett, SM, Macreadie, PI, Ralph, PJ & Seymour, JR 2014, 'Detachment and flow cytometric quantification of seagrass-associated bacteria', Journal of Microbiological Methods, vol. 102, pp. 23-25.View/Download from: UTS OPUS or Publisher's site
A new protocol was developed to detach bacteria from seagrass tissue and subsequently enumerate cells using flow cytometry (FCM). A method involving addition of the surfactant Tween 80 and vortexing resulted in maximum detachment efficiency of seagrass attached bacteria, providing a robust protocol for precisely enumerating seagrass-associated bacteria with FCM. Using this approach we detected cell concentrations between 2.0 × 105 and 8.0 × 106 cells mg- 1 DW tissue.
Petrou, K, Trimborn, S, Kühl, M & Ralph, PJ 2014, 'Desiccation stress in two intertidal beachrock biofilms', Marine Biology, vol. 161, no. 8, pp. 176-1773.View/Download from: UTS OPUS or Publisher's site
Chlorophyll a fluorescence was used to look at the effect of desiccation on the photophysiology in two beachrock microbial biofilms from the intertidal rock platform of Heron Island, Australia. The photophysiological response to desiccation differed between the beachrock microbial communities. The black biofilm from the upper shoreline, dominated by Calothrix sp., showed a response typical of desiccation-tolerant cyanobacteria, where photosynthesis closed down during air exposure with a rapid and complete recovery upon rehydration. In contrast, the pink biofilm from the mid-intertidal zone, dominated by Blennothrix sp., showed no distinct response to desiccation stress and instead maintained reduced photosynthesis throughout drying and re-wetting cycles. Spatial differences in photosynthetic activity within the black biofilm were evident with a faster recovery rate of photosynthesis in the surface cyanobacteria than in the deeper layers of the biofilm. There was no variation with depth in the pink biofilm. The photophysiological differences in desiccation responses between the beachrock biofilms exemplify the ecological niche specialisation of these complex microbial communities, where the functional differences help to explain their vertical distribution on the intertidal shoreline.
Schrameyer, V, Wangpraseurt, D, Hill, R, Kuehl, M, Larkum, AWD & Ralph, PJ 2014, 'Light Respiratory Processes and Gross Photosynthesis in Two Scleractinian Corals', PLOS ONE, vol. 9, no. 10.View/Download from: UTS OPUS or Publisher's site
Sinutok, S, Hill, R, Kuhl, M, Doblin, MA & Ralph, PJ 2014, 'Ocean acidification and warming alter photosynthesis and calcification of the symbiont-bearing foraminifera Marginopora vertebralis', Marine Biology, vol. 161, pp. 2143-2154.View/Download from: UTS OPUS or Publisher's site
Szabo, M, Wangpraseurt, D, Tamburic, B, Larkum, A, Schreiber, U, Suggett, DJ, Kühl, M & Ralph, PJ 2014, 'Effective light absorption and absolute electron transport rates in the coral Pocillopora damicornis', Plant Physiology and Biochemistry, vol. 83, pp. 159-167.View/Download from: UTS OPUS or Publisher's site
Pulse Amplitude Modulation (PAM) fluorometry has been widely used to estimate the relative photosynthetic efficiency of corals. However, both the optical properties of intact corals as well as past technical constrains to PAM fluorometers have prevented calculations of the electron turnover rate of PSII. We used a new Multi-colour PAM (MC-PAM) in parallel with light microsensors to determine for the first time the wavelength-specific effective absorption cross-section of PSII photochemistry, sII(?), and thus PAM-based absolute electron transport rates of the coral photosymbiont Symbiodinium both in culture and in hospite in the coral Pocillopora damicornis. In both cases, sII of Symbiodinium was highest in the blue spectral region and showed a progressive decrease towards red wavelengths. Absolute values for sII at 440 nm were up to 1.5-times higher in culture than in hospite. Scalar irradiance within the living coral tissue was reduced by 20% in the blue when compared to the incident downwelling irradiance. Absolute electron transport rates of P. damicornis at 440 nm revealed a maximum PSII turnover rate of ca. 250 electrons PSII-1 s-1, consistent with one PSII turnover for every 4 photons absorbed by PSII; this likely reflects the limiting steps in electron transfer between PSII and PSI. Our results show that optical properties of the coral host strongly affect light use efficiency of Symbiodinium. Therefore, relative electron transport rates do not reflect the productivity rates (or indeed how the photosynthesis-light response is parameterised). Here we provide a non-invasive approach to estimate absolute electron transport rates in corals.
Wangpraseurt, D, Tamburic, B, Szabo, M, Suggett, DJ, Ralph, PJ & Kuhl, M 2014, 'Spectral Effects on Symbiodinium Photobiology Studied with a Programmable Light Engine', PLoS One.View/Download from: UTS OPUS or Publisher's site
The spectral light field of Symbiodinium within the tissue of the coral animal host can deviate strongly from the ambient light field on a coral reef and that of artificial light sources used in lab studies on coral photobiology. Here, we used a novel approach involving light microsensor measurements and a programmable light engine to reconstruct the spectral light field that Symbiodinium is exposed to inside the coral host and the light field of a conventional halogen lamp in a comparative study of Symbiodinium photobiology. We found that extracellular gross photosynthetic O2 evolution was unchanged under different spectral illumination, while the more red-weighted halogen lamp spectrum decreased PSII electron transport rates and there was a trend towards increased light-enhanced dark respiration rates under excess irradiance. The approach provided here allows for reconstructing and comparing intra-tissue coral light fields and other complex spectral compositions of incident irradiance. This novel combination of sensor technologies provides a framework to studying the influence of macro- and microscale optics on Symbiodinium photobiology with unprecedented spectral resolution.
Hill, R, Szabo, M, Rehman, A, Vass, I, Ralph, PJ & Larkum, A 2014, 'Inhibition of photosynthetic CO2 fixation in the coral Pocillopora damicornis and its relationship to thermal bleaching', Journal of Experimental Biology, vol. 217, pp. 2150-2162.View/Download from: UTS OPUS or Publisher's site
Two inhibitors of the CalvinBenson cycle [glycolaldehyde (GA) and potassium cyanide (KCN)] were used in cultured Symbiodinium cells and in nubbins of the coral Pocillopora damicornis to test the hypothesis that inhibition of the CalvinBenson cycle triggers coral bleaching. Inhibitor concentration range-finding trials aimed to determine the appropriate concentration to generate inhibition of the CalvinBenson cycle, but avoid other metabolic impacts to the symbiont and the animal host. Both 3 mmol l-1 GA and 20 µmol l-1 KCN caused minimal inhibition of host respiration, but did induce photosynthetic impairment, measured by a loss of photosystem II function and oxygen production. GA did not affect the severity of bleaching, nor induce bleaching in the absence of thermal stress, suggesting inhibition of the CalvinBenson cycle by GA does not initiate bleaching in P. damicornis. In contrast, KCN did activate a bleaching response through symbiont expulsion, which occurred in the presence and absence of thermal stress. While KCN is an inhibitor of the CalvinBenson cycle, it also promotes reactive oxygen species formation, and it is likely that this was the principal agent in the coral bleaching process. These findings do not support the hypothesis that temperature-induced inhibition of the CalvinBenson cycle alone induces coral bleaching.
Macreadie, PI, Baird, ME, Trevathan-Tackett, SM, Larkum, A & Ralph, PJ 2014, 'Quantifying and modelling the carbon sequestration capacity of seagrass meadows - A critical assessment', Marine Pollution Bulletin, vol. 83, pp. 430-439.View/Download from: UTS OPUS or Publisher's site
Seagrasses are among the planets most effective natural ecosystems for sequestering (capturing and storing) carbon (C); but if degraded, they could leak stored C into the atmosphere and accelerate global warming. Quantifying and modelling the C sequestration capacity is therefore critical for successfully managing seagrass ecosystems to maintain their substantial abatement potential. At present, there is no mechanism to support carbon financing linked to seagrass. For seagrasses to be recognised by the IPCC and the voluntary C market, standard stock assessment methodologies and inventories of seagrass C stocks are required. Developing accurate C budgets for seagrass meadows is indeed complex; we discuss these complexities, and, in addition, we review techniques and methodologies that will aid development of C budgets. We also consider a simple process-based data assimilation model for predicting how seagrasses will respond to future change, accompanied by a practical list of research priorities.
Szabo, M, Parker, KB, Guruprasad, S, Kuzhiumparambil, U, Lilley, RM, Tamburic, B, Schliep, MT, Larkum, A, Schreiber, U, Raven, J & Ralph, PJ 2014, 'Photosynthetic acclimation of Nannochloropsis oculata investigated by multi-wavelength chlorophyll fluorescence analysis', Bioresource Technology, vol. 167, pp. 521-529.View/Download from: UTS OPUS or Publisher's site
Multi-wavelength chlorophyll fluorescence analysis was utilised to examine the photosynthetic efficiency of the biofuel-producing alga Nannochloropsis oculata, grown under two light regimes; low (LL) and high (HL) irradiance levels. Wavelength dependency was evident in the functional absorption cross-section of Photosystem II (sII (?)), absolute electron transfer rates (ETR(II)), and non-photochemical quenching (NPQ) of chlorophyll fluorescence in both HL and LL cells. While sII(?) was not significantly different between the two growth conditions, HL cells upregulated ETR(II) 1.6 to 1.8-fold compared to LL cells, most significantly in the wavelength range of 440-540 nm. This indicates preferential utilisation of blue-green light, a highly relevant spectral region for visible light in algal pond conditions. Under these conditions, the HL cells accumulated saturated fatty acids, whereas polyunsaturated fatty acids were more abundant in LL cells. This knowledge is of importance for the use of N. oculata for fatty acid production in the biofuel industry.
Tamburic, B, Guruprasad, S, Radford, DT, Szabo, M, Lilley, R, Larkum, A, Franklin, J, Kramer, D, Blackburn, S, Raven, J, Schliep, MT & Ralph, PJ 2014, 'The effect of diel temperature and light cycles on the growth of Nannochloropsis oculata in a photobioreactor matrix', PLoS One, vol. 9, no. 1, p. e86047.View/Download from: UTS OPUS or Publisher's site
Tamburic, B, Szabo, M, Tran, A, Larkum, A, Suggett, DJ & Ralph, PJ 2014, 'Action spectra of oxygen production and chlorophyll a fluorescence in the green microalga Nannochloropsis oculata', Bioresource Technology, vol. 169, pp. 320-327.View/Download from: UTS OPUS or Publisher's site
The first complete action spectrum of oxygen evolution and chlorophyll a fluorescence was measured for the biofuel candidate alga Nannochloropsis oculata. A novel analytical procedure was used to generate a representative and reproducible action spectrum for microalgal cultures. The action spectrum was measured at 14 discrete wavelengths across the visible spectrum, at an equivalent photon flux density of 60 µmol photons m-2 s-1. Blue light (~414 nm) was absorbed more efficiently and directed to photosystem II more effectively than red light (~679 nm) at light intensities below the photosaturation limit. Conversion of absorbed photons into photosynthetic oxygen evolution was maximised at 625 nm; however, this maximum is unstable since neighbouring wavelengths (646 nm) resulted in the lowest photosystem II operating efficiency. Identifying the wavelength-dependence of photosynthesis has clear implications to optimising growth efficiency and hence important economic implications to the algal biofuels and bioproducts industries.
Kanazawa, A, Blanchard, GJ, Szabo, M, Ralph, PJ & Kramer, DM 2014, 'The site of regulation of light capture in Symbiodinium: Does the peridinin-chlorophyll a-protein detach to regulate light capture?', Biochimica et Biophysica Acta - Bioenergetics, vol. 1837, no. 8, pp. 1227-1234.View/Download from: UTS OPUS or Publisher's site
Dinoflagellates from the genus Symbiodinium form symbiotic associations with cnidarians including corals and anemones. The photosynthetic apparatuses of these dinoflagellates possess a unique photosynthetic antenna system incorporating the peridininchlorophyll aprotein (PCP). It has been proposed that the appearance of a PCP-specific 77 K fluorescence emission band around 672675 nm indicates that high light treatment results in PCP dissociation from intrinsic membrane antenna complexes, blocking excitation transfer to the intrinsic membrane-bound antenna complexes, chlorophyll achlorophyll c2peridininprotein-complex (acpPC) and associated photosystems (Reynolds et al., 2008 Proc Natl Acad Sci USA 105:1367413678).We have tested this model using time-resolved fluorescence decay kinetics in conjunction with global fitting to compare the timeevolution of the PCP spectral bands before and after high light exposure. Our results show that no long-lived PCP fluorescence emission components appear either before or after high light treatment, indicating that the efficiency of excitation transfer from PCP to membrane antenna systems remains efficient and rapid even after exposure to high light. The apparent increased relative emission at around 675 nmwas, instead, caused by strong preferential exciton quenching of the membrane antenna complexes associatedwith acpPC and reaction centers. This strong non-photochemical quenching (NPQ) is consistent with the activation of xanthophyll-associated quenching mechanisms and the generally-observed avoidance in nature of long-lived photoexcited states that can lead to oxidative damage. The acpPC component appears to be the most strongly quenched under high light exposure suggesting that it houses the photoprotective exciton quencher.
Robinson, C, Suggett, DJ, Cherukuru, N, Ralph, PJ & Doblin, MA 2014, 'Performance of Fast Repetition Rate fluorometry based estimates of primary productivity in coastal waters', JOURNAL OF MARINE SYSTEMS, vol. 139, pp. 299-310.View/Download from: UTS OPUS or Publisher's site
Brodersen, KE, Nielsen, DA, Ralph, PJ & Kuhl, M 2014, 'A split flow chamber with artificial sediment to examine the below-ground microenvironment of aquatic macrophytes', MARINE BIOLOGY, vol. 161, no. 12, pp. 2921-2930.View/Download from: UTS OPUS or Publisher's site
Wangpraseurt, D, Polerecky, L, Larkum, A, Ralph, PJ, Nielsen, DA, Pernice, M & Kuhl, M 2014, 'The in situ light microenvironment of corals', Limnology and Oceanography, vol. 59, no. 3, pp. 917-926.View/Download from: UTS OPUS or Publisher's site
We used a novel diver-operated microsensor system to collect in situ spectrally resolved light fields on corals with a micrometer spatial resolution. The light microenvironment differed between polyp and coenosarc tissues with scalar irradiance (400700 nm) over polyp tissue, attenuating between 5.1- and 7.8-fold from top to base of small hemispherical coral colonies, whereas attenuation was at most 1.5-fold for coenosarc tissue. Fluctuations in ambient solar irradiance induced changes in light and oxygen microenvironments, which were more pronounced and faster in coenosarc compared with polyp tissue. Backscattered light from the surrounding benthos contributed . 20% of total scalar irradiance at the coral tissue surface and enhanced symbiont photosynthesis and the local O2 concentration, indicating an important role of benthos optics for coral ecophysiology. Light fields on corals are species and tissue specific and exhibit pronounced variation on scales from micrometers to decimeters. Consequently, the distribution, genetic diversity, and physiology of coral symbionts must be coupled with the measurements of their actual light microenvironment to achieve a more comprehensive understanding of coral ecophysiology.
Baird, ME, Ralph, PJ, Rizwi, F, Wild-Allen, K & Steven, A 2013, 'A dynamic model of the cellular carbon to chlorophyll ratio applied to a batch culture and a continental shelf ecosystem', Limnology and Oceanography, vol. 58, no. 4, pp. 1215-1226.View/Download from: UTS OPUS or Publisher's site
A novel parameterization of the dynamical relationship between cellular carbon (C) and chlorophyll (Chl) is developed using a Chl synthesis term that includes the physiological status of the cell and the effect of packaging of pigments within cells. The geometric derivation highlights the non-linear relationship between Chl content and absorption due to the package effect. When parameterized for a generic 3 mm radius phytoplankton cell, the model reproduces the magnitude and daily variations of C: Chl and C: nitrogen ratios of the diatom Skeletonema costatum in published laboratory experiments. The parameterization is then applied in a three-dimensional biogeochemical model containing three phytoplankton classes in the coastal waters off southeast Tasmania, Australia, which demonstrates the behavior of the dynamic Chl parameterization over a range of light- and nutrient-limiting environments for phytoplankton of different sizes and growth rates. The model produces C: Chl ratios of , 1220 (weight : weight) and , 6080 for phytoplankton communities dominated by fast-growing small and fast-growing large cells, respectively, close to the ratios of 17 and 76 observed at two sampling stations during periods with diatom- and flagellate-dominated communities. Throughout the simulation, community C: Chl ratios generally vary between 12 and 200, which is similar to the range observed globally. In the new parameterization, C: Chl ratios are most influenced by the package effect for light-limited, slow-growing large microalgae, with physiological processes becoming important for smaller, nutrient-limited, fast-growing microalgae.
Clark, J, Poore, AG, Ralph, PJ & Doblin, MA 2013, 'Potential for adaptation in response to thermal stress in an intertidal macroalga', Journal of Phycology, vol. 49, no. 4, pp. 630-639.View/Download from: UTS OPUS or Publisher's site
Understanding responses of marine algae to changing ocean temperatures requires knowledge of the impacts of elevated temperatures and the likelihood of adaptation to thermal stress. The potential for rapid evolution of thermal tolerance is dependent on the levels of heritable genetic variation in response to thermal stress within a population. Here, we use a quantitative genetic breeding design to establish whether there is a heritable variation in thermal sensitivity in two populations of a habitat-forming intertidal macroalga, Hormosira banksii (Turner) Descaisne. Gametes from multiple parents were mixed and growth and photosynthetic performance were measured in the resulting embryos, which were incubated under control and elevated temperature (20°C and 28°C). Embryo growth was reduced at 28°C, but significant interactions between male genotype and temperature in one population indicated the presence of genetic variation in thermal sensitivity. Selection for more tolerant genotypes thus has the ability to result in the evolution of increased thermal tolerance. Furthermore, genetic correlations between embryos grown in the two temperatures were positive, indicating that those genotypes that performed well in elevated temperature also performed well in control temperature. Chlorophyll a fluorescence measurements showed a marked decrease in maximum quantum yield of photosystem II (PSII) under elevated temperature. There was an increase in the proportion of energy directed to photoinhibition (nonregulated nonphotochemical quenching) and a concomitant decrease in energy used to drive photochemistry and xanthophyll cycling (regulated nonphotochemical quenching). However, PSII performance between genotypes was similar, suggesting that thermal sensitivity is related to processes other than photosynthesis.
Gustafsson, MS, Baird, ME & Ralph, PJ 2013, 'The interchangeability of autotrophic and heterotrophic nitrogen sources in Scleractinian coral symbiotic relationships: A numerical study', Ecological Modelling, vol. 250, pp. 183-194.View/Download from: UTS OPUS or Publisher's site
The success of corals in tropical oligotrophic waters depends largely on their symbiotic relationship with the dinoflagellate algae residing in their tissues. Understanding the dynamics of this symbiosis is essential to predict how corals respond to environmental stressors, such as changes in nutrients availability, water temperatures and irradiance. This study presents a numerical model of the symbiotic relationship between a heterotrophic coral (cnidarian) host and autotrophic symbiotic dinoflagellates, including the major metabolic and physical functions of the system, under non-bleaching conditions. The coral acquires nitrogen (N) through two processes, uptake of dissolved inorganic nitrogen (VH DIN) and heterotrophic feeding (ZN). Numerical experiments were used to highlight the importance of these different sources of N for coral survival and growth. The model was analyzed for four external nutrient supply scenarios, using combinations of two VH DIN rates (high and low) and two ZN rates (high and low), and for a range of light levels. The model outputs showed the importance of the algae symbionts to the coral host as a source of both N and C when the feeding rate was limited, with heterotrophic feeding providing only 14% of the N needed to sustain the host biomass for the low ZN + high VH DIN scenario. In contrast, with no light or low light, conditions under which the symbiont population dies, the host was able to survive if ZN was high. Living inside the host the symbiont population thrived as long as there was enough light, as well as, DIN and DIC in the host tissues, independent of whether N was supplied as ZN or VH DIN. Translocation and recycling of nutrient were two of the most important features of this model, emphasizing why it is essential to resolve host and symbiont in a coral model. The model highlights that the interchangeability of N sources, and the ability to exchange and recycle nutrients in the host-symbiont system, is the key to coral su...
Hong, Y, Burford, MA, Ralph, PJ, Udy, JW & Doblin, MA 2013, 'The cyanobacterium Cylindrospermopsis raciborskii is facilitated by copepod selective grazing', Harmful Algae, vol. 29, no. 1, pp. 14-21.View/Download from: UTS OPUS or Publisher's site
Blooms of the toxin-producing cyanobacterium Cylindrospermopsis raciborskii occur in tropical and subtropical lakes during spring-summer but the mechanisms behind bloom formation are unclear. This study tests the hypothesis that C. raciborskii accumulations in freshwater systems are facilitated by selective copepod grazing. Prey selection was examined in a series of experiments with C. raciborskii and the green alga, Chlamydomonas reinhardtii, as well as within natural phytoplankton assemblages. Clearance rates of the copepod Boeckella sp. on a C. raciborskii diet were 24 times lower than that of a common cladoceran Ceriodaphnia sp. when both grazers had prey choice. More C. raciborskii was cleared by Boeckella sp. when in mixed natural phytoplankton assemblages, but the clearance rate declined when nutrient replete C. reinhardtii was added, demonstrating that when alternate high quality algae were present, so did C. raciborskii consumption. The clearance rates of Boeckella sp. on two toxic C. raciborskii strains were significantly lower than on a non-toxic strain, and on C. raciborskii with low cellular P content. When we tested the grazing preference of a copepod dominated mixed zooplankton community on C. raciborskii during the early bloom period, clearance rates were relatively low (0.050.20 ml individual-1 h-1), and decreased significantly as the proportion of C. raciborskii increased above 5%. These results suggest that C. raciborskii persistence could be promoted by copepods preferentially grazing on other algae, with significant loss of top-down control as C. raciborskii abundance increases.
Kramer, W, Schrameyer, V, Hill, R, Ralph, PJ & Bischof, K 2013, 'PSII Activity And Pigment Dynamics Of Symbiodinium In Two Indo-pacific Corals Exposed To Short-term High-light Stress', Marine Biology, vol. 160, no. 3, pp. 563-577.View/Download from: UTS OPUS or Publisher's site
This study examined the capacity for photoprotection and repair of photo-inactivated photosystem II in the same Symbiodinium clade associated with two coexisting coral species during high-light stress in order to test for the modulation of the symbionts photobiological response by the coral host. After 4 days exposure to in situ irradiance, symbionts of the bleaching-sensitive Pocillopora damicornis showed rapid synthesis of photoprotective pigments (by 44 %) and strongly enhanced rates of xanthophyll cycling (by 446 %) while being insufficient to prevent photoinhibition (sustained loss in F v/F m at night) and loss of symbionts after 4 days. By contrast, Pavona decussata showed no significant changes in F v/F m, symbiont density or xanthophyll cycling. Given the association with the same Symbiodinium clade in both coral species, our findings suggest that symbionts in the two species examined may experience different in hospite light conditions as a result of different biometric properties of the coral host.
Petrou, K, Jimenez-denness, I, Chartrand, KM, Mccormack, C, Rasheed, M & Ralph, PJ 2013, 'Seasonal heterogeneity in the photophysiological response to air exposure in two tropical intertidal seagrass species', Marine Ecology Progress Series, vol. 482, pp. 93-106.View/Download from: UTS OPUS or Publisher's site
Photosynthesis, chlorophyll a fluorescence, leaf bio-optical properties and pigments were measured in 2 tropical intertidal seagrass species, Zostera muelleri ssp. capricorni and Halophila ovalis before, during and after air-exposure over a tidal cycle. Data were collected across 4 seasons (October and January-growing seasons; May and July-senescent seasons) to determine seasonal dynamics in physiological responses to air exposure. Both species showed clear light-dependent responses with a decline in photosynthetic efficiency and increased photoprotection during periods of combined maximum daily irradiance and air exposure for all seasons. In Z. muelleri ssp. capricorni there was a negative correlation between air-exposed effective quan - tum yield and light intensity, suggesting exposure was driving this decline. Conversely, sensitivity (decline in effective quantum yield of photosystem II) to increased irradiance dominated the response in H. ovalis, with no change in the magnitude of this response between air-exposed and submerged blades. The response to air exposure observed in Z. muelleri ssp. capricorni showed seasonal variation, with a greater decline in photosynthesis during the spring (October). Tidal exposure did not provide intertidal seagrasses a 'window' of photosynthetic respite (increase in photosynthesis) from high natural or anthropogenic turbidity. However, the periods immediately prior to and after exposure were important for providing an optimum period for net photosynthetic gain.
Sackett, O, Petrou, K, Reedy, B, De Grazia, A, Hill, R, Doblin, M, Beardall, J, Ralph, P & Heraud, P 2013, 'Phenotypic Plasticity of Southern Ocean Diatoms: Key to Success in the Sea Ice Habitat?', PLOS ONE, vol. 8, no. 11.View/Download from: UTS OPUS or Publisher's site
Sinutok, S, Hill, R, Doblin, MA & Ralph, PJ 2013, 'Diurnal photosynthetic response of the motile symbiotic benthic foraminiferan Marginopora vertebralis', Marine Ecology Progress Series, vol. 478, pp. 127-138.View/Download from: UTS OPUS or Publisher's site
Movement of the symbiont-bearing foraminiferan Marginopora vertebralis and photo physiological response to diurnal fluctuations in irradiance were investigated in field and laboratory experiments. The abundance of M. vertebralis from both light-exposed and sheltered habitats was determined 5 times during the day, from pre-dawn to post-dusk. M. vertebralis abundance was significantly higher in sheltered compared to exposed habitats at midday under high irradiance, and this movement enabled the algal symbionts to avoid excessive photoinhibition. The diurnal changes in photosynthetic efficiency were not consistent with the typical midday solar maximum downregulation of photosystem II observed in other photoautotrophs and was likely due to the negatively phototactic capacity of the foraminifera. To confirm the light-dependent movement of foraminifera, individuals in exposed and sheltered habitats were exposed to the photosynthetic inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) in the laboratory. The lack of movement in DCMU-exposed specimens confirmed light-dependent movement and subsequent disruption of signalling between the host foraminiferan and the algal symbionts. Analysis of chlorophyll and xanthophyll pigments, as well as symbiont density, indicated that under high irradiance, foraminiferal symbionts have the capacity to reduce light stress by activating photo-protective mechanisms. The negatively phototactic behaviour prevented chlorophyll degradation, symbiont loss and bleaching, suggesting that it is the primary mechanism for controlling light exposure in these foraminifera. This behaviour provides a competitive advantage over other sessile organisms in avoiding photoinhibition and bleaching by moving away from over-saturating irradiance, towards less damaging light fields.
York, PH, Gruber, RK, Hill, R, Ralph, PJ, Booth, DJ & Macreadie, PI 2013, 'Physiological and Morphological Responses of the Temperate Seagrass Zostera muelleri to Multiple Stressors: Investigating the Interactive Effects of Light and Temperature', PLOS ONE, vol. 8, no. 10.View/Download from: UTS OPUS or Publisher's site
Buxton, LJ, Takahashi, S, Hill, R & Ralph, PJ 2012, 'Variability in the primary site of photosynthetic damage in Symbiodinium sp. (Dinophyceae) exposed to thermal stress', Journal of Phycology, vol. 48, no. 1, pp. 117-126.View/Download from: UTS OPUS or Publisher's site
Exposure to elevated temperature is known to cause photosynthetic inhibition in the coral symbiont Symbiodinium sp. Through the use of the artificial electron acceptor, methyl viologen, this study identified how reduced photosynthetic capacity occurs as a result of inhibition up- and/or downstream of ferredoxin in Symbiodinium sp. in hospite and in culture. Heterogeneity between coral species and symbiont clades was identified in the thermal sensitivity of photosynthesis in the symbionts of the scleractinian corals Stylophora pistillata and Pocillopora damicornis, as well as among Symbiodinium cultures of clades A, B, and C. The in hospite symbionts of S. pistillata and the cultured clade C Symbiodinium both exhibited similar patterns in that their primary site of thermal inhibition occurred downstream of ferredoxin at 32 degrees C. In contrast, the primary site of thermal inhibition occurred upstream of ferredoxin in clades A and B at 32 degrees C, while at 34 degrees C, all samples showed combined up- and downstream inhibition. Although clade C is common to both P. damicornis and S. pistillata, the manner of thermal inhibition was not consistent when observed in hospite. Results showed that there is heterogeneity in the primal site of thermal damage in Symbiodinium among coral species and symbiont clades.
This study examined the response of a coral holobiont to thermal stress when the bacterial community was treated with antibiotics. Colonies of Pocillopora damicornis were exposed to broad and narrow-spectrum antibiotics targeting coral-associated a and c-Proteobacteria. Corals were gradually heated from the control temperature of 26 to 31 C, and measurements were made of host, zooxanthellar and microbial condition. Antibiotics artificially reduced the abundance and activity of bacteria, but had minimal effect on zooxanthellae photosynthetic efficiency or host tissue protein content. Heated corals without antibiotics showed significant declines in FV/FM, typical of thermal stress. However, heated corals treated with antibiotics showed severe tissue loss in addition to a decline in FV/ FM. This study demonstrated that a disruption to the microbial consortium diminished the resilience of the holobiont. Corals exposed to antibiotics under control temperature did not bleach, suggesting that temperature may be an important factor influencing the activity, diversity and ecological function of the holobiont bacterial community.
Macreadie, PI, Allen, K, Kelaher, BP, Ralph, PJ & Skilbeck, G 2012, 'Paleoreconstruction of estuarine sediments reveal human-induced weakening of coastal carbon sinks', Global Change Biology, vol. 18, no. 3, pp. 891-901.View/Download from: UTS OPUS or Publisher's site
Human activities in coastal areas frequently cause loss of benthic macrophytes (e.g. seagrasses) and concomitant increases in microalgal production through eutrophication. Whether such changes translate into shifts in the composition of sediment detritus is largely unknown, yet such changes could impact the role these ecosystems play in sequestrating CO2. We reconstructed the sedimentary records of cores taken from two sites within Botany Bay, Sydney the site of European settlement of Australia to look for human-induced changes in dominant sources of detritus in this estuary. Cores covered a period from the present day back to the middle Holocene (6000years) according to 210Pb profiles and radiocarbon (14C) dating. Depositional histories at both sites could not be characterized by a linear sedimentation rate; sedimentation rates in the last 3050years were considerably higher than during the rest of the Holocene. C:N ratios declined and began to exhibit a microalgal source signature from around the time of European settlement, which could be explained by increased nutrient flows into the Bay caused by anthropogenic activity. Analysis of stable isotopic ratios of 12C/13C showed that the relative contribution of seagrass and C3 terrestrial plants (mangroves, saltmarsh) to detritus declined around the time of rapid industrial expansion (1950s), coinciding with an increase in the contribution of microalgal sources. We conclude that the relative contribution of microalgae to detritus has increased within Botany Bay, and that this shift is the sign of increased industrialization and concomitant eutrophication.
McMinn, A, Ashworth, C, Bhagooli, R, Martin, A, Salleh, S, Ralph, PJ & Ryan, KG 2012, 'Antarctic Coastal Microalgal Primary Production And Photosynthesis', Marine Biology, vol. 159, no. 12, pp. 2827-2837.View/Download from: UTS OPUS or Publisher's site
Primary production in coastal Antarctica is primarily contributed from three sources: sea ice algae, phytoplankton, and microphytobenthos. Compared to other eastern Antarctic sites, the sea ice microalgal biomass at Casey Station, in spring 2005 was rela
Petrou, K, Kranz, SA, Doblin, MA & Ralph, PJ 2012, 'Photophysiological responses of Fragilariopsis cylindrus (Bacillariophyceae) to nitrogen depletion at two temperatures', Journal of Phycology, vol. 48, no. 1, pp. 127-136.View/Download from: UTS OPUS or Publisher's site
The photosynthetic efficiency and photoprotective capacity of the sea-ice diatom, Fragilariopsis cylindrus (Grunow) W. Krieg., grown in a matrix of nitrogen repletion and depletion at two different temperatures (-1 degrees C and +6 degrees C) was investigated. Temperature showed no significant effect on photosynthetic efficiency or photoprotection in F. cylindrus. Cultures under nitrogen depletion showed enhanced photoprotective capacity with an increase in nonphotochemical quenching (NPQ) when compared with nitrogen-replete cultures. This phenomenon was achieved at no apparent cost to the photosynthetic efficiency of PSII (FV/FM). Nitrogen depletion yielded a partially reduced electron transport chain in which maximum fluorescence (FM) could only be obtained by adding 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). reoxidation curves showed the presence of QB nonreducing PSII centers under nitrogen depletion. Fast induction curves (FICs) and electron transport rates (ETRs) revealed slowing of the electrons transferred from the primary (QA) to the secondary (QB) quinone electron acceptors of PSII. The data presented show that nitrogen depletion in F. cylindrus leads to the formation of QB nonreducing PSII centers within the photosystem. On a physiological level, the formation of QB nonreducing PSII centers in F. cylindrus provides the cell with protection against photoinhibition by facilitating the rapid induction of NPQ. This strategy provides an important ecological advantage, especially during the Antarctic spring, maintaining photosynthetic efficiency under high light and nutrient-limiting conditions.
Verhoeven, MP, Kelaher, BP, Bishop, M & Ralph, PJ 2012, 'Epiphyte Grazing Enhances Productivity Of Remnant Seagrass Patches', Austral Ecology, vol. 37, no. 8, pp. 885-892.View/Download from: UTS OPUS or Publisher's site
Anthropogenic nutrient enrichment is increasingly modifying community structure and ecosystem functioning in terrestrial and aquatic ecosystems. In marine ecosystems, the paradigm is that nutrient enrichment leads to a decline of seagrasses by stimulatin
Wilson, KG & Ralph, PJ 2012, 'Laboratory testing protocol for the impact of dispersed petrochemicals on seagrass', Marine Pollution Bulletin, vol. 64, no. 11, pp. 2421-2427.View/Download from: UTS OPUS or Publisher's site
To improve the effectiveness of oil spill mitigation, we developed a rapid, logistically simple protocol to detect petrochemical stress on seagrass. Sections of leaf blades from Zostera muelleri subsp. capricorni were exposed to the water accommodated fraction (WAF) of non-dispersed and dispersed Tapis crude oil and fuel oil (IFO-380) for 5 h. Photosynthetic health was monitored by assessing changes in effective quantum yield of photosystem II () and chlorophyll a pigment concentrations. Loss of total petroleum hydrocarbons (TPH) was measured using an oil-in-water fluorometer, whilst GCMS analyses quantified the hydrocarbon components within each treatment. Few significant differences were detected in the chlorophyll a pigment analyses; however, appeared sensitive to petrochemical exposure. Dispersing both types of oil resulted in a substantial increase in the TPH of the WAF and was generally correlated with a greater physiological impact to the seagrass health, compared with the oil alone.
Seymour, JR, Doblin, MA, Jeffries, TC, Brown, MV, Newton, K, Ralph, PJ, Baird, ME & Mitchell, JG 2012, 'Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current', Environmental Microbiology Reports, vol. 4, pp. 548-555.View/Download from: UTS OPUS or Publisher's site
Different oceanographic provinces host discrete microbial assemblages that are adapted to local physicochemical conditions. We sequenced and compared the metagenomes of two microbial communities inhabiting adjacent water masses in the Tasman Sea, where the recent strengthening of the East Australian Current (EAC) has altered the ecology of coastal environments. Despite the comparable latitude of the samples, significant phylogenetic differences were apparent, including shifts in the relative frequency of matches to Cyanobacteria, Crenarchaeota and Euryarchaeota. Fine-scale variability in the structure of SAR11, Prochlorococcus and Synechococcus populations, with more matches to `warm-water ecotypes observed in the EAC, indicates the EAC may drive an intrusion of tropical microbes into temperate regions of the Tasman Sea. Furthermore, significant shifts in the relative importance of 17 metabolic categories indicate that the EAC prokaryotic community has different physiological properties than surrounding waters
Jimenez Denness, IM, Larkum, A, Ralph, PJ & Kuhl, M 2012, 'In situ thermal dynamics of shallow water corals is affected by tidal patterns and irradiance', Marine Biology, vol. 159, pp. 1773-1782.View/Download from: UTS OPUS or Publisher's site
We studied the diel variation of in situ coral temperature, irradiance and photosynthetic performance of hemispherical colonies of Porites lobata and branching colonies of Porites cylindrica during different bulk water temperature and tidal scenarios on the shallow reef flat of Heron Island, Great Barrier Reef, Australia. Our study presents in situ evidence that coral tissue surface temperatures can exceed that of the surrounding water under environmental conditions typically occurring during low tide in shallow reef or lagoon environments. Such heating may be a regular occurrence on shallow reef flats, triggered by the combined effects of high irradiance and low water flow characteristic of low Spring tides. At these times, solar heating of corals coincides with times of maximum water temperature and high irradiance, where the slow flow and consequent thick boundary layers impede heat exchange between corals and the surrounding water. Despite similar light-absorbing properties, the heating effect was more pronounced for the hemispherical P. lobata than for the branching P. cylindrica. This is consistent with previous laboratory experiments showing the evidence of interspecific variation in coral thermal environment and may result from morphologically influenced variation in convective heat transfer and/or thermal properties of the skeleton. Maximum coral surface warming did not coincide with maximum irradiance, but with maximum water temperature, well into the low-tide period with extremely low water flow in the partially drained reef flat, just prior to flushing by the rising tide. The timing of low tide thus influences the thermal exposure and photophysiological performance of corals, and the timing of tidally driven coral surface warming could potentially have different physiological impacts in the morning or in the afternoon.
Jimenez Denness, IM, Larkum, A, Ralph, PJ & Kuhl, M 2012, 'Thermal effects of tissue optics in symbiont-bearing reef-building corals', Limnology and Oceanography, vol. 57, no. 6, pp. 1816-1825.View/Download from: UTS OPUS or Publisher's site
Reflectance spectroscopy and microscale temperature measurements were used to investigate links between optical and thermal properties of corals. Coral tissue heating showed a species-specific linear correlation to the absorptance of incident irradiance. Heat budgets estimated from absorptance and thermal boundary layer measurements indicated differences in the relative contribution of convection and conduction to heat loss in Porites lobata and Stylophora pistillata, and a higher heat conduction into the skeleton of the thin-tissued branching S. pistillata as compared to the massive thick-tissued P. lobata. Decreasing absorptance associated with bleaching resulted in decreased surface warming of coral tissue. Action spectra of coral tissue heating showed elevated efficiency of heating at wavelengths corresponding to absorption maxima of major zooxanthellae photopigments. Generally, energy-rich radiation (, 500 nm) showed the highest heating efficiency. Speciesspecific relationships between coral tissue heating and absorptance can be strongly affected by differences in the thermal properties of the skeleton and/or tissue arrangement within the skeletal matrix, indicating a yet unresolved potential for coral shape, size, and tissue thickness to affect heat dissipation and especially the conduction of heat into the coral skeleton.
Sinutok, S, Hill, R, Doblin, MA, Kuhl, M & Ralph, PJ 2012, 'Microenvironmental changes support evidence of photosynthesis and calcification inhibition in Halimeda under ocean acidification and warming', Coral Reefs, vol. 31, pp. 1201-1213.View/Download from: UTS OPUS or Publisher's site
The effects of elevated CO 2 and temperature on photosynthesis and calcification of two important calcifying reef algae (Halimedamacroloba and Halimeda cylindracea) were investigated with O 2 microsensors and chlorophyll a fluorometry through a combination of two pCO 2 (400 and 1,200 µatm) and two temperature treatments (28 and 32 °C) equivalent to the present and predicted conditions during the 2100 austral summer. Combined exposure to pCO 2 and elevated temperature impaired calcification and photosynthesis in the two Halimeda species due to changes in the microenvironment around the algal segments and a reduction in physiological performance. There were no significant changes in controls over the 5-week experiment, but there was a 50-70 % decrease in photochemical efficiency (maximum quantum yield), a 70-80 % decrease in O 2 production and a threefold reduction in calcification rate in the elevated CO 2 and high temperature treatment. Calcification in these species is closely coupled with photosynthesis, such that a decrease in photosynthetic efficiency leads to a decrease in calcification. Although pH seems to be the main factor affecting Halimeda species, heat stress also has an impact on their photosystem II photochemical efficiency. There was a strong combined effect of elevated CO 2 and temperature in both species, where exposure to elevated CO 2 or temperature alone decreased photosynthesis and calcification, but exposure to both elevated CO 2 and temperature caused a greater decline in photosynthesis and calcification than in each stress individually. Our study shows that ocean acidification and ocean warming are drivers of calcification and photosynthesis inhibition in Halimeda. Predicted climate change scenarios for 2100 would therefore severely affect the fitness of Halimeda, which can result in a strongly reduced production of carbonate sediments on coral reefs under such changed climate conditions.
Wangpraseurt, D, Larkum, A, Ralph, PJ & Kuhl, M 2012, 'Light gradients and optical microniches in coral tissues', Frontiers in Microbiology, vol. 3, no. 316, pp. 1-9.View/Download from: UTS OPUS or Publisher's site
Light quantity and quality are among the most important factors determining the physiology and stress response of zooxanthellate corals. Yet, almost nothing is known about the light ?eld that Symbiodinium experiences within their coral host, and the basic optical properties of coral tissue are unknown. We used scalar irradiance microprobes to characterize vertical and lateral light gradients within and across tissues of several coral species. Our results revealed the presence of steep light gradients with photosynthetically available radiation decreasing by about one order of magnitude from the tissue surface to the coral skeleton. Surface scalar irradiance was consistently higher over polyp tissue than over coenosarc tissue in faviid corals. Coral bleaching increased surface scalar irradiance by ~150% (between 500 and 700 nm) relative to a healthy coral. Photosynthesis peaked around 300 µm within the tissue, which corresponded to a zone exhibiting strongest depletion of scalar irradiance. Deeper coral tissue layers, e.g., ~1000 µm into aboral polyp tissues, harbor optical microniches, where only ~10% of the incident irradiance remains. We conclude that the optical microenvironment of corals exhibits strong lateral and vertical gradients of scalar irradiance, which are affected by both tissue and skeleton optical properties. Our results imply that zooxanthellae populations inhabit a strongly heterogeneous light environment and highlight the presence of different optical microniches in corals; an important ?nding for understanding the photobiology, stress response, as well as the phenotypic and genotypic plasticity of coral symbionts.
Hill, R, Larkum, A, Prasil, O, Kramer, DM, Szabo, M, Kumar, V & Ralph, PJ 2012, 'Light-induced dissociation of antenna complexes in the symbionts of scleractinian corals correlates with sensitivity to coral bleaching', Coral Reefs, vol. 31, pp. 963-975.View/Download from: UTS OPUS or Publisher's site
Elevated temperatures in combination with moderate to high irradiance are known to cause bleaching events in scleractinian corals, characterised by damage to photosystem II (PSII). Photoprotective mechanisms of the symbiont can reduce the excitation pressure impinging upon PSII. In the bleaching sensitive species, Acropora millepora and Pocillopora damicornis, high light alone induced photoprotection through the xanthophyll cycle, increased content of the antioxidant carotenoid, ß-carotene, as well as the dissociation of the light-harvesting chlorophyll complexes. The evidence is compatible with either the membrane-bound chlorophyll a-chlorophyll c 2-peridinin-protein (acpPC) complex or the peripheral peridinin-chlorophyll-protein complex, or both, disconnecting from PSII under high light. The acpPC complex potentially showed a state transition response with redistribution towards photosystem I to reduce PSII over-excitation. This apparent acpPC dissociation/reassociation was promoted by the addition of the xanthophyll cycle inhibitor, dithiothreitol, under high irradiance. Exposure to thermal stress as well as high light promoted xanthophyll de-epoxidation and increased ß-carotene content, although it did not influence light-harvesting chlorophyll complex (LHC) dissociation, indicating light, rather than temperature, controls LHC dissociation. Photoinhibition was avoided in the bleaching tolerant species, Pavona decussata, suggesting xanthophyll cycling along with LHC dissociation may have been sufficient to prevent photodamage to PSII. Symbionts of P. decussata also displayed the greatest detachment of antenna complexes, while the more thermally sensitive species, Pocillopora damicornis and A. millepora, showed less LHC dissociation, suggesting antenna movement influences bleaching susceptibility.
Doblin, MA, Petrou, K, Shelly, K, Westwood, K, van den Enden, R, Wright, S, Griffiths, B & Ralph, PJ 2011, 'Diel variation of chlorophyll-a fluorescence, phytoplankton pigments and productivity in the Sub-Antarctic and Polar Front Zones south of Tasmania, Australia', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 58, no. 21-22, pp. 2189-2199.View/Download from: UTS OPUS or Publisher's site
Marine primary production is a fundamental measure of the oceanâs capacity to convert carbon dioxide to particulate organic carbon for the marine foodweb, and as such is an essential variable used in ecosystem and biogeochemical models to assess trophic dynamics and carbon cycling. The Sub-Antarctic Zone (SAZ) is a major sink for atmospheric carbon and exhibits large gradients in ocean conditions on both temporal and spatial scales. In this dynamic system, an understanding of small-scale temporal changes is critical for modelling primary production at larger scales. Thus, we investigated diel effects on maximum quantum yield of PSII (FV/FM), photosynthetic pigment pools and primary productivity in the western (Diel 1) and eastern SAZ region (Diel 3) south of Tasmania, Australia, and compared this to a station at the polar front (Diel 2). Phytoplankton in the eastern SAZ had the greatest diel response, with cells showing decreased FV/FM and increased biosynthesis and transformation of xanthophyll and other photoprotective pigments during the day, but only in the surface waters (0 and 10m). Diel responses diminished by 30 m. Cells in the western SAZ had similar responses across the depths sampled, increasing their FV/FM during the night and increasing their xanthophyll pigment content during the day. Phytoplankton at the polar front (Diel 2) showed intermediate diel-related variations in photophysiology, with xanthophyll conversion and increases in photoprotective pigments during the day but constant FV/FM.
Earp, AA, Hanson, CE, Ralph, PJ, Brando, VE, Allen, S, Baird, ME, Clementson, L, Daniel, P, Dekker, AG, Fearns, PR, Parslow, JS, Strutton, PG, Thompson, P, Underwood, M, Weeks, S & Doblin, MA 2011, 'Review of fluorescent standards for calibration of in situ fluorometers: Recommendations applied in coastal and ocean observing programs', Optics Express, vol. 19, no. 27, pp. 26768-26782.View/Download from: UTS OPUS or Publisher's site
Fluorometers are widely used in ecosystem observing to monitor fluorescence signals from organic compounds, as well as to infer geophysical parameters such as chlorophyll or CDOM concentration, but measurements are susceptible to variation caused by biofouling, instrument design, sensor drift, operating environment, and calibration rigor. To collect high quality data, such sensors need frequent checking and regular calibration. In this study, a wide variety of both liquid and solid fluorescent materials were trialed to assess their suitability as reference standards for performance assessment of in situ fluorometers. Criteria used to evaluate the standards included the spectral excitation/emission responses of the materials relative to fluorescence sensors and to targeted ocean properties, the linearity of the fluorometerâs optical response with increasing concentration, stability and consistency, availability and ease of use, as well as cost. Findings are summarized as a series of recommended reference standards for sensors deployed on stationary and mobile platforms, to suit a variety of in situ coastal to ocean sensor configurations. Repeated determinations of chlorophyll scale factor using the recommended liquid standard, Fluorescein, achieved an accuracy of 2.5%. Repeated measurements with the recommended solid standard, Plexiglas Satinice® plum 4H01 DC (polymethylmethacrylate), over an 18 day period varied from the mean value by 1.0% for chlorophyll sensors and 3.3% for CDOM sensors.
Hill, R, Brown, CM, DeZeeuw, K, Campbell, DA & Ralph, PJ 2011, 'Increased rate of D1 repair in coral symbionts during bleaching is insufficient to counter accelerated photo-inactivation', Limnology and Oceanography, vol. 56, no. 1, pp. 139-146.View/Download from: UTS OPUS or Publisher's site
We dissect the primary photo-inactivation and the counteracting metabolic repair rates in fragments of the scleractinian coral, Pocillopora damicornis, subjected to a combined stress of a shift to elevated temperature (from 26 degrees C to 32 degrees C) and increased light (from 200 mu mol photons m(-2) s(-1) to 400 mmol photons m(-2) s(-1)) to induce bleaching. During the bleaching treatment the dinoflagellate symbionts showed a 5.5-fold acceleration in their photosystem II (PSII) repair rate constant, demonstrating that they maintain strong metabolic capacity to clear and replace photo-damaged D1 protein at the elevated temperature and light conditions. Nevertheless, the symbionts concurrently suffered a seven-fold increase in the rate constant for PSII photo-inactivation. This rapid photo-inactivation exceeded the PSII repair capacity, therefore tipping the symbionts, and by implication the symbiosis, into net photo-inhibition. Increased photo-inactivation in hospite, rather than an inhibition of PSII repair, is the principle trigger for net photo-inhibition under bleaching conditions.
Petrou, K & Ralph, PJ 2011, 'Photosynthesis and net primary productivity in three Antarctic diatoms: possible significance for their distribution in the Antarctic marine ecosystem', Marine Ecology Progress Series, vol. 437, pp. 27-40.View/Download from: UTS OPUS or Publisher's site
Photosynthesis and net primary productivity were measured in 3 Antarctic diatoms, Fragilariopsis cylindrus, Pseudo-nitzschia subcurvata and Chaetoceros sp., exposed to rapid changes in temperature and salinity representing a range of conditions found during a seasonal cycle. Measured differences in fluorescence-derived photosynthetic activity and oxygen evolution suggested that some alternative electron cycling activity was present under high irradiances. F. cylindrus displayed the highest rates of relative electron transport and net primary productivity under all salinity and temperature combinations and showed adaptive traits towards the sea-ice-like environment. P. subcurvata displayed a preference for low saline conditions where production rates were greatest. However, there was evidence of photosynthetic sensitivity to the lowest temperatures and highest salinities, suggesting a lack of adaptation for dealing with sea-ice-like conditions. Chaetoceros sp. showed high plasticity, acclimating well to all conditions but performing best under pelagic conditions. The study shows species-specific sensitivities to environmental change, highlighting photosynthetic capacity as a potentially important mechanism in ecological niche adaptation. When these data were modelled over different seasons, integrated daily net primary production was greatest under summer pelagic conditions. The findings from this study support the general observations of light control and seasonal development of net primary productivity and species succession in the Antarctic marine ecosystem.
Petrou, K, Doblin, MA & Ralph, PJ 2011, 'Heterogeneity in the photoprotective capacity of three Antarctic diatoms during short-term changes in salinity and temperature', Marine Biology, vol. 158, no. 5, pp. 1029-1041.View/Download from: UTS OPUS or Publisher's site
The Antarctic marine ecosystem changes seasonally, forming a temporal continuum of specialised niche habitats including open ocean, sea ice and meltwater environments. The ability for phytoplankton to acclimate rapidly to the changed conditions of these environments depends on the speciesâ physiology and photosynthetic plasticity and may ultimately determine their long-term ecological niche adaptation. This study investigated the photophysiological plasticity and rapid acclimation response of three Antarctic diatomsâFragilariopsis cylindrus, Pseudo-nitzschia subcurvata and Chaetoceros sp.âto a selected range of temperatures and salinities representative of the sea ice, meltwater and pelagic habitats in the Antarctic. Fragilariopsis cylindrus displayed physiological traits typical of adaptation to the sea ice environment. Equally, this species showed photosynthetic plasticity, acclimating to the range of environmental conditions, explaining the prevalence of this species in all Antarctic habitats. Pseudo-nitzschia subcurvata displayed a preference for the meltwater environment, but unlike F. cylindrus, photoprotective capacity was low and regulated via changes in PSII antenna size. Chaetoceros sp. had high plasticity in non-photochemical quenching, suggesting adaptation to variable light conditions experienced in the wind-mixed pelagic environment. While only capturing short-term responses, this study highlights the diversity in photoprotective capacity that exists amongst three dominant Antarctic diatom species and provides insight into links between ecological niche adaptation and speciesâ distribution
Petrou, K, Hassler, CS, Doblin, MA, Shelly, K, Schoemann, V, van den Enden, R, Wright, S & Ralph, PJ 2011, 'Iron-limitation and high light stress on phytoplankton populations from the Australian Sub-Antarctic Zone (SAZ)', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 58, no. 21-22, pp. 2200-2211.View/Download from: UTS OPUS or Publisher's site
The high nutrient low chlorophyll (HNLC) surface waters of the Southern Ocean are characterised by high concentrations of nitrate and phosphate, low concentrations of dissolved iron and deep vertical mixing. Future climate scenarios predict increased sur
Petrou, K, Hill, R, Doblin, MA, McMinn, A, Johnson, R, Wright, SW & Ralph, PJ 2011, 'Photoprotection of sea-ice microalgal communities from the east Antarctic pack ice', Journal of Phycology, vol. 47, no. 1, pp. 77-86.View/Download from: UTS OPUS or Publisher's site
All photosynthetic organisms endeavor to balance energy supply with demand. For sea-ice diatoms, as with all marine photoautotrophs, light is the most important factor for determining growth and carbonfixation rates. Light varies from extremely low to often relatively high irradiances within the sea-ice environment, meaning that sea-ice algae require moderate physiological plasticity that is necessary for rapid light acclimation and photoprotection. This study investigated photoprotective mechanisms employed by bottom Antarctic sea-ice algae in response to relatively high irradiances to understand how they acclimate to the environmental conditions presented during early spring, as the light climate begins to intensify and snow and sea-ice thinning commences.
Sinutok, S, Hill, R, Doblin, MA, Wuhrer, R & Ralph, PJ 2011, 'Warmer more acidic conditions cause decreased productivity and calcification in subtropical coral reef sediment-dwelling calcifiers', Limnology and Oceanography, vol. 56, no. 4, pp. 1200-1212.View/Download from: UTS OPUS or Publisher's site
The effects of elevated CO(2) and temperature on photosynthesis and calcification in the calcifying algae Halimeda macroloba and Halimeda cylindracea and the symbiont-bearing benthic foraminifera Marginopora vertebralis were investigated through exposure to a combination of four temperatures (28 degrees C, 30 degrees C, 32 degrees C, and 34 degrees C) and four CO(2) levels (39, 61, 101, and 203 Pa; pH 8.1, 7.9, 7.7, and 7.4, respectively). Elevated CO(2) caused a profound decline in photosynthetic efficiency (F(V) : F(M)), calcification, and growth in all species. After five weeks at 34 degrees C under all CO(2) levels, all species died. Chlorophyll (Chl) a and b concentration in Halimeda spp. significantly decreased in 203 Pa, 32 degrees C and 34 degrees C treatments, but Chl a and Chl c(2) concentration in M. vertebralis was not affected by temperature alone, with significant declines in the 61, 101, and 203 Pa treatments at 28 degrees C. Significant decreases in F(V) : F(M) in all species were found after 5 weeks of exposure to elevated CO(2) (203 Pa in all temperature treatments) and temperature (32 degrees C and 34 degrees C in all pH treatments). The rate of oxygen production declined at 61, 101, and 203 Pa in all temperature treatments for all species. The elevated CO(2) and temperature treatments greatly reduced calcification (growth and crystal size) in M. vertebralis and, to a lesser extent, in Halimeda spp. These findings indicate that 32 degrees C and 101 Pa CO(2), are the upper limits for survival of these species on Heron Island reef, and we conclude that these species will be highly vulnerable to the predicted future climate change scenarios of elevated temperature and ocean acidification.
Behrendt, L, Larkum, A, Norman, A, Qvortrup, K, Chen, M, Ralph, PJ, Sorensen, SJ, Trampe, E & Kuhl, M 2011, 'Endolithic chlorophyll d-containing phototrophs', ISME Journal, vol. 5, no. 6, pp. 1072-1076.View/Download from: UTS OPUS or Publisher's site
Cyanobacteria in the genus Acaryochloris are the only known oxyphototrophs that have exchanged chlorophyll a (Chl a) with Chl d as their primary photopigment, facilitating oxygenic photosynthesis with near infrared (NIR) light. Yet their ecology and natural habitats are largely unknown. We used hyperspectral and variable chlorophyll fluorescence imaging, scanning electron microscopy, photopigment analysis and DNA sequencing to show that Acaryochloris-like cyanobacteria thrive underneath crustose coralline algae in a widespread endolithic habitat on coral reefs. This finding suggests an important role of Chl d-containing cyanobacteria in a range of hitherto unexplored endolithic habitats, where NIR light-driven oxygenic photosynthesis may be significant.
Jimenez Denness, IM, Kuhl, M, Larkum, A & Ralph, PJ 2011, 'Effects of flow and colony morphology on the thermal boundary layer of corals', Journal of the Royal Society Interface, vol. 8, no. 65, pp. 1785-1795.View/Download from: UTS OPUS or Publisher's site
The thermal microenvironment of corals and the thermal effects of changing flow and radiation are critical to understanding heat-induced coral bleaching, a stress response resulting from the destruction of the symbiosis between corals and their photosynt
Ulstrup, K, Kuhl, M, van Oppen, MJ, Cooper, TF & Ralph, PJ 2011, 'Variation in photosynthesis and respiration in geographically distinct populations of two reef-building coral species', Aquatic Biology, vol. 12, pp. 241-248.View/Download from: UTS OPUS or Publisher's site
Studies of the regulation and importance of physiological processes such as coral photosynthesis and respiration on coral reefs require knowledge of spatio-temporal patterns of variability at different scales. Oxygen microelectrodes were used to measure photosynthesis and dark respiration of 2 corals, Pocillopora damicornis and Turbinaria reniformis, in the northern (Lizard Island) and central (Davies and Broadhurst Reefs) regions of the Great Barrier Reef (GBR) in winter and summer. Genetic characterisation of Symbiodinium revealed that P. damicornis hosted a single symbiont type (Symbiodinium C1) in both regions, whereas T. reniformis harboured 2 types, dependent on location. Colonies at Lizard Island harboured Symbiodinium D, whereas colonies at Davies Reef harboured Symbiodinium C2. Rates of gross photosynthesis were greater in the central than in the northern GBR in summer. A similar pattern was detected for dark respiration rates in T. reniformis. No seasonal change in either photosynthesis or dark respiration was evident in the northern GBR, possibly due to less annual variability in light conditions, and for T. reniformis, additionally the presence of Symbiodinium D. These results highlight that environmental conditions coupled with regional-scale distribution of Symbiodinium are likely to exert important influences on respiration and photosynthetic performance of reef-building corals.
Csaszar, N, Ralph, PJ, Frankham, R, Berkelmans, R & van Oppen, MJ 2010, 'Estimating the Potential for Adaptation of Corals to Climate Warming', PLoS ONE, vol. 5, no. 3, pp. 1-8.View/Download from: UTS OPUS or Publisher's site
The persistence of tropical coral reefs is threatened by rapidly increasing climate warming, causing a functional breakdown of the obligate symbiosis between corals and their algal photosymbionts (Symbiodinium) through a process known as coral bleaching. Yet the potential of the coral-algal symbiosis to genetically adapt in an evolutionary sense to warming oceans is unknown. Using a quantitative genetics approach, we estimated the proportion of the variance in thermal tolerance traits that has a genetics basis (i.e. heritability) as a proxy for their adaptive potential in the widespread Indo-Pacific reef-building coral Acropora millepora. We chose two physiologically different populations that associate respectively with one thermotolerant (Symbiodinium clade D) and one less tolerant symbiont type (Symbiodinium C2). In both symbiont types, pulse amplitude modulated (PAM) fluorometry and high performance liquid chromatography (HPLC) analysis revealed significant heritabilities for traits related to both photosynthesis and photoprotective pigment profile. However, quantitative real-time polymerase chain reaction (qRT - PCR) assays showed a lack of heritability in both coral host populations for their own expression of fundamental stress genes. Coral colony growth, contributed to by both symbiotic partners, displayed heritability. High heritabilities for functional key traits of algal symbionts, along with their short clonal generation time and high population sizes allow for their rapid thermal adaptation. However, the low overall heritability of coral host traits, along with the corals' long generation time, raise concern about the timely adaptation of the coral-algal symbiosis in the face of continued rapid climate warming.
Herrera-Silveira, JA, Cebrian, J, Hauxwell, J, Ramirez-Ramirez, J & Ralph, PJ 2010, 'Evidence of negative impacts of ecological tourism on turtlegrass (Thalassia testudinum) beds in a marine protected area of the Mexican Caribbean', Aquatic Ecology, vol. 44, no. 1, pp. 23-31.View/Download from: UTS OPUS or Publisher's site
Many marine protected areas (MPAs) have been established in recent years. Some MPAs are open to tourists to foster environmental education and generate revenue for the MPA. This has been coined âecological tourismâ. Here, we examine the impact of ecological tourism on turtlegrass (Thalassia testudinum) health in one area of the âCosta Occidental de Isla Mujeres, Punta CancÃºn y Punta Nizucâ MPA in the Mexican Caribbean. A heavily visited location was compared with an unvisited location. Turtlegrass leaves at the visited location were sparser, shorter, grew more slowly, and had more epiphytes than at the unvisited location. Vertical and horizontal rhizomes of turtlegrass also grew more slowly at the visited than at the unvisited location. There is reasonable evidence to suggest that the observed differences are likely due to the deleterious impacts of novice and careless snorkelers. If continuing, these impacts could cause severe degradation of the visited areas in this MPA and, thus, changes in management policies seem in order.
McMinn, A, Pankowskii, A, Ashworth, C, Bhagooli, R, Ralph, PJ & Ryan, K 2010, 'In situ net primary productivity and photosynthesis of Antarctic sea ice algal, phytoplankton and benthic algal communities', Marine Biology, vol. 157, no. 6, pp. 1345-1356.View/Download from: UTS OPUS or Publisher's site
Primary production at Antarctic coastal sites is contributed from sea ice algae, phytoplankton and benthic algae. Oxygen microelectrodes were used to estimate sea ice and benthic primary production at several sites around Casey, a coastal area in eastern Antarctica. Maximum oxygen export from sea ice was 0.95 mmol O2 m-2 h-1 (*11.7 mg C m-2 h-1) while from the sediment it was 6.08 mmol O2 m-2 h-1 (*70.8 mg C m-2 h-1). When the ice was present O2 export from the benthos was either low or negative. Sea ice algae assimilation rates were up to 3.77 mg C (mg Chl-a)-1 h-1 while those from the benthos were up to 1.53 mg C (mg Chl-a)-1 h-1. The contribution of the major components of primary productivity was assessed using fluorometric techniques. When the ice was present approximately 55â65% of total daily primary production occurred in the sea ice with the remainder unequally partitioned between the sediment and the water column. When the ice was absent, the benthos contributed nearly 90% of the primary production.
Petrou, K, Hill, R, Brown, CM, Campbell, DA, Doblin, MA & Ralph, PJ 2010, 'Rapid photoprotection in sea-ice diatoms from the East Antarctic pack ice', Limnology and Oceanography, vol. 55, no. 3, pp. 1400-1407.View/Download from: UTS OPUS or Publisher's site
Photoinhibition and D1 protein re-synthesis were investigated in bottom-dwelling sea-ice microalgal communities from the East Antarctic pack ice during early spring. Bottom-dwelling sea-ice microalgal communities were dominated by diatoms that exhibited rapid photoprotection when exposed to a range of different light levels (10 µmol photons m-2 s-1, 50 µmol photons m-2 s-1, 100 µmol photons m-2 s-1, and 200 µmol photons m-2 s-1). Photosynthetic capacity of photosystem II (PSII) dropped significantly over 3 h under 200 µmol photons m-2 s-1, but largely recovered when placed in a low-light environment (10 µmol photons m-2 s-1) for an additional 3 h. PSII repair rates increased with increasing irradiance, and the D1-protein pool remained steady even under high light (200 µmol photons m-2 s-1). Sea-ice diatoms showed a low intrinsic susceptibility to photoinactivation of PSII across all the light treatments, and a strong and irradiance-dependent induction of nonphotochemical quenching, which did not depend upon chloroplast protein synthesis, was also seen. These highly plastic organisms, once thought to be adapted to shade, are in fact well equipped to withstand rapid and relatively large changes in light at low temperatures with minimal long-term effect on their photosynthetic machinery.
Seery, CR & Ralph, PJ 2010, 'Ecological relevance of a chlorophyll a fluorescence ecotoxicological endpoint', Toxicological and Environmental Chemistry, vol. 92, no. 8, pp. 1529-1540.View/Download from: UTS OPUS or Publisher's site
With the increasing use of new techniques to assess toxic stress and the effects of pollution, it is important to ensure that any âânewââ endpoint employed is able to demonstrate a level of eco-relevance. Though recent application of chlorophyll a fluorescence parameters to macroalgal bioassays has been successful, a level of eco-relevance for such use has not been experimentally shown. As such, this article presents a series of experiments designed to establish a link between fluorescence parameters and higher-level effects (supra-individual level). The results show that fluorescence parameters are capable of predicting germination success of macroalgal gametes and can do so much sooner than the actual event of germination. Furthermore, a decline in DF=F0m is shown to be strongly associated with a reduced germination success. Thus, a level of eco-relevance has been established for the fluorescence endpoint that is at least equal to that of the widely accepted germination-based macroalgal bioassays.
Wright, JT, Byers, JE, Koukoumaftsis, L, Ralph, PJ & Gribben, PE 2010, 'Native species behaviour mitigates the impact of habitat-forming invasive seaweed', Oecologia, vol. 163, no. 2, pp. 527-534.View/Download from: UTS OPUS or Publisher's site
Habitat-forming invasive species cause large, novel changes to the abiotic environment. These changes may elicit important behavioural responses in native fauna, yet little is known about mechanisms driving this behaviour and how such trait-mediated responses influence the fitness of native species. Low dissolved oxygen is a key abiotic change created by the habitat-forming invasive seaweed, Caulerpa taxifolia, which influences an important behavioural response (burrowing depth) in the native infaunal bivalve Anadara trapezia. In Caulerpa-colonised areas, Anadara often emerged completely from the sediment, and we experimentally demonstrate that water column hypoxia beneath the Caulerpa canopy is the mechanism instigating this pop-up behaviour. Importantly, pop-up in Caulerpa allowed similar survivorship to that in unvegetated sediment; however, when we prevented Anadara from popping-up, they suffered >50% mortality in just 1 month. Our findings not only highlight the substantial environmental alteration by Caulerpa, but also an important role for the behaviour of native species in mitigating the effects of habitat-forming invasive species.
Lilley, R, Ralph, PJ & Larkum, A 2010, 'The determination of activity of the enzyme Rubisco in cell extracts of the dinoflagellate alga Symbiodinium sp. by manganese chemiluminescence and its response to short-term thermal stress of the alga', Plant Cell and Environment, vol. 33, no. 6, pp. 995-1004.View/Download from: UTS OPUS or Publisher's site
The dinoflagellate alga Symbiodinium sp., living in symbiosis with corals, clams and other invertebrates, is a primary producer in coral reefs and other marine ecosystems. The function of the carbon-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in dinoflagellates is difficult to study because its activity is rapidly lost after extraction from the cell. We report procedures for the extraction of Rubisco from Symbiodinium cells and for stable storage. We describe a continuous assay for Rubisco activity in these crude cell extracts using the Mn2+ chemiluminescence of Rubisco oxygenase. Chemiluminescence time courses exhibited initial transients resembling bacterial Form II Rubisco, followed by several minutes of linearly decreasing activity. The initial activity was determined from extrapolation of this linear section of the time course. The activity of fast-frozen cell extracts was stable at -80 °C and, after thawing and storage on ice, remained stable for up to 1 h before declining non-linearly. Crude cell extracts bound [14C] 2-carboxy-D-arabitinol 1,5-bisphosphate to a high molecular mass fraction separable by gel filtration chromatography. After pre-treatment of Symbiodinium cell cultures in darkness at temperatures above 30 °C, the extracted Rubisco activities decreased, with almost complete loss of activity above 36 °C. The implications for the sensitivity to elevated temperature of Symbiodinium photosynthesis are assessed.
Baird, AH, Bhagooli, R, Ralph, PJ & Takahashi, S 2009, 'Coral bleaching: the role of the host', Trends In Ecology & Evolution, vol. 24, no. 1, pp. 16-20.View/Download from: UTS OPUS or Publisher's site
Coral bleaching caused by global warming is one of the major threats to coral reefs. Very recently, research has focused on the possibility of corals switching symbionts as a means of adjusting to accelerating increases in sea surface temperature. Although symbionts are clearly of fundamental importance, many aspects of coral bleaching cannot be readily explained by differences in symbionts among coral species. Here we outline several potential mechanisms by which the host might influence the bleaching response, and conclude that predicting the fate of corals in response to climate change requires both members of the symbiosis to be considered equally.
Buxton, LJ, Badger, M & Ralph, PJ 2009, 'Effects Of Moderate Heat Stress And Dissolved Inorganic Carbon Concentration On Photosynthesis And Respiration Of Symbiodinium Sp (Dinophyceae) In Culture And In Symbiosis', Journal of Phycology, vol. 45, no. 2, pp. 357-365.View/Download from: UTS OPUS or Publisher's site
The influence of temperature and inorganic carbon (C-i) concentration on photosynthesis was examined in whole corals and samples of cultured symbiotic dinoflagellates (Symbiodinium sp.) using combined measurements from a membrane inlet mass spectrometer and chl a fluorometer. In whole corals, O-2 production at 26 degrees C was significantly limited at C-i concentrations below ambient seawater (similar to 2.2 mM). Further additions of C-i up to similar to 10 mM caused no further stimulation of oxygenic photosynthesis. Following exposure to 30 degrees C (2 d), net oxygen production decreased significantly in whole corals, as a result of reduced production of photosynthetically derived oxygen rather than increased host consumption. Whole corals maintained a rate of oxygen evolution around eight times lower than cultured Symbiodinium sp. at inorganic carbon concentrations < 2 mM, but cultures displayed greater levels of photoinhibition following heat treatment (30 degrees C, 2 d). Whole corals and cultured zooxanthellae differed considerably in their responses to C-i concentration and moderate heat stress, demonstrating that cultured Symbiodinium make an incongruous model for those in hospite. Reduced net oxygen evolution, in whole corals, under conditions of low C-i (< 2 mM) has been interpreted in terms of possible sink limitation leading to increased nonphotochemical energy dissipation. The advantages of combined measurement of net gas exchange and fluorometry offered by this method are discussed.
Collier, C, Lavery, P, Ralph, PJ & Masini, R 2009, 'Shade-induced response and recovery of the seagrass Posidonia sinuosa', Journal Of Experimental Marine Biology And Ecology, vol. 370, no. 1-2, pp. 89-103.View/Download from: UTS OPUS or Publisher's site
The effect of shading on the seagrass Posidonia sinuosa Cambridge et Kuo was investigated to identify mechanisms that prolong its survival during periods of low light and permit its subsequent recovery. We also tested whether the responses were consistent in plants growing at different depths. Shade treatments were low (LS; 70 - 100% of ambient Photosynthetic Photon Flux Density), medium (MS; 12 - 39%) and heavy (HS; 5 - 4%) at the shallow (3 - 4 m) site, whilst the deep (7 - 8 m) site had no HS treatment. HS at the shallow and MS at the deep site were below minimum light requirements (MLR) for the long-term survival of P. sinuoso.
Hill, R, Ulstrup, K & Ralph, PJ 2009, 'Temperature Induced Changes In Thylakoid Membrane Thermostability Of Cultured, Freshly Isolated, And Expelled Zooxanthellae From Scleractinian Corals', Bulletin of Marine Science, vol. 85, no. 3, pp. 223-244.View/Download from: UTS OPUS
Coral bleaching events are characterized by a dysfunction between the cnidarian coral host and the symbiotic dinoflagellate algae, known as zooxanthellae (genus Symbiodinium). Elevated temperature and intense light induce coral bleaching, where zooxanthellae are expelled from the host tissue. The primary cellular process in zooxanthellae which leads to coral bleaching is unresolved, and here, we investigated the sensitivity of the thylakoid membrane in a Symbiodinium culture and in genetically identified freshly isolated and expelled Symbiodinium cells. The fluorescence-temperature curve technique was used to measure the critical temperature (Tc) at which irreversible damage to the thylakoid membrane occurred. The accuracy of this technique was confirmed through the collection of scanning transmission electron micrographs which demonstrated the clear relationship between Tc and thylakoid membrane degradation. Analysis of 10 coral species with a diverse range of genetically distinct Symbiodinium communities showed a decline in Tc from summer to winter. A Symbiodinium culture and fragments of Pocillopora damicornis (Linnaeus, 1758) were exposed to a series of light and temperature treatments, where Tc increased from approximately 37 Â°C to 42 Â°C upon exposure to elevated temperature. Under bleaching conditions, the thermostability of the thylakoid membrane increased within 4 hrs by 5.1 Â°C, to a temperature far above bleaching thresholds, in both freshly isolated and photosynthetically competent zooxanthellae expelled from P. damicornis under these conditions. It is demonstrated that the thermostability of the thylakoid membrane increases in cultured, freshly isolated, and expelled zooxanthellae exposed to bleaching stress, suggesting it is not the primary site of impact during coral bleaching events.
Strom, D, Ralph, PJ & Stauber, JL 2009, 'Development of a Toxicity Identification Evaluation Protocol Using Chlorophyll-a Fluorescence in a Marine Microalga', Archives Of Environmental Contamination And Toxic..., vol. 56, no. 1, pp. 30-38.View/Download from: UTS OPUS or Publisher's site
Growth inhibition bioassays with the microalga Nitzschia closterium have recently been applied in marine Toxicity Identification Evaluation (TIE) testing. However, the 48-h test duration can result in substantial loss of toxicants over time, which might lead to an underestimation of the sample toxicity. Although shorter-term microalgal bioassays can minimize such losses, there are few bioassays available and none are adapted for marine TIE testing. The acute (5-min) chlorophyll-a fluorescence bioassay is one alternative; however, this bioassay was developed for detecting herbicides in freshwater aquatic systems and its suitability for marine TIE testing was not known. In this study, a chlorophyll-a fluorescence bioassay using the marine microalga Isochrysis galbana was able to detect contaminants other than herbicides at environmentally relevant concentrations and tolerated the physical and chemical manipulations needed for a Phase I TIE. Phase I TIE procedures were successfully developed using this chlorophyll-a fluorescence bioassay and used to identify all classes of contaminants present in a synthetic mixture of known chemical composition. In addition, TIEs with both the acute fluorescence bioassay and the standard growth inhibition bioassay identified the same classes of toxicants in a sample of an unknown complex effluent. Even though the acute chlorophyll-a fluorescence end point was less sensitive than the chronic cell division end point, TIEs with the chlorophyll-a fluorescence bioassay provided a rapid and attractive alternative to longer-duration bioassays.
Collier, C, Lavery, P, Ralph, PJ & Masini, R 2008, 'Physiological characteristics of the seagrass Posidonia sinuosa along a depth-related gradient of light availability', Marine Ecology-Progress Series, vol. 353, pp. 65-79.View/Download from: UTS OPUS or Publisher's site
Physiological plasticity has the capacity to prolong seagrass survival under reduced light conditions. However, when light is attenuated across a depth gradient, the relative importance of this over other mechanisms for tolerating long-term light reducti
Hill, R & Ralph, PJ 2008, 'Dark-induced reduction of the plastoquinone pool in zooxanthellae of scleractinian corals and implications for measurements of chlorophyll a fluorescence', Symbiosis, vol. 46, pp. 45-56.View/Download from: UTS OPUS
Fluorometric measurements of maximum quantum yield (Fv/Fm) and fast induction curves (FICs) require coral samples to be dark-adapted (DA). Pathways causing dark-reduction of the plastoquinone (PQ) pool are shown here to be active in corals. Early morning sunlight and far-red light successfully increased Fv/Fm and lowered the O and J steps of FICs in corals that were darkened overnight. The thick-tissued massive coral, Cyphastrea serailia, was shown to be more prone to reduction of the PQ pool, with significant reductions in Fv/Fm occurring after 10 min of DA, and elevated J steps occurring within 200 s following a far-red flash. In thinner-tissued branching species, Pocillopora damicornis and Acropora nobilis, elevation of the J step also occurred within 200 s of DA, but a drop in Fv/Fm was only manifested after 30 min. Pre-exposure to far-red light is an effective and simple procedure to ensure determination of the true maximum quantum yield of Photosystem II (PSII) and accurate FICs which require a fully oxidised inter-system electron transport chain and open PSII reaction centres.
Hill, R & Ralph, PJ 2008, 'Impact of bleaching stress on the function of the oxygen evolving complex of zooxanthellae from scleractinian corals', Journal of Phycology, vol. 44, no. 2, pp. 299-310.View/Download from: UTS OPUS or Publisher's site
Global climate change is leading to the rise of ocean temperatures and is triggering mass coral bleaching events on reefs around the world. The expulsion of the symbiotic dinoflagellate algae is believed to occur as a result of damage to the photosynthetic apparatus of these symbionts, although the specific site of initial impact is yet to be conclusively resolved. Here, the sensitivity of the oxygen evolving complex (OEC) to bleaching stress was studied as well as its natural variation between seasons. The artificial electron donor, diphenyl carbazide (DPC), was added to cultured, freshly isolated and expelled (bleaching treatments only) zooxanthellae suspensions. Chl a fluorescence and oxygen production measurements showed that upon addition of DPC, no restoration of diminished photochemical efficiency occurred under control or bleaching conditions. This result was consistent between 12h and 5d bleaching treatments on Pocilloporadamicornis, indicating that the OEC is not the primary site of damage, and that zooxanthellae expulsion from the host is a nonselective process with respect to the functioning of the OEC. Further experiments measuring fast induction curves (FICs) revealed that in both summer and winter, the temperature when OEC function was lost occurred between 7°C and 14°C above the sea surface temperature. FIC and oxygen production measurements of P. damicornis during exposure to bleaching stress demonstrated that the thermotolerance of the OEC increased above the temperature of the bleaching treatment over a 4h period. This finding indicates that the OEC has the capacity to acclimate between seasons and remains functional at temperatures well above bleaching thresholds.
Petrou, K, Doblin, MA, Smith, RA, Ralph, PJ, Shelly, K & Beardall, J 2008, 'State transitions and nonphotochemical quenching during a nutrient-induced fluorescence transient in phosphorus-starved Dunaliella tertiolecta', Journal of Phycology, vol. 44, pp. 1204-1211.View/Download from: UTS OPUS or Publisher's site
Assessments of nutrient-limitation in microalgae using chl a fluorescence have revealed that nitrogen and phosphorus depletion can be detected as a change in chl a fluorescence signal when nutrient-starved algae are resupplied with the limiting nutrient.
Roff, G, Ulstrup, K, Fine, M, Ralph, PJ & Hoegh-Guldberg, O 2008, 'Spatial heterogeneity of photosynthetic activity within diseased corals from the great barrier reef', Journal Of Phycology, vol. 44, no. 2, pp. 526-538.View/Download from: UTS OPUS or Publisher's site
Morphological diagnosis and descriptions of seven disease-like syndromes affecting scleractinian corals were characterized from the southern Great Barrier Reef (GBR). Chl a fluorescence of PSII was measured using an Imaging-PAM (pulse amplitude modulated
Jimenez Denness, IM, Kuhl, M, Larkum, A & Ralph, PJ 2008, 'Heat budget and thermal microenvironment of shallow-water corals: Do massive corals get warmer than branching corals?', Limnology And Oceanography, vol. 53, no. 4, pp. 1548-1561.View/Download from: UTS OPUS or Publisher's site
Coral surface temperature was investigated with multiple temperature sensors mounted on hemispherical and branching corals under (a) artificial lighting and controlled flow; (b) natural sunlight and controlled flow; and (c) in situ conditions in a shallo
Kuhl, M, Holst, G, Larkum, A & Ralph, PJ 2008, 'Imaging of oxygen dynamics within the endolithic algal community of the massive coral porites lobata', Journal of Phycology, vol. 44, no. 3, pp. 541-550.View/Download from: UTS OPUS or Publisher's site
We used transparent planar oxygen optodes and a luminescence lifetime imaging system to map (at a pixel resolution of <200 ?m) the two-dimensional distribution of O2 within the skeleton of a Porites lobata colony. The O2 distribution was closely correlated to the distribution of the predominant endolithic microalga, Ostreobium quekettii Bornet et Flahault that formed a distinct green band inside the skeleton. Oxygen production followed the outline of the Ostreobium band, and photosynthetic O2 production was detected at only 0.2 ?mol photons m-2 · s-1, while saturation occurred at ?37 ?mol photons m-2 · s-1. Oxygen levels varied from ?60% to 0% air saturation in the illuminated section of the coral skeleton in comparison to the darkened section. The O2 production within the Ostreobium band was lower in the region below the upward facing surface of the coral and elevated on the sides. Oxygen consumption in darkness was also greatest within the Ostreobium zone, as well as in the white skeleton zone immediately below the corallites. The rate of O2 depletion was not constant within zones and between zones, showing pronounced heterogeneity in endolithic respiration. When the coral was placed in darkness after a period of illumination, O2 levels declined by 50% within 20 min and approached steady-state after 4050 min in darkness. Our study demonstrates the use of an important new tool in endolith photobiology and presents the first data of spatially resolved O2 concentration and its correlation to the physical structures and specific zones responsible for O2 production and consumption within the coral skeleton.
Ulstrup, K, Hill, R, van Oppen, MJ, Larkum, A & Ralph, PJ 2008, 'Seasonal variation in the photo-physiology of homogeneous and heterogeneous Symbiodinium consortia in two scleractinian corals', Marine Ecology Progress Series, vol. 361, pp. 139-150.View/Download from: UTS OPUS or Publisher's site
Seasonal variation in the composition of the algal endosymbiont community and photophysiology was determined in the corals Pocillopora damicornis,w hich show high local fidelity to one symbiont type (Symbiodinium C1) and Acropora valida, with a mixed Symbiodinium synbiont community, compromising members of both clades A and C. The relative abundances of Symbiodinium types varied overtime. A significant decline in symbiont densities in both coral species during the summer of 2005 coincided with a NOAA 'hotspot' warning for Heron Island. This also coincided with a relayiove increase in the presence and dominance of clade A in A. valida particularl in sun-adapted surfaces.
Bishop, M, Kelaher, BP, Alquezar, R, York, PH, Ralph, PJ & Skilbeck, G 2007, 'Trophic cul-de-sac, Pyrazus ebeninus, limits trophic transfer through an estuarine detritus-based food web', OIKOS, vol. 116, no. 3, pp. 427-438.View/Download from: UTS OPUS or Publisher's site
The importance to food-webs of trophic cul-de-sacs, species that channel energy flow away from higher trophic levels, is seldom considered outside of the pelagic systems in which they were first identified. On intertidal mudflats, inputs of detritus from saltmarshes, macroalgae or microphytobenthos are generally regarded as a major structuring force underpinning food-webs and there has been no consideration of trophic cul-de-sacs to date. A fully orthogonal three-factor experiment manipulating the density of the abundant gastropod, Pyrazus ebeninus, detritus and macrobenthic predators on a Sydney mudflat revealed large deleterious effects of the gastropod, irrespective of detrital loading or the presence of predators. Two months after experimental manipulation, the standing-stock of microphytobenthos in plots with high (44 per m(2)) densities of P. ebeninus was 20% less than in plots with low (4 per m(2)) densities. Increasing densities of P. ebeninus from low to high halved the abundance of macroinvertebrates and the average number of species. In contrast, the addition of detritus had differing effects on microphytobenthos (positively affected) and macroinvertebrates (negatively affected). Over the two-months of our experiment, no predatory mortality of P. ebeninus was observed and high densities of P. ebeninus decreased impacts of predators on macroinvertebrate abundances. Given that the dynamics of southeast Australian mudflats are driven more by disturbance than seasonality in predators and their interactions with prey, it is likely that Pyrazus would be similarly resistant to predation and have negative effects on benthic assemblages at other times of the year, outside of our study period. Thus, in reducing microphytobenthos and the abundance and species richness of macrofauna, high abundances of the detritivore P. ebeninus may severely limit the flow of energy up the food chain to commercially-important species.
Collier, C, Lavery, P, Masini, R & Ralph, PJ 2007, 'Morphological, growth and meadow characteristics of the seagrass Posidonia sinuosa along a depth-related gradient of light availability', Marine Ecology: Progress Series, vol. 337, pp. 103-115.View/Download from: UTS OPUS or Publisher's site
Morphological and growth characteristics of the meadow-forming seagrass Posidonia sinuosa (Cambridge et Kuo), were measured along a depth-related gradient of light to infer its response to long-term differences in light availability. Morphometric measurements were carried out at 6 depths between 1.6 and 9.0 m in summer and winter at Cockburn Sound and summer only at Warnbro Sound in south-western Australia. The minimum light requirement for P. sinuosa of 8.5% sub-surface light was among the lower range reported for seagrasses. Its slow growth rate (0.5?1.5 mgdry shoot?1 d?1), relative to similarly sized species, may contribute to the low light requirements of this species. Shoot density, leaf area index and biomass showed pronounced and consistent differences among depths (up to 88-fold reduction of above-ground biomass from shallow to deep sites). At the deeper sites, the reduced shoot density probably reduces respiratory demand and alleviates self-shading. Morphological differences (leaf length, width and thickness and number of leaves per shoot) did not follow a clear and consistent trend with depth. Despite a 70% reduction in light availability at the canopy level between the shallowest and deepest sites, leaf growth rate was unaffected by depth during summer, and in winter differed between only a few depths. We propose that the reduction in shoot density partially alleviates the effects of self-shading and permits comparable leaf growth rates across the depth range. These results suggest that for interpreting long-term responses to light availability, shoot density is the most sensitive of the morphological characteristics measured here.
Hill, R & Ralph, PJ 2007, 'Post-bleaching viability of expelled zooxanthellae from the scleractinian coral Pocillopora damicornis', Marine Ecology Progress Series, vol. 352, pp. 137-144.View/Download from: UTS OPUS or Publisher's site
Coral bleaching events have been linked to elevated seawater temperatures in combination with intense light and can be characterised by the loss of symbionts (zooxanthellae, genus Symbiodinium) from the host tissue, as well as a reduction in photosynthetic pigments in these zooxanthellae. The long-term (days) viability of expelled zooxanthellae in the water column from the scleractiman coral Pocillopora damicornis was explored in this study through measurements of photosynthetic health and morphological condition. After initial expulsion, zooxanthellae were found to be photosynthetically competent and structurally intact. However, within 6 to 12 h following this time, photosystem II photochemical efficiency dramatically declined in these cells and photosynthetic damage was gradually manifested in the loss of structural integrity of the cell. The time of expulsion during bleaching exposure, as well as ambient water temperature, greatly influenced survivorship. Expelled zooxanthellae were collected at 4 different time intervals (0-6, 6-12, 12-24 and 24-36 h) following the onset of exposure to bleaching conditions (32 degrees C and 400 mu mol photons m(-2) s(-1)) and then maintained at 28, 30 or 32 degrees C and 100 mu mol photons m(-2) s(-1) for up to 96 h. Those cells expelled within the first 6 h of bleaching and held at 28 degrees C (lagoon temperature) had the greatest longevity, although even in this treatment, long-term photosynthetic viability was restricted to 5 d in the water column. This suggests that unless expelled zooxanthellae inhabit other environments of coral reefs (such as sediments) which may be more favourable for survival, their capacity for persistence in the environment is extremely limited.
McMinn, A, Ryan, KG, Ralph, PJ & pankowski, A 2007, 'Spring sea ice photosynthesis, primary productivity and biomass distribution in eastern Antarctica, 2002-2004', Marine Biology, vol. 151, no. 3, pp. 985-995.View/Download from: UTS OPUS or Publisher's site
While it is known that Antarctic sea ice biomass and productivity are highly variable over small spatial and temporal scales, there have been very few measurements from eastern Antarctic. Here we attempt to quantify the biomass and productivity and relat
Ralph, PJ, Durako, M, Enriquez, S, Collier, C & Doblin, MA 2007, 'Impact of light limitation on seagrasses', Journal of Experimental Marine Biology and Ecology, vol. 350, no. 1-2, pp. 176-193.View/Download from: UTS OPUS or Publisher's site
Seagrass distribution is controlled by light availability, especially at the deepest edge of the meadow. Light attenuation due to both natural and anthropogenically-driven processes leads to reduced photosynthesis. Adaptation allows seagrasses to exist under these sub-optimal conditions. Understanding the minimum quantum requirements for growth (MQR) is revealed when light conditions are insufficient to maintain a positive carbon balance, leading to a decline in seagrass growth and distribution. Respiratory demands of photosynthetic and non-photosynthetic tissues strongly influence the carbon balance, as do resource allocations between above- and below-ground biomass. Seagrass light acclimation occurs on varying temporal scales, as well as across spatial scales, from the position along a single leaf blade to within the canopy and finally across the meadow. Leaf absorptance is regulated by factors such as pigment content, morphology and physical properties. Chlorophyll content and morphological characteristics of leaves such as leaf thickness change at the deepest edge. We present a series of conceptual models describing the factors driving the light climate and seagrass responses under current and future conditions, with special attention on the deepest edge of the meadow.
Ralph, PJ, Ryan, KG, Martin, AJ & Fenton, G 2007, 'Melting out of sea ice causes greater photosynthetic stress in algae than freezing in', Journal Of Phycology, vol. 43, no. 5, pp. 948-956.View/Download from: UTS OPUS or Publisher's site
Sea ice is the dominant feature of polar oceans and contains significant quantities of microalgae. When sea ice forms and melts, the microalgal cells within the ice matrix are exposed to altered salinity and irradiance conditions, and subsequently, their
Ralph, PJ, Smith, RA, Macinnis-Ng, CM & Seery, CR 2007, 'Use of fluorescence-based ecotoxicological bioassays in monitoring toxicants and pollution in aquatic systems: Review', Toxicological and Environmental Chemistry, vol. 89, no. 4, pp. 631-649.View/Download from: UTS OPUS or Publisher's site
Chlorophyll a fluorescence has the potential to become a valuable ecotoxicological endpoint, which could be used with a range of aquatic phototrophs. Chlorophyll a fluorescence bioassays have been applied in the assessment of heavy metals, herbicides, petrochemicals and nutrients. The strengths of this endpoint are that it is rapid, non-invasive and non-destructive, while the major weakness is the lack of clear ecological relevance. We provide an overview of chlorophyll a fluorescence applications in ecotoxicology. We reviewed test conditions, parameters and protocols used to date and found standardised protocols to be lacking. The most favoured fluorescence parameters were maximum quantum yield (Fv/Fm) and effective quantum yield (?PSII); microalgae were the most widely used tested organism, herbicides the most commonly tested toxicant, while most studies lacked a summary statistic (such as EC50). We recommend that future research in aquatic chlorophyll a fluorescence ecotoxicology focus on standardisation of test protocols and statistical techniques.
Ralph, PJ, Larkum, A & Kuhl, M 2007, 'Photobiology of endolithic microorganisms in living coral skeletons: 1. Pigmentation, spectral reflectance and variable chlorophyll fluorescence analysis of endoliths in the massive corals Cyphastrea serailia, Porites lutea and Goniastrea australensi', Marine Biology, vol. 152, no. 2, pp. 395-404.View/Download from: UTS OPUS or Publisher's site
We used microscopy, reflectance spectroscopy, pigment analysis, and photosynthesis-irradiance curves measured with variable fluorescence techniques to characterise the endolithic communities of phototrophic microorganisms in the skeleton of three massive
Ulstrup, K, Ralph, PJ, van Oppen, MJ & Kuhl, M 2007, 'Inter-polyp genetic and physiological characterisation of Symbiodinium in an Acropora valida colony', Marine Biology: international journal on life in oceans and coastal waters, vol. 153, no. 2, pp. 225-234.View/Download from: UTS OPUS or Publisher's site
Corals harbouring genetically mixed communities of endosymbiotic algae (Symbiodinium) often show distribution patterns in accordance with differences in light climate across an individual colony. However, the physiology of these genetically characterised communities is not well understood. Single stranded conformation polymorphism (SSCP) and real time quantitative polymerase chain reaction (qPCR) analyses were used to examine the genetic diversity of the Symbiodinium community in hospite across an individual colony of Acropora valida at the spatial scale of single polyps. The physiological characteristics of the polyps were examined prior to sampling with a combined O2 microelectrode with a fibre-optic microprobe (combined sensor diameter 50-100 Î¼m) enabling simultaneous measurements of O2 concentration, gross photosynthesis rate and photosystem II (PSII) quantum yield at the coral surface as a function of increasing irradiances. Both sun- and shade-adapted polyps were found to harbour either Symbiodinium clade C types alone or clades A and C simultaneously. Polyps were grouped in two categories according to (1) their orientation towardps light, or (2) their symbiont community composition. Physiological differences were not detected between sun- and shade-adapted polyps, but O2 concentration at 1,100 Î¼mol photons m-2 s-1 was higher in polyps that harboured both clades A and C symbionts than in polyps that harboured clade C only. These results suggest that the acclimatisation of zooxanthellae of individual polyps of an A. valida colony to ambient light levels may not be the only determinant of the photosynthetic capacity of zooxanthellae. Here, we found that photosynthetic capacity is also likely to have a strong genetic basis and differs between genetically distinct Symbiodinium types.
Charles, AL, Markich, SJ & Ralph, PJ 2006, 'Toxicity of uranium and copper individually, and in combination, to a tropical freshwater macrophyte (Lemna aequinoctialis)', Chemosphere, vol. 62, no. 8, pp. 1224-1233.View/Download from: UTS OPUS or Publisher's site
Copper (Cu) and uranium (U) are of potential ecotoxicological concern to tropical freshwater biota in northern Australia, as a result of mining activities. Few data are available on the toxicity of U, and no data are available on the toxic interaction of
Hill, R & Ralph, PJ 2006, 'Photosystem II Heterogeneity of in hospite Zooxanthellae in Scleractinian Corals Exposed to Bleaching Conditions', Photochemistry and Photobiology, vol. 82, no. 6, pp. 1577-1585.View/Download from: UTS OPUS or Publisher's site
Increased ocean temperatures are thought to be triggering mass coral bleaching events around the world. The intracellular symbiotic zooxanthellae (genus Symbiodinium) are expelled from the coral host, which is believed to be a response to photosynthetic damage within these symbionts. Several sites of impact have been proposed, and here we probe the functional heterogeneity of Photosystem II (PSII) in three coral species exposed to bleaching conditions. As length of exposure to bleaching conditions (32 degrees C and 350 mu mol photons m(-2) s(-1)) increased, the Q(A)(-) reoxidation kinetics showed a rise in the proportion of inactive PSII centers (PSIIX), where Q(B) was unable to accept electrons. PSIIX contributed up to 20% of the total PSII centers in Pocillopora damicornis, 35% in Acropora nobilis and 14% in Cyphastrea serailia. Changes in F-V/F-M and amplitude of the J step along fast induction curves were found to be highly dependent upon the proportion of PSIIx centers within the total pool of PSII reaction centers. Determination of PSII antenna size revealed that under control conditions in the three coral species up to 60% of PSII centers were lacking peripheral light-harvesting complexes (PSII beta). In P. damicornis, the proportion of PSII beta increased under bleaching conditions and this could be a photoprotective mechanism in response to excess light. The rapid increases in PSIIX and PSII beta observed in these corals under bleaching conditions indicates these physiological processes are involved in the initial photochemical damage to zooxanthellae.
Ryan, KG, Hegseth, E, Martin, A, Davy, S, O'Toole, R, Ralph, PJ, McMinn, A & Thorn, C 2006, 'Comparison of the microalgal community within fast ice two sites along the Ross Sea coast, Antarctia', Antarctic Science, vol. 18, no. 4, pp. 583-594.View/Download from: UTS OPUS or Publisher's site
Seery, CR, Gunthorpe, L & Ralph, PJ 2006, 'Herbicide impact on Hormosira banksii gametes measured by fluorescence and germination bioassays', Environmental Pollution, vol. 140, no. 1, pp. 43-51.View/Download from: UTS OPUS or Publisher's site
The innovative bioassay described here involves chlorophyll a fluorescence measurements of gametes from the macroalgae, Hormosira banksii, where gametes (eggs) were exposed to Diuron, Irgarol and Bromacil. Response was assessed as percent inhibition from
Ulstrup, K, Berkelmans, R, Ralph, PJ & van Oppen, MJ 2006, 'Variation in bleaching sensitivity of two coral species across a latitudinal gradient on the Great Barrier Reef: the role of zooxanthellae', Marine Ecology Progress Series, vol. 314, pp. 135-148.View/Download from: UTS OPUS or Publisher's site
The ability of corals to cope with environmental change, such as increased temperature, relies on the physiological mechanisms of acclimatisation and long-term genetic adaptation. We experimentally examined the bleaching sensitivity exhibited by 2 species of coral, Pocillopora damicornis and Turbinaria reniformis, at 3 locations across a latitudinal gradient of almost 6 degrees on the Great Barrier Reef (GBR), Target bleaching temperature was reached by using a ramping rate of 0.2 degrees C/h. We found that the bleaching sensitivity and recovery of both species differed between corals with clade D symbionts and those with clade C. However, in F damicornis bleaching susceptibility corresponded more strongly with latitude than with zooxanthella type and hence, temperature history, suggesting that local adaptation has occurred. The observed bleaching sensitivity was shown by a decrease in photochemical efficiency (F-v/F-m) in both species of coral. The rate of recovery in T reniformis was highest in explants containing clade D symbionts. The occurrence of clade D in the northern section of the GBR may reflect a long-term response to high sea water temperatures, while the presence of clade D in low abundance in T reniformis at Heralds Prong Reef and Percy Island may be a result of recent bleaching events.
Bengtson Nash, S, Schreiber, U, Ralph, PJ & Muller, JF 2005, 'The combined SPE: Tox Y-PAM phytotoxicity assay; application and appraisal of a novel Biomonitoring tool for the aquatic environment', Biosensors and Bioelectronics, vol. 20, no. 7, pp. 1443-1451.View/Download from: UTS OPUS or Publisher's site
Mounting concerns regarding the environment impact of herbicides has meant a growing requirement for accurate, timely information regarding herbicide residue contamination of, in particular, aquatic systems. Conventional methods of detection remain limited in temrns of practicality due to high costs of oeration and the specialised information that analysis provides. A new phytotoxicity bioassay wa trialled for the detection of herbicide residues in filter-purified (Milli-Q) as sell as antural waters. The performance of the system, which combines solid-phase extraction (SPE) wtih the ToxY-PAM dual-channel yield annalyser (Heinz Walz GmbH), was tested alongside the traditional method of liquid chromatography-mass spectometry (LC-MS). The assay methodology was found to be highly sensitive (LOD 0.1 ngL-1 diuron) with good reproducibility. The study showed that the assay protocol is time effective and can be employed for the aquatic screening of herbicide residues in purified as well as natural waters.
Hill, R & Ralph, PJ 2005, 'Diel and seasonal changes in fluorescence rise kinetics of three scleractinian corals', Functional Plant Biology, vol. 32, no. 6, pp. 549-559.View/Download from: UTS OPUS or Publisher's site
The effect of diel oscillations in light on the photosynthetic response of three coral species during summer and winter was studied. Fast induction curves revealed detailed information on primary photochemistry as well as redox states of electron accepto
Hill, R, Frankart, C & Ralph, PJ 2005, 'Impact of bleaching conditions on the components of non-photochemical quenching in the zooxanthellae of a coral', Journal Of Experimental Marine Biology And Ecology, vol. 322, no. 1, pp. 83-92.View/Download from: UTS OPUS or Publisher's site
Mass coral bleaching events are a worldwide phenomenon, which generally occur during periods of elevated sea surface temperature and intense sunlight. These conditions result in a decline in photochemical efficiency of symbiotic microalgae (zooxanthellae
Macinnis-Ng, CM, Morrison, DJ & Ralph, PJ 2005, 'Temporal and spatial variation in the morphology of the brown macroalga Hormosira banksii (Fucales, Phaeophyta)', Botanica Marina, vol. 48, no. 3, pp. 198-207.View/Download from: UTS OPUS or Publisher's site
Hormosira banksii is a morphologically variable macroalgal species from southeastern and southern Australia, which has been previously categorised into ecoforms according to habitat. This study is by far the largest quantitative evaluation of morphologic
Rapid light curves provide detailed information on the saturation characteristics of electron transport, as well as the overall photosynthetic performance of a plant. Rapid light curves were collected from samples of Zostera marina grown under low and hi
Ralph, PJ, Macinnis-Ng, CM & Frankart, C 2005, 'Fluorescence imaging application: effect of leaf age on seagrass photokinetics', Aquatic Botany, vol. 81, no. 1, pp. 69-84.View/Download from: UTS OPUS or Publisher's site
We used the Imaging-PAM fluorometer to map spatial variability of photosynthesis in three seagrass species, Halophila ovalis, Zostera capricorni and Posidonia australis. Photosynthesis was described by relative photosynthetic rate (PS/50), effective quan
Ralph, PJ, McMinn, A, Ryan, KG & Ashworth, C 2005, 'Short-term effect of temperature on the photokinetics of microalgae from the surface layers of Antarctic pack ice', Journal Of Phycology, vol. 41, no. 4, pp. 763-769.View/Download from: UTS OPUS or Publisher's site
Microalgae growing within brine channels (85 psu salinity) of the surface ice layers of Antarctic pack ice showed considerable photosynthetic tolerance to the extreme environmental condition. Brine microalgae exposed to temperatures above -5 degrees C an
Ulstrup, K, Hill, R & Ralph, PJ 2005, 'Photosynthetic impact of hypoxia on in hospite zooxanthellae in the scleractinian coral Pocillopora damicornis', Marine Ecology-Progress Series, vol. 286, pp. 125-132.View/Download from: UTS OPUS or Publisher's site
Shallow water coral reefs may experience hypoxia under conditions of calm weather doldrums. Anaerobic responses of endosymbionts (i.e. zooxanthellae) within Pocillopora damicornis coral colonies were tested using both slow and fast chlorophyll a fluoresc
The cyanobacterium known as Acaryochloris marina is a unique phototroph that uses chlorophyll d as its principal light-harvesting pigment instead of chlorophyll a, the form commonly found in plants, algae and other cyanobacteria; this means that it depends on far-red light for photosynthesis. Here we demonstrate photosynthetic activity in Acaryochloris-like phototrophs that live underneath minute coral-reef invertebrates (didemnid ascidians) in a shaded niche enriched in near-infrared light. This discovery clarifies how these cyanobacteria are able to thrive as free-living organisms in their natural habitat.
Ralph, PJ, Larkum, A & Kuehl, M 2005, 'Temporal patterns in effective quantum yield of individual zooxanthellae expelled during bleaching', Journal Of Experimental Marine Biology And Ecology, vol. 316, no. 1, pp. 17-28.View/Download from: UTS OPUS or Publisher's site
Bleaching is a worldwide phenomenon affecting coral reefs. During elevated temperature and light conditions (bleaching), expelled zooxanthellae show distinct patterns in photosynthetic health. An innovative new device was used to collect individual expel
Macinnis-Ng, CM & Ralph, PJ 2004, 'In situ impact of multiple pulses of metal and herbicide on the seagrass| Zostera capricorni', Aquatic Toxicology, vol. 67, pp. 227-237.View/Download from: UTS OPUS or Publisher's site
Ryan, KG, Ralph, PJ & McMinn, A 2004, 'Acclimation of Antarctic bottom-ice algal communities to lowered salinities during melting', Polar Biology, vol. 27, pp. 679-686.View/Download from: UTS OPUS or Publisher's site
Hill, R, Larkum, A, Frankart, C, Kuehl, M & Ralph, PJ 2004, 'Loss of functional Photosystem II reaction centres in zooxanthellae of corals exposed to bleaching conditions: using fluorescence rise kinetics', Photosynthesis Research, vol. 82, pp. 59-72.View/Download from: UTS OPUS or Publisher's site
Hill, R, Schreiber, U, Gademann, R, Larkum, A, Kuehl, M & Ralph, PJ 2004, 'Spatial heterogeneity of photosynthesis and the effect of temperature-induced bleaching condition in three species of corals', Marine Biology, vol. 144, pp. 633-640.View/Download from: UTS OPUS or Publisher's site
Choinski, JS, Ralph, PJ & Eamus, D 2003, 'Changes in photosynthesis during leaf expansion in Corymbia gummifera', Australian Journal Of Botany, vol. 51, no. 1, pp. 111-118.View/Download from: UTS OPUS or Publisher's site
Hohnberg, D, Ralph, PJ & Jones, H 2003, 'Toxicity of the herbicide atrazine at environmental concentrations to Vallisneria Gigantea, assessed using chlorophyll fluorescence', Australasian Journal of Ecotoxicology, vol. 9, pp. 93-100.View/Download from: UTS OPUS
Macinnis-Ng, CM & Ralph, PJ 2003, 'In situ impact of petrochemicals on the photosynthesis of the seagrass Zostera capricorni', Marine Pollution Bulletin, vol. 46, no. 11, pp. 1395-1407.View/Download from: UTS OPUS or Publisher's site
Macinnis-Ng, CM & Ralph, PJ 2003, 'Short-term response and recovery of Zostera capricorni photosynthesis after herbicide exposure', Aquatic Botany, vol. 76, no. 1, pp. 1-15.View/Download from: UTS OPUS or Publisher's site
Macinnis-Ng, CM & Ralph, PJ 2002, 'Towards a more ecologically relevant assessment of the impact of heavy metals on the photosynthesis of seagrass, Zostera capricorni', Marine Pollution Bulletin, vol. 45, no. N/A, pp. 100-106.
This in situ study used photosynthetic activity (measured as chlorophyll a fluorescence) and photosynthetic pigment concentrations to assess the effect of copper, cadmium, lead and zinc on the seagrass Zostera capricorni. Custom-made portable in situ exposure (PIE) chambers were developed so seagrasses could be dosed within the meadow. Z. capricorni was exposed to 0.1 and 1 mg l-1 of metal solutions for 10 h. During this time and for the subsequent four-day recovery period, the effective quantum yield of photosystem II (PS II) (?F/Fm?) was measured. While the results were variable, copper and zinc exposed samples had a depressed ?F/Fm? during the exposure period. Samples exposed to zinc recovered to pre-exposure levels but those exposed to copper did not. Cadmium and lead did not impact on the chlorophyll a fluorescence and the chlorophyll pigment data supported these findings. This study presents an innovative new application of chlorophyll a fluorescence stress assessment.
Ralph, PJ & Short, FT 2002, 'Impact of the wasting disease pathogen Labyrinthula zosterae on the photobiology of eelgrass Zostera marina', Marine Ecology Progress Series, vol. 226, no. N/A, pp. 265-271.
Labyrinthula zosterae is clearly shown to be a primary pathogen of eelgrass Zostera marina L., not merely a secondary infection of senescent leaves or an indication of decomposition, The results of this investigation using a Diving-PAM fluorometer indicate that the regions of tissue photosynthetically compromised by Labyrinthula are substantially larger than previously thought. Labyrinthula moves through Zostera marine tissue at a rate of up to 0.8 h-1 during daylight periods. The photosynthetic efficiency of apparently healthy green leaf tissue can be reduced by almost 50% in areas up to 3 mm from a necrotic region infected with Labyrinthula. Once a necrotic spot expands to bisect the eelgrass leaf, the condition of all acropertal tissue diminished; lead tissue up to 5 cm away has severely reduced photosynthetic activity.
Ralph, PJ, Polk, SM, Moore, KA, Orth, RJ & Smith, WO 2002, 'Operation of the xanthophyll cycle in the seagrass Zostera marina in response to variable irradiance', Journal of Experimental Marine Biology and Ecology, vol. 271, no. 2, pp. 189-207.View/Download from: Publisher's site
Changes in the photobiology and photosynthetic pigments of the seagrass Zostera marina from Chesapeake Bay (USA) were examined under a range of natural and manipulated irradiance regimes. Photosynthetic activity was assessed using chlorophyll-a fluorescence, and photosynthetic pigments were measured by HPLC. Large changes in the violaxanthin, zeaxanthin, and antheraxanthin content were concomitant with the modulation of non-photochemical quenching (NPQ). Photokinetics (Fv/Fm, rapid light curves (RLC), and non-photochemical quenching) varied as a result of oscillating irradiance and were highly correlated to xanthophyll pigment content. Zeaxanthin and antheraxanthin concentrations increased under elevated light conditions, while violaxanthin increased in darkened conditions. Unusually high concentrations of antheraxanthin were found in Z. marina under a wide range of light conditions, and this was associated with the partial conversion of violaxanthin to zeaxanthin. These results support the idea that xanthophyll intermediate pigments induce a photoprotective response during exposure to high irradiances in this seagrass.
Ralph, PJ, Gademann, R, Larkum, A & Kuehl, M 2002, 'Spatial heterogeneity in active chlorophyll fluorescence and PSII activity of coral tissues', Marine Biology, vol. 141, no. N/A, pp. 639-646.View/Download from: UTS OPUS or Publisher's site
Schreiber, U, Gademann, R, Bird, P, Ralph, PJ, Larkum, A & Kuehl, M 2002, 'Apparent light requirement for activation of photosynthesis upon rehydration of desicated beachrock microbial mats', Journal of Phycology, vol. 38, no. N/A, pp. 125-134.View/Download from: UTS OPUS
Ralph, PJ, Gademann, R & Larkum, A 2001, 'Zooxanthellae Expelled from Bleached Corals at 33°C Are Photosynthetically Competent', Marine Ecology Progress Series, vol. 220, pp. 163-168.View/Download from: UTS OPUS or Publisher's site
Haynes, D, Ralph, PJ, Prange, J & Dennison, B 2000, 'The Impact of the Herbicide Diuron on Photosynthesis in Three Species of Tropical Seagrass', Marine Pollution Bulletin, vol. 41, no. 0, pp. 288-293.
The impact and recovery from exposure to the herbicide diuron [DCMU; 3-(30,40-dichlorophenyl)-1,1-dimethyl- urea] was assessed for three tropical seagrasses, maintained in outdoor aquaria over a 10-day period. Photosynthetic stress was detected using chlorophyll a Puorescence, measured with a Diving-PAM (pulse am- plitude modulated Puorometer). Exposure to 10 and 100 lg ly1 diuron resulted in a decline in eective quantum yield (F=Fm0 ) within 2 h of herbicide exposure in Cy- modocea serrulata, Halophila ovalis and Zostera capri- corni. Eective quantum yield also declined over the Rrst 24 h of exposure in H. ovalis at even lower diuron con- centrations (0.1 and 1.0 lg ly1). Eective quantum yield in H. ovalis and Z. capricorni was signiRcantly depressed at all diuron concentrations (0.1}100 lg ly1) after 5 days exposure, whereas eective quantum yield in C. serrulata was only signiRcantly lower in plants exposed to highest diuron concentrations (10 and 100 lg ly1). Eective quantum yield depression was present 5 days after plants exposed to 10 and 100 lg ly1 diuron were returned to fresh seawater. These results indicate that exposure to herbicide concentrations present in nearshore Queensland sediments present a potential risk to seagrass functioning.
This paper details experiments performed to investigate the short-term stress effects of both high and low-light regimes on laboratory-cultured Halophila ovalis using chlorophyll fluorescence. Increasing irradiance up to 400 mu mol quanta m(-2) s(-1) on
Combinations of stresses showed an additive effect in comparison to the individual stress responses. It is apparent from these results that thermal, elevated-light or osmotic stress increases the sensitivity of Halophila ovalis to any of the other stress
Ralph, PJ, Gademann, R, Larkum, A & Schreiber, U 1999, 'In situ underwater measurements of photosynthetic activity of coral zooxanthellae and other reef-dwelling dinoflagellate endosymbionts', Marine Ecology-Progress Series, vol. 180, pp. 139-147.View/Download from: Publisher's site
Chlorophyll fluorescence was used to assess the iu situ photosynthesis of a range of reef-dwelling endosymbionts. Such non-intrusive in situ measurements became possible after the recent development of a submersible pulse modulated fluorometer (DIVING-PA
Chlorophyll a fluorescence was able to rapidly detect responses of laboratory-cultured Halophila ovalis to acute changes in temperature. Six heating (27.5, 30.0, 32.5, 35.0, 37.5 and 40.0 degrees C) and 6 chilling (10.0, 12.5, 15.0, 17.5, 20.0 and 22.5 d
Ralph, PJ 1998, 'Photosynthetic responses of Halophila ovalis (R. Br.) Hook. f. to osmotic stress', Journal Of Experimental Marine Biology And Ecology, vol. 227, no. 2, pp. 203-220.View/Download from: Publisher's site
Chlorophyll fluorescence was used to monitor the onset, development and recovery from hyper- and hypo-osmotic stress effects of the seagrass, Halophila ovalis (R. Br.) Hook. f. H. ovalis was able to tolerate rapid transfer from normal (35 ppt) seawater t
Ralph, PJ & Burchett, M 1998, 'Impact of petrochemicals on the photosynthesis of Halophila ovalis using chlorophyll fluorescence', Marine Pollution Bulletin, vol. 36, no. 6, pp. 429-436.View/Download from: Publisher's site
Laboratory-cultured Halophila ovalis showed tolerance to petrochemical exposure up to 1% (w/v) solution of Bass Strait crude oil, an oil dispersant (Corexit 9527) and a mixture of crude oil and dispersant, Quantum yield, as measured by chlorophyll fluore
This paper deals with the photosynthetic effects of a range of heavy metals on the seagrass Halophila ovalis. In this study, the photosynthetic response of laboratory-cultured II. ovalis to four heavy metals (Cu, Cd, Pb, Zn) was investigated. The results
Ralph, PJ, Gademann, R & Dennison, WC 1998, 'In situ seagrass photosynthesis measured using a submersible, pulse-amplitude modulated fluorometer', Marine Biology, vol. 132, no. 3, pp. 367-373.View/Download from: Publisher's site
Assessments of photosynthetic activity in marine plants can now be made in situ using a newly developed, submersible, pulse-amplitude modulated (PAM) fluorometer: Diving-PAM. PAM fluorometry provides a measure of chlorophyll a fluorescence using rapid-li
Ralph, PJ, Morrison, DJ & Addison, A 1998, 'A quantitative study of the patterns of morphological variation within Hormosira banksii (Turner) Decaisne (Fucales : Phaeophyta) in south-eastern Australia', Journal Of Experimental Marine Biology And Ecology, vol. 225, no. 2, pp. 285-300.View/Download from: Publisher's site
Homzosira banksii shows a considerable degree of morphological variability throughout its range in south-eastern Australia, apparently in relation to the local habitat, and there have been several previous qualitative attempts to categorize this variatio
Schreiber, U, Gademann, R, Ralph, PJ & Larkum, A 1997, 'Assessment of photosynthetic performance of Prochloron in Lissoclinum patella in hospite by chlorophyll fluorescence measurements', Plant And Cell Physiology, vol. 38, no. 8, pp. 945-951.View/Download from: Publisher's site
Two new PAM fluorometers (pulse amplitude modulated) were used in an investigation of photosynthetic performance of Prochloron resident as a symbiont in the ascidian Lissoclinum patella, growing in a coral reef of Heron Island on the Great Barrier Reef.
Ralph, PJ & Burchett, M 1995, 'Photosynthetic Responses Of The Seagrass Halophila-Ovalis (R Br) Hook F To High Irradiance Stress, Using Chlorophyll-A Fluorescence', Aquatic Botany, vol. 51, no. 1-Feb, pp. 55-66.View/Download from: Publisher's site
With the increasing threat of destruction to diminishing seagrass resources, there is a need for an accurate stress monitoring procedure to be developed for species of this community. In this study chlorophyll a fluorescence (20 degrees C) was used to mo
Ralph, PJ, Burchett, M & Pulkownik, A 1992, 'Distribution Of Extractable Carbohydrate Reserves Within The Rhizome Of The Seagrass Posidonia-Australis Hook F', Aquatic Botany, vol. 42, no. 4, pp. 385-392.View/Download from: Publisher's site
Rhizomes of Posidonia australis Hook. f., collected from Botany Bay on the eastern coast of Australia, were analysed for extractable carbohydrates. The concentration of extractable carbohydrate in the stelar tissue of the rhizome was significantly higher
Wilkinson, S, Ralph, P & Biloria, NM 2019, 'Algae Building: Is This the New Smart Sustainable Technology' in Biloria, N (ed), Data-Driven Multivalence in the Built Environment, Springer Nature, Switzerland, pp. 245-268.View/Download from: UTS OPUS or Publisher's site
Building energy use contributes around 40% of total greenhouse gas (GHG) emissions (UNEP 2009) and reducing building-related GHG emissions could mitigate global warming significantly. With a three degree increase in global temperature by 2100 predicted by the United Nations Intergovernmental Panel on Climate Change we need to explore ways to mitigate these impacts. An option for the built environment is to build and retrofit using innovative technologies to adopt onsite energy generation and reduce energy use (UNEP 2015). Increasing energy efficiency and using renewable energy are ways to reduce GHG emissions.
Technological innovations change over time, and innovations that start as expensive and inefficient can become economic and highly productive, solar energy is an example. In the mid 1800s the photovoltaic (PV) effect was discovered but it took a century to invent a suitable storage device, after which rapid innovation in efficiency and costs followed. Could the same happen for bio-energy? Global biomass energy production reached 88 GW in 2014 (Rosillo et al, 2016); and bio-energy is no longer a transition energy source. In 2013, a residential building in Hamburg Germany adopted algae, as a renewable energy source. Several questions arise; how does algae produce energy for buildings? And how much energy is produced? How does it compare to other renewable energy sources? Furthermore, which building types are suited to adoption of algae as an energy source? This chapter explores the feasibility of algae building technology explaining the technology and how it works; the strengths and weaknesses. Then the chapter sets out the drivers and barriers to adopting Algae Building Technology, and; to assesses opportunities across a range of building types.
Ralph, P 2018, 'Estimating Seagrass Blue Carbon and Policy Implications: The Australian Perspective' in Seagrasses of Australia: Structure, Ecology and Conservation, Springer, Switzerland, pp. 743-758.View/Download from: UTS OPUS or Publisher's site
Larkum, AWD, Pernice, M, Schliep, M, Davey, P, Szabo, M, Raven, JA, Lichtenberg, M, Brodersen, KE & Ralph, PJ 2018, 'Photosynthesis and metabolism of seagrasses' in Seagrasses of Australia: Structure, Ecology and Conservation, Springer, Switzerland, pp. 315-342.View/Download from: UTS OPUS or Publisher's site
© Springer International Publishing AG, part of Springer Nature 2018. Seagrasses have a unique leaf morphology where the major site for chloroplasts is in the epidermal cells, stomata are absent and aerenchyma is present inside the epidermis. This means that the major site for photosynthesis is in the epidermis. Furthermore the lack of stomata means that the route for carbon uptake is via inorganic carbon (C i ) uptake across the vestigial cuticle and through the outer plasma membranes. Since the leaf may at times be in an unstirred situation diffusion through an unstirred layer outside the leaf may be a large obstacle to carbon uptake. The existence of a carbon concentrating mechanism is discussed, but its existence to date is not proven. Active bicarbonate uptake across the plasmalemma does not seem to operate; an external carbonic anhydrase and an extrusion of protons seem to play a role in enhancing CO 2 uptake. There is some evidence that a C4 mechanism plays a role in carbon fixation but more evidence from "omics" is required. Photorespiration certainly occurs in seagrasses and an active xanthophyll cycle is present to cope with damaging high light, but both these biochemical mechanisms need further work. Finally, epiphytes pose a problem which impedes the uptake of C i and modifies the light environment inside the leaves.
Kumar, M, Ralph, P & Kuzhiumparambil, U 2017, 'Polyamines-stress metabolites in marine macrophytes' in ALGAL GREEN CHEMISTRY: RECENT PROGRESS IN BIOTECHNOLOGY, Elsevier.View/Download from: UTS OPUS or Publisher's site
Kuzhiumparambil, U, Kumar, M & Ralph, P 2017, 'Gas and liquid chromatography-mass spectrometry-based metabolic profiling of marine angiosperm Zostera Muelleri (alismatales, zosteraceae)' in Systems Biology of Marine Ecosystems, pp. 189-203.View/Download from: UTS OPUS or Publisher's site
© Springer International Publishing AG 2017. Seagrasses are monocotyledonous marine flowering plants that are considered lungs of the sea and are the most intense carbon sinks on the planet, delivering a range of ecologically and economically valuable biological services. In this study, we report the chemical fingerprint of Zostera muelleri using an untargeted metabolomic approach. High-performance liquid chromatography-mass spectrometry (HPLC-MS) and gas chromatography-mass spectrometry (GC-MS) were performed to study the metabolic profile of Z. muelleri. A total of 98 metabolites belonging to various chemical classes including flavonoids, phenolics, lipids, fatty acids, sugar alcohols and amino acids were identified, including two characteristic marker compounds of the genus, zosteric acid and rosmarinic acid. Chromatographic profiling yield a comprehensive map for the chemical constituents of Z. muelleri, and this method can be used as an effective and convenient approach to gain insights into the chemical composition of other seagrasses.
Ralph, PJ, Hill, R, Doblin, MA & Davy, SK 2016, 'Theory and Application of Pulse Amplitude Modulated Chlorophyll Fluorometry in Coral Health Assessment' in Woodley, CM, Downs, CA, Bruckner, AW, Porter, JW & Galloway, SB (eds), Diseases of Coral, John Wiley & Sons, Hoboken, New Jersey, pp. 506-523.View/Download from: Publisher's site
© 2016 John Wiley & Sons, Inc. Scleractinian corals exist in symbiosis with dinoflagellate alga (genus Symbiodinium), which provides access to nutrients by the host but also makes it makes the holobiont vulnerable to photosynthetic stress, providing an opportunity for rapid health assessment using chlorophyll a (chl-a) fluorescence techniques. Common photosynthetic stressors of corals are high irradiance, ultraviolet light, temperature extremes, chemical pollution and low salinity, which are further compounded by other major anthropogenic pressures on coral reefs. Coral Symbiodinium cells contain chlorophyll (chl) a, c2 and a range of accessory pigments. The chl-a within the pigment complex absorbs light maximally in the blue (peak at 440 nm) and red (peak at 678 nm) regions of the spectrum and re-emits light energy in the form of fluorescence, maximally in the red bandwidth (630 to 770 m with a peak at 680 nm). In vivo chl-a has a variable fluorescence yield that is dependent upon the wavelength of excitation irradiance and varies over time as a result of the complex interaction of the photosynthetic pathways (Kautsky effect). When a chloroplast captures a photon of energy, the chl a molecule is excited from its ground state to an excited state. There are three competing and complementary energy dissipation processes for that excited molecule: (i) driving photosynthesis via the electron transport chain leading to carbon fixation, (ii) heat dissipation, or (iii) returning to the ground state and re-emitting some of the energy as fluorescence. This is why chl a fluorescence can be used as a proxy for photochemistry (and energy dissipation). During periods of high incident irradiance, if the amount of absorbed light exceeds the maximum rate of electron transport, then the excess energy must be dissipated, or photodamage can occur. Pulse-amplitude modulated (PAM) fluorometry provides a versatile technique for monitoring and assessing zooxanthellae health. It measure...
Ralph, PJ, Wilhelm, C, Lavaud, J, Jakob, T, Petrou, K & Kranz, SA 2011, 'Fluorescence as a Tool to Understand Changes in Photosynthetic Electron Flow Regulation' in Suggett, DJ, Borowitzka, MA & Prasil, O (eds), Chlorophyll a Fluorescence in Aquatic Sciences : Methods and Applications, Springer, United Kingdom, pp. 75-89.View/Download from: UTS OPUS or Publisher's site
This chapter investigates the use of chlorophyll a fluorescence to better understand changes in the regulation of photosynthetic electron transport. It describes the different electron pathways utilised by photosynthetic organisms, including pathways used in photosynthesis as well as alternative electron cycling (AEC). The major photoprotective processes are described, in particular, non-photochemical quenching (NPQ) and its three components, energy-dependent quenching (qE), state-transition quenching (qT), and photoinhibition (qI). Fluorescence and NPQ responses to light stress are compared across a higher plant, diatom and cyanobacteria. Photosynthesis is a complex interaction of complementary processes making the identification and isolation of a particular photosynthetic pathway or process inherently difficult. Therefore, we describe the use of chemicals which allow for the differentiation of mechanistic photosynthetic processes, such as electron transport pathways, CO2 fixation and the use of trans-thylakoid proton gradients, which can be effectively understood and quantified using chlorophyll fluorescence detection techniques.
Warner, ME, Lesser, MP & Ralph, PJ 2011, 'Chlorophyll fluorescence in reef building corals' in Suggett, DJ, Borowitzka, MA & Prasil, O (eds), Chlorophyll a Fluorescence in Aquatic Sciences : Methods and Applications, Springer, UK, pp. 209-221.View/Download from: UTS OPUS or Publisher's site
The ecological success of reef-building corals throughout the tropics is due in large part to the endosymbiotic dinoflagellates that reside within the gastrodermal cells of these cnidarian hosts. These algae, belonging to the genus Symbiodinium, are often referred to by the common term of zooxanthellae. This mutualism between Symbiodinium spp. and tropical and sub-tropical coral species has been a key component to the evolutionary persistence of reef-building corals since the Triassic (Stanely 2003). The importance of these algae in the long-term success of reef-building corals cannot be over emphasized, as they can contribute a significant portion of photosynthetically derived carbon to the host via translocation. The coral metabolizes this carbon, thereby meeting up to 90 percent or more of the animals daily metabolic demand from the byproducts of photosynthesis by the symbionts (Muscatine 1990).
Ralph, PJ, Tomasko, D, Moore, KA, Seddon, S & Macinnis-Ng, CM 2006, 'Human impacts on seagrasses: Eutrophication, sedimentation and contamination' in Larkum, AWD, Orth, RJ & Duarte, CM (eds), Seagrasses: Biology, Ecology and Conservation, Springer, The Netherlands, pp. 567-593.View/Download from: UTS OPUS
Larkum, A, Drew, E & Ralph, PJ 2006, 'Photosynthesis and Metabolism in Seagrasses at the Cellular Level' in Larkum, AWD, Orth, RJ & Dyarte, CM (eds), Seagrasses:Biology, Ecology and Conservation, Springer, Dordrecht, The Netherlands, pp. 323-345.View/Download from: UTS OPUS
Beer, S, Bjork, M, Gademann, R & Ralph, PJ 2001, 'Measurements of Photosynthetic Rates in Seagrasses' in Short, FT & Coles, RG (eds), Global Seagrass Research Methods, Elsevier Science, Netherlands, pp. 183-198.
Awan, Z, Kahlke, T, Ralph, PJ & Kennedy, PJ 2019, 'Chemical named entity recognition with deep contextualized neural embeddings', IC3K 2019 - Proceedings of the 11th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management, pp. 135-144.
Copyright © 2019 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved Chemical named entity recognition (ChemNER) is a preliminary step in chemical information extraction pipelines. ChemNER has been approached using rule-based, dictionary-based, and feature-engineered based machine learning, and more recently also deep learning based methods. Traditional word-embeddings, like word2vec and Glove, are inherently problematic because they ignore the context in which an entity appears. Contextualized embeddings called embedded language models (ELMo) have been recently introduced to represent contextual information of a word in its embedding space. In this work, we quantify the impact of contextualized embeddings for ChemNER by using Bi-LSTM-CRF (bidirectional long short term memory networks - conditional random fields) networks. We benchmarked our approach using four well-known corpora for chemical named entity recognition. Our results show that incorporation of ELMo results in statistically significant improvements in F1 score in all of the tested datasets.
Verma, A, Kohli, G, Hoppenrath, M, Harwood, T, Kuzhiumparambil, U, Ralph, P & Murray, S 2016, 'Systematics and diversity of the genus Ostreopsis in the East Australian Current region', Marine and Fresh-Water Harmful Algae. Proceedings of the 17th International Conference on Harmful Algae., International Conference on Harmful Algae, International Society for Study of Harmful Algae, Brazil, pp. 84-88.View/Download from: UTS OPUS
Chia, Q, Brown, P, Labeeuw, L, Bajada, C, Ghannam, S, Pham, H, Wright, A & Ralph, P 2018, 'Comparing alternative algal cultivation systems for biodiesel production by utilizing an integrated model of sustainability', 17th Australasian - Centre for Social and Environmental Accounting Research Conference, Melbourne.
Howes, JM, Stuart, BH & Ralph, PJ 2013, 'Assessing metabolic variation of endosymbiotic and cultured Symbiodinium microadriaticum using synchrotron imaging FTIR spectroscopy', 7th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator-Based Sources Abstracts, 7th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator-Based Sources.
Howes, JM, Stuart, BH & Ralph, PJ 2013, 'Macromolecular composition varies significantly between genetic clades of Symbiodinium microadriaticum', 10th International Phycological Congress Abstracts, 10th International Phycological Congress.
Chartrand, KM, Rasheed, M, Petrou, K & Ralph, PJ 2012, 'Establishing tropical seagrass light requirements in a dynamic port environment', Proceedings of the 12th International Coral Reef Symposium, Cairns, Australia, 9-13 July 2012, International Coral Reef Symposium, ReefBase, Cairns.View/Download from: UTS OPUS
Tropical seagrasses inhabit naturally turbid waters with dynamic light environments and variable water quality in coastal waters adjacent to the Great Barrier Reef. Large tidal fluxes amplify the magnitude of these conditions with extreme high and low light over relatively short time scales (i.e. hours). Large port developments in the region have the potential to confound the complex relationships between seagrass physiology and this dynamic light field with the onset of dredging and their associated turbid plumes. Understanding the capacity for seagrasses to respond to changes in the quantity and quality of the light environment will allow for prediction of how seagrass species and populations will tolerate changes in light attenuation that may occur during dredging. We present a strategy for determining seasonal-specific light requirements for an intertidal tropical seagrass community in a port environment. Locally relevant light requirements are established by describing the relationships among photosynthetic inputs and losses, tidal exposure, shifts in spectral light quality, seasonality and the capacity to utilise below ground carbon reserves. The outcomes of the study provide guidelines for a mitigation strategy that is focused on maintaining critical windows of light to support seagrass growth and the longer term survival of these productive coastal ecosystems.
Hill, R, Brown, C, DeZeeuw, K, Campbell, D & Ralph, PJ 2010, 'Increased rate of D1 repair in coral symbionts during bleaching is insufficient to counter accelerated photoinactivation', Euro ISRS Symposium 2010, Grafisch Service Center, Wageningen, The Netherlands, pp. 87-87.
Schrameyer, V, Kraemer, W, Hill, R, Doblin, MA, Kai, B & Ralph, PJ 2010, 'Nutritional status of hard and soft corals influences photosynthesis capacity of Symbiodinium sp. and vitality of the holobiont', Euro ISRS Symposium 2010, Grafisch Service Center, Wageningen, The Netherlands, pp. 108-108.
Sinutok, S, Hill, R, Doblin, MA & Ralph, PJ 2010, 'Rising ocean temperature and ocean acidification will reduce productivity and calcification in Halimeda sp. and benthic foraminifera from the Great Barrier Reef', Euro ISRS Symposium 2010, Grafisch Service Center, Wageningen, The Netherlands, pp. 191-191.
Doblin, MA, Ralph, PJ, Oubelkheir, K, Hassler, CS, Suthers, I & Thompson, P 2009, 'Using IMOS to bridge the gap between direct measurements of marine primary production and models', Adelaide, Australia.
Petrou, K, Doblin, MA, Hassler, CS & Ralph, PJ 2009, 'Multiple stressors on the sea ice diatom Fragilariopsis cylindrus - photophysiological impacts of seasonal freezing and melting of sea ice', Japan.
Sinutok, S, Hill, R & Ralph, PJ 2009, 'The effect of light intensity on photosynthetic efficiency and calcification in three reef building species of Halimeda', ASPAB 2009 Conference, Townsville, Australia.
Calcareous green algae from the genus Halimeda are widely distributed in tropical and subtropical marine environments. Halimeda is important as a carbonate sediment producer, as a source of food for herbivores, as a phototroph, and as a provider of shelter and nursery ground for invertebrates on coral reefs. Halimeda cylindracea, H. macroloba, and H. opuntia collected from the intertidal zone at Heron Island reef in the southern Great Barrier Reef of Australia were maintained in flow-through seawater tanks under three different irradiances (50, 400 and 900 Âµmol photon m-2 s-1) for a 4 day period. Measures of photosynthetic efficiency were investigated using Pulse Amplitude Modulated (PAM) fluorometry and chlorophyll concentrations (a and b) were determined after 4 days on an apical lobe of the thallus. Growth and calcification were examined by staining the thallus with Alizarin Red-S solution. Pigmentation, growth, and calcification were found to be independent of irradiance, remaining constant over time between treatments, except for chlorophyll a in H. cylindracea which was higher in low light than in higher light treatments. The results indicate that each species responded differently under the high light treatment at midday, with H. cylindracea and H. macroloba showing a reduction in photochemical quenching (Y(II)), indicating downregulation in photosynthetic efficiency. This was mirrored by an increase in non-regulated energy dissipation yield of PSII (Y(NO)), suggesting that photoinhibition was occurring. In comparison to this species, H. opuntia showed no changes in Y(II) and Y(NO) while H. macroloba showed higher Y(II) and lower Y(NO) only in the morning and the evening. Non-photochemical quenching yield (Y(NPQ)) was low in all treatments and in all three species which may indicate a low potential for photoprotection mechanisms in these algae. However, further investigation is required which run over an extended period of time and between seasons.
Wilson, KG & Ralph, PJ 2008, 'A comparison of the effects of Tapis crude oil and dispersed crude oil on subtidal Zostera capricorni', International Oil Spill Conference - IOSC 2008, Proceedings, pp. 859-864.
The toxic effects of Tapis crude oil and dispersed Tapis crude oil on subtidal Zostera capricorni were studied. Limited photosynthetic impact was detected in Z. capricorni exposed to the water soluble fraction of the non-dispersed Tapis crude oil treatments. No significant photosynthetic impact was evident in the dispersed Tapis crude oil treatment even though the total petroleum hydrocarbon (TPH) concentration in these treatments was higher than in the non-dispersed Tapis crude oil treatments. Plants from both treatments recovered following replenishment from the surrounding sea water. A substantial reduction of the TPH within the mesoscosms over the 10 hr exposure period was apparent and would likely suggest a rapid loss of the toxic mixture to the sediments rather than assimilation by the sea grass. This is an abstract of a paper presented at the International Oil Spill Conference 2008 Proceedings (Savannah, GA 5/4-8/2008).
Petrou, K, Shelly, K, Hassler, CS, Schoemann, V, Doblin, MA & Ralph, PJ 2007, 'Ocean productivity in a changing world: Iron-limitation of Southern Ocean phytoplankton and implication for Antarctic meltwater productivity', Australia.
Macinnis-Ng, CMO & Ralph, PJ 2001, 'Towards a more ecologically relevant assessment of the impact of heavy metals on the photosynthesis of the seagrass, Zostera capricorni', MARINE POLLUTION BULLETIN, 3rd International Conference on Marine Pollution and Ecotoxicology, PERGAMON-ELSEVIER SCIENCE LTD, HONG KONG, PEOPLES R CHINA, pp. 100-106.View/Download from: Publisher's site
Ralph, P, de Beyer, L & Hardtke, L 2018, 'Living Lights', Vivid Sydney.
Living Lights is a ‘forest’ made entirely of living, breathing algae that welcomes visitors with an energetic, bubbling ‘blurp’.
Growing and sustaining itself by harvesting the energy of the sun, in just three weeks Living Lights will produce more oxygen than a suburban park does in a year!
Created by the University of Technology Sydney and the Deep Green Biotech Hub this installation aims to increase public awareness of algae as a highly versatile and sustainable resource for a wide range of industries.
In nature, algae are responsible for half of the air we breathe; But it’s only now that the global potential of these naturally occurring organisms is being realised as they are harvested for use in next-generation medicines, cosmetics, food and drink.
The installation has 18 reactors of varying heights up to 2.5 metres tall, containing three different strains of algae – two sourced from CSIRO’s Australian National Algae Culture Collection. The organisms’ naturally varying colours of bright red, gold and fluorescent green are lit up with LEDs.
Visitors to Living Lights will be drawn to the illuminated beauty of this little-known organism, which has the potential to shape our sustainable future.
Wilkinson, SJ, Stoller, P, Ralph, P & Hamdorf, B UTS 2016, Feasibility of Algae Building Technology in Sydney, Feasibility of Algae Building Technology in Sydney, no. 1, pp. 1-56, Sydney Australia.View/Download from: UTS OPUS
Ralph, PJ & Sinutok, S AccessUTS Pty Limited 2013, Vallisneria and submerged macrophyte management in Penrith Lakes, Sydney.
Chartrand, KM, McKenna, SA, Petrou, K, Jimenez Denness, IM, Franklin, J, Sankey, TL, Hedge, SA, Rasheed, M & Ralph, PJ DEEDI Publication 2010, Port Curtis Benthic Primary Producer Habitat Assessment and Health Studies Update: Interim Report December 2010, pp. 1-128, Cairns.View/Download from: UTS OPUS
Abstract Eukaryotic microalgae dominate primary photosynthetic productivity in fluctuating nutrient-rich environments, including coastal, estuarine and polar regions, where competition and complexity are presumably adaptive and dynamic traits. Numerous genomes and transcriptomes of these species have been carefully sequenced, providing an unprecedented view into the vast genetic repertoires and the diverse transcriptional programs operating inside these organisms. Here we collected, re-mapped, quantified and clustered publicly available transcriptome data for ten different eukaryotic microalgae in order to develop new insights into their molecular systems biology, as well as to provide a large new resource of integrated information to facilitate the efforts of others to further compare and contextualize the results of individual and new experiments within and between species. This is summarized herein and provided for public use by the eukaryotic microalgae research community.