The over-arching goal of our research is to understand how the seas smallest inhabitants ultimately control the ecology and biogeochemistry of the Ocean
My research interests incorporate aquatic microbial ecology and biological oceanography, and my research team tackles the important questions of who are the key microbial populations in different ocean ecosystems, and what they are doing? To answer these questions we examine the ecology of microbes across a range of marine environments (tropical coral reefs to Antarctica) and a continuum of spatiotemporal scales. At the ocean-basin scale we investigate how large-scale oceanographic processes (e.g. boundary currents and mesoscale eddies) influence microbial community dynamics and functionality. At the scale of individual drops of seawater, we consider the behaviours of individual microbes within a patchy chemical seascape. Finally, we are interested in the relationships (both positive and negative) between microorganisms and marine animals and plants.
Test tube reef
The crucial role of the tiniest denizens of the deep
How a Marine Bacteria’s Mealtime Dash is a Swimming Success
Tiny Ecosystem may shed light on climate change
A Plankton Eat Plankton World
Tiny MIT Ecosystem may shed light on climate change
Can supervise: YES
The principle goal of my research team is to understand the ecological and biogeochemical function of microbes in marine environments. Our research tackles the important questions of who are the key microbial populations in different ocean ecosystems, and what they are doing?
Key Research Themes:
My research investigates processes that have profound implications for the function of the ocean and our planet, and can be defined under five key research themes including:
(i) Microbial Oceanography: How the physical, chemical and biological characteristics of different oceanic provinces influence, and are influenced by, the composition and functionality of marine microbial assemblages.
(ii) Marine Microbial Ecology: Understanding the ecological interactions between different microbial groups, including Bacteria, Archaea, Viruses and Eukaryotes.
(iii) Marine Microbe – Animal Interactions: Understanding the roles of microbes in the ecology and health of marine animals, including corals and fish
(iv) Marine Microbe – Plant Interactions: Understanding the roles of microbes in the ecology and health of marine plants, including seagrasses and macroalgae
(v) Marine Microbe – Human Interactions: Examination of the occurrence and dynamics of potentially harmful indigenous and introduced bacteria in coastal marine environments, with specific focus on the influence of shifting environmental conditions (e.g. pollution and climate change processes).
Subject Coordinator and Chief Lecturer for Microbial Ecology (91170)
Guest Lecturer in Ecology (91154) and General Microbiology (91314)
Labbate, M, Seymour, JR, Lauro, F & Brown, MV 2016, Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments, Frontiers Media SA, Lausanne, Switzerland.View/Download from: UTS OPUS or Publisher's site
Aquatic ecosystems are currently experiencing unprecedented levels of impact from human activities including over-exploitation of resources, habitat destruction, pollution and the influence of climate change. The impacts of these activities on the microbial ecology of aquatic environments are only now beginning to be defined. One of the many implications of environmental degradation and climate change is the geographical expansion of disease- causing microbes such as those from the Vibrio genus. Elevating sea surface temperatures correlate with increasing Vibrio numbers and disease in marine animals (e.g. corals) and humans. Contamination of aquatic environments with heavy metals and other pollutants affects microbial ecology with downstream effects on biogeochemical cycles and nutrient turnover. Also of importance is the pollution of aquatic environments with antibiotics, resistance genes and the mobile genetic elements that house resistance genes from human and animal waste. Such contaminated environments act as a source of resistance genes long after an antibiotic has ceased being used in the community. Environments contaminated with mobile genetic elements that are adapted to human commensals and pathogens function to capture new resistance genes for potential reintroduction back into clinical environments. This research topic encompasses these diverse topics and describes the affect(s) of human activity on the microbial ecology and function in aquatic environments and, describes methods of restoration and for modelling disturbances.
Green, TJ, Siboni, N, King, WL, Labbate, M, Seymour, JR & Raftos, D 2019, 'Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event.', Microbial ecology.View/Download from: UTS OPUS or Publisher's site
Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.
King, WL, Jenkins, C, Go, J, Siboni, N, Seymour, JR & Labbate, M 2019, 'Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event.', Microbial Ecology.View/Download from: UTS OPUS or Publisher's site
The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013-2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1-V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.
King, WL, Jenkins, C, Seymour, JR & Labbate, M 2019, 'Oyster disease in a changing environment: Decrypting the link between pathogen, microbiome and environment.', Marine environmental research.View/Download from: UTS OPUS or Publisher's site
Shifting environmental conditions are known to be important triggers of oyster diseases. The mechanism(s) behind these synergistic effects (interplay between host, environment and pathogen/s) are often not clear, although there is evidence that shifts in environmental conditions can affect oyster immunity, and pathogen growth and virulence. However, the impact of shifting environmental parameters on the oyster microbiome and how this affects oyster health and susceptibility to infectious pathogens remains understudied. In this review, we summarise the major diseases afflicting oysters with a focus on the role of environmental factors that can catalyse or amplify disease outbreaks. We also consider the potential role of the oyster microbiome in buffering or augmenting oyster disease outbreaks and suggest that a deeper understanding of the oyster microbiome, its links to the environment and its effect on oyster health and disease susceptibility, is required to develop new frameworks for the prevention and management of oyster diseases.
King, WL, Siboni, N, Williams, NLR, Kahlke, T, Nguyen, KV, Jenkins, C, Dove, M, O'Connor, W, Seymour, JR & Labbate, M 2019, 'Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 mu var Disease', FRONTIERS IN MICROBIOLOGY, vol. 10.View/Download from: UTS OPUS or 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
Macreadie, PI, Atwood, TB, Seymour, JR, Fontes, MLS, Sanderman, J, Nielsen, DA & Connolly, RM 2019, 'Vulnerability of seagrass blue carbon to microbial attack following exposure to warming and oxygen.', The Science of the total environment, vol. 686, pp. 264-275.View/Download from: Publisher's site
Seagrass meadows store globally-significant quantities of organic 'blue' carbon. These blue carbon stocks are potentially vulnerable to anthropogenic stressors (e.g. coastal development, climate change). Here, we tested the impact of oxygen exposure and warming (major consequences of human disturbance) on rates of microbial carbon break-down in seagrass sediments. Active microbes occurred throughout seagrass sediment profiles, but deep, ancient sediments (~5000 yrs. old) contained only 3% of the abundance of active microbes as young, surface sediments (<2 yrs. old). Metagenomic analysis revealed that microbial community structure and function changed with depth, with a shift from proteobacteria and high levels of genes involved in sulfur cycling in the near surface samples, to a higher proportion of firmicutes and euraracheota and genes involved in methanogenesis at depth. Ancient carbon consisted almost entirely (97%) of carbon considered 'thermally recalcitrant', and therefore presumably inaccessible to microbial attack. Experimental warming had little impact on carbon; however, exposure of ancient sediments to oxygen increased microbial abundance, carbon uptake and sediment carbon turnover (34-38 fold). Overall, this study provides detailed characterization of seagrass blue carbon (chemical stability, age, associated microbes) and suggests that environmental disturbances that expose coastal sediments to oxygen (e.g. dredging) have the capacity to diminish seagrass sediment carbon stocks by facilitating microbial remineralisation.
Moore, LR, Huang, T, Ostrowski, M, Mazard, S, Kumar, SS, Gamage, HKAH, Brown, MV, Messer, LF, Seymour, JR & Paulsen, IT 2019, 'Unicellular Cyanobacteria Are Important Components of Phytoplankton Communities in Australia's Northern Oceanic Ecoregions.', Frontiers in microbiology, vol. 9, pp. 3356-3356.View/Download from: UTS OPUS or Publisher's site
The tropical marine environments of northern Australia encompasses a diverse range of geomorphological and oceanographic conditions and high levels of productivity and nitrogen fixation. However, efforts to characterize phytoplankton assemblages in these waters have been restricted to studies using microscopic and pigment analyses, leading to the current consensus that this region is dominated by large diatoms, dinoflagellates, and the marine cyanobacterium Trichodesmium. During an oceanographic transect from the Arafura Sea through the Torres Strait to the Coral Sea, we characterized prokaryotic and eukaryotic phytoplankton communities in surface waters using a combination of flow cytometry and Illumina based 16S and 18S ribosomal RNA amplicon sequencing. Similar to observations in other marine regions around Australian, phytoplankton assemblages throughout this entire region were rich in unicellular picocyanobacterial primary producers while picoeukaryotic phytoplankton formed a consistent, though smaller proportion of the photosynthetic biomass. Major taxonomic groups displayed distinct biogeographic patterns linked to oceanographic and nutrient conditions. Unicellular picocyanobacteria dominated in both flow cytometric abundance and carbon biomass, with members of the Synechococcus genus dominating in the shallower Arafura Sea and Torres Strait where chlorophyll a was relatively higher (averaging 0.4 ± 0.2 mg m-3), and Prochlorococcus dominating in the oligotrophic Coral Sea where chlorophyll a averaged 0.13 ± 0.07 mg m-3. Consistent with previous microscopic and pigment-based observations, we found from sequence analysis that a variety of diatoms (Bacillariophyceae) exhibited high relative abundance in the Arafura Sea and Torres Strait, while dinoflagellates (Dinophyceae) and prymnesiophytes (Prymnesiophyceae) were more abundant in the Coral Sea. Ordination analysis identified temperature, nutrient concentrations and water depth as key drivers of the region'...
Raina, JB, Fernandez, V, Lambert, B, Stocker, R & Seymour, JR 2019, 'The role of microbial motility and chemotaxis in symbiosis', Nature Reviews Microbiology.View/Download from: UTS OPUS or Publisher's site
© 2019, Springer Nature Limited. Many symbiotic relationships rely on the acquisition of microbial partners from the environment. However, the mechanisms by which microbial symbionts find and colonize their hosts are often unknown. We propose that the acquisition of environmental symbionts often necessitates active migration and colonization by the symbionts through motility and chemotaxis. The pivotal role of these behaviours in the onset and maintenance of symbiotic interactions is well established in a small number of model systems but remains largely overlooked for the many symbioses that involve the recruitment of microbial partners from the environment. In this Review, we highlight when, where and how chemotaxis and motility can enable symbiont recruitment and propose that these symbiont behaviours are important across a wide range of hosts and environments.
Rinke, C, Rubino, F, Messer, LF, Youssef, N, Parks, DH, Chuvochina, M, Brown, M, Jeffries, T, Tyson, GW, Seymour, JR & Hugenholtz, P 2019, 'A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).', The ISME Journal, vol. 13, no. 3, pp. 663-675.View/Download from: UTS OPUS or Publisher's site
Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to occupy a variety of ecological niches and to become the most succes...
Copeland, E, Leonard, K, Carney, R, Kong, J, Forer, M, Naidoo, Y, Oliver, BGG, Seymour, JR, Woodcock, S, Burke, CM & Stow, NW 2018, 'Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites', Frontiers in Cellular and Infection Microbiology, vol. 8, pp. 1-14.View/Download from: UTS OPUS or Publisher's site
Ajani, PA, Kahlke, T, Siboni, N, Carney, R, Murray, S & Seymour, J 2018, 'The microbiome of the cosmopolitan diatom Leptocylindrus reveals significant spatial and temporal variability', Frontiers in Microbiology, vol. 9.View/Download from: UTS OPUS or Publisher's site
Brown, MV, van de Kamp, J, Ostrowski, M, Seymour, JR, Ingleton, T, Messer, LF, Jeffries, T, Siboni, N, Laverock, B, Bibiloni-Isaksson, J, Nelson, TM, Coman, F, Davies, CH, Frampton, D, Rayner, M, Goossen, K, Robert, S, Holmes, B, Abell, GCJ, Craw, P, Kahlke, T, Sow, SLS, McAllister, K, Windsor, J, Skuza, M, Crossing, R, Patten, N, Malthouse, P, van Ruth, PD, Paulsen, I, Fuhrman, JA, Richardson, A, Koval, J, Bissett, A, Fitzgerald, A, Moltmann, T & Bodrossy, L 2018, 'Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative.', Scientific data, vol. 5, pp. 180130-180130.View/Download from: UTS OPUS or Publisher's site
Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.
Dann, LM, McKerral, JC, Smith, RJ, Tobe, SS, Paterson, JS, Seymour, JR, Oliver, RL & Mitchell, JG 2018, 'Microbial micropatches within microbial hotspots.', PLoS ONE, vol. 13, no. 5, pp. 1-22.View/Download from: UTS OPUS or Publisher's site
The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have 'hotspots' of high abundance, and 'coldspots' of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.
Giardina, M, Cheong, S, Marjo, CE, Clode, PL, Guagliardo, P, Pickford, R, Pernice, M, Seymour, JR & Raina, J-B 2018, 'Quantifying Inorganic Nitrogen Assimilation by Synechococcus Using Bulk and Single-Cell Mass Spectrometry: A Comparative Study.', Frontiers in microbiology, vol. 9.View/Download from: UTS OPUS or Publisher's site
Microorganisms drive most of the major biogeochemical cycles in the ocean, but the rates at which individual species assimilate and transform key elements is generally poorly quantified. One of these important elements is nitrogen, with its availability limiting primary production across a large proportion of the ocean. Nitrogen uptake by marine microbes is typically quantified using bulk-scale approaches, such as Elemental Analyzer-Isotope Ratio Mass Spectrometry (EA-IRMS), which averages uptake over entire communities, masking microbial heterogeneity. However, more recent techniques, such as secondary ion mass spectrometry (SIMS), allow for elucidation of assimilation rates at the scale at which they occur: the single-cell level. Here, we combine and compare the application of bulk (EA-IRMS) and single-cell approaches (NanoSIMS and Time-of-Flight-SIMS) for quantifying the assimilation of inorganic nitrogen by the ubiquitous marine primary producer Synechococcus. We aimed to contrast the advantages and disadvantages of these techniques and showcase their complementarity. Our results show that the average assimilation of 15N by Synechococcus differed based on the technique used: values derived from EA-IRMS were consistently higher than those derived from SIMS, likely due to a combination of previously reported systematic depletion as well as differences in sample preparation. However, single-cell approaches offered additional layers of information, whereby NanoSIMS allowed for the quantification of the metabolic heterogeneity among individual cells and ToF-SIMS enabled identification of nitrogen assimilation into peptides. We suggest that this coupling of stable isotope-based approaches has great potential to elucidate the metabolic capacity and heterogeneity of microbial cells in natural environments.
Haydon, TD, Seymour, JR & Suggett, DJ 2018, 'Soft corals are significant DMSP producers in tropical and temperate reefs', Marine Biology, vol. 165, no. 7.View/Download from: UTS OPUS or Publisher's site
© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. Corals synthesise large quantities of the sulphur metabolite dimethylsulphoniopropionate (DMSP), which contributes to key roles in coral reef ecology including the capacity of corals to withstand various stressors. While closely related to scleractinian corals and often occupying similar ecological niche space, it is currently poorly defined to what extent soft corals produce DMSP. We, therefore, examined DMSP content within four key species of soft coral in February and July–August of 2017, including two temperate species from Sydney Harbour (Erythropodium hicksoni, Capnella gaboensis) and two tropical species from the Great Barrier Reef (Sinularia sp., Sarcophyton sp.). We compared DMSP content of these soft coral species to that of commonly occurring temperate (Plesiastrea versipora) and tropical (Acropora aspera) scleractinian coral species. DMSP content was normalised to coral protein content, with soft coral DMSP content highly variable across species and locations [56–539 nmol (mg protein)−1], and lower than for the tropical [1242–4710 nmol (mg protein)−1], but not temperate [465–1984 nmol (mg protein)−1] scleractinian species. Further comparison with previously published values demonstrated that soft coral DMSP content falls within the 'low–mid range' of scleractinian corals. Notably, DMSP content was also higher in summer samples than winter samples for the scleractinian corals, but did not differ between seasons for soft corals. Such contrasting dynamics of DMSP production by soft corals compared to scleractinian corals indicates that the regulation of DMSP content differs between these two important benthic cnidarian groups, potentially as a consequence of dissimilar ecophysiological roles for this compound.
Lawson, CA, Raina, J-B, Kahlke, T, Seymour, JR & Suggett, DJ 2018, 'Defining the core microbiome of the symbiotic dinoflagellate, Symbiodinium.', Environmental microbiology reports, vol. 10, no. 1, pp. 7-11.View/Download from: UTS OPUS or Publisher's site
Dinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterized the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome. Similar to other systems, bacteria were nearly two orders of magnitude more numerically abundant than Symbiodinium cells and we identified three operational taxonomic units (OTUs) which were present in all cultures. These represented the α-proteobacterium Labrenzia and the γ-proteobacteria Marinobacter and Chromatiaceae. Based on the abundance and functional potential of bacteria harboured in these cultures, their contribution to Symbiodinium physiology can no longer be ignored.
Newton, K, Jeffries, TC, Smith, RJ, Seymour, JR, Seuront, L & Mitchell, JG 2018, 'Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs', Journal of Oceanology and Limnology, vol. 36, no. 6, pp. 2033-2049.View/Download from: UTS OPUS or Publisher's site
© 2018, Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag GmbH Germany, part of Springer Nature. The Coorong estuary lies at the terminus of Australia's largest river system, the Murray-Darling; both are strongly influenced by human activities; including farming and extensive flow modification. Metagenomic approaches were used to determine the planktonic bacterial community composition and potential metabolic function at two extremes in the Coorong, the river mouth which exhibits marine-like salinity, and the hypersaline upper-reaches of the estuary. Significant shifts in taxa and metabolic function were seen between the two sites. The river mouth exhibited an increase in abundance of Rhodobacteriaceae and Alteromonadaceae; families readily able to adapt to change in nutrient conditions; and the potentially pathogenic families Brucellaceae, Enterobacteriaceae and Vibrionaceae. Metabolisms over-represented include motility and chemotaxis, RNA metabolism and membrane transport, all of which are involved in actively searching for and obtaining nutrients. Also over-represented were metabolisms involved in population succession and stress response. An over-representation of taxa and metabolisms indicative of environmental change is reflective of anthropogenically affected riverine input. In the hypersaline upper reaches of the estuary, the halophilic family Ectothiorhodospiraceae was over-represented, as were the families Flavobacteriaceae, Cytophagaceae and Nocardioidaceae, members of which are able to survive over a wide salinity range. Metabolisms over-represented here were reflective of increased bacterial growth, characteristic of hypersaline environments, and included DNA metabolism, nucleotide and nucleoside synthesis and cell cycle. Coorong metagenomes clustered taxonomically and metabolically with other planktonic metagenomes, but remained an outlier of this group with only 71% and 84% similarity, respectively. This indicates tha...
Varkey, D, Mazard, S, Jeffries, T, Hughes, D, Seymour, J, Paulsen, IT & Ostrowski, M 2018, 'Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary', PLoS ONE, vol. 13, no. 12, pp. e0209857-e0209857.View/Download from: UTS OPUS or Publisher's site
Sydney Harbour is subjected to persistent stress associated with anthropogenic activity and global climate change, but is particularly subjected to pulse stress events associated with stormwater input during episodic periods of high rainfall. Photosynthetic microbes underpin metazoan diversity within estuarine systems and are therefore important bioindicators of ecosystem health; yet how stormwater input affects their occurrence and distribution in Sydney Harbour remains poorly understood. We utilised molecular tools (16S/18S rRNA and petB genes) to examine how the phytoplankton community structure (both prokaryotes and eukaryotes) within Sydney Harbour varies between high and low rainfall periods. The relative proportion of phytoplankton sequences was more abundant during the high rainfall period, comprising mainly of diatoms, an important functional group supporting increased productivity within estuarine systems, together with cyanobacteria. Increased spatial variability in the phytoplankton community composition was observed, potentially driven by the steepened physico-chemical gradients associated with stormwater inflow. Conversely, during a low rainfall period, the proportion of planktonic photosynthetic microbes was significantly lower and the persistent phytoplankton were predominantly represented by chlorophyte and dinoflagellate sequences, with lower overall diversity. Differences in phytoplankton composition between the high and low rainfall periods were correlated with temperature, salinity, total nitrogen and silicate. These results suggest that increased frequency of high-rainfall events may change the composition, productivity and health of the estuary. Our study begins to populate the knowledge gap in the phytoplankton community structure and substantial changes associated with transient environmental perturbations, an essential step towards unravelling the dynamics of primary production in a highly urbanised estuarine ecosystem in response to cli...
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.
Tran, NAT, Seymour, JR, Siboni, N, Evenhuis, CR & Tamburic, B 2017, 'Photosynthetic carbon uptake induces autoflocculation of the marine microalga Nannochloropsis oculata', Algal Research, vol. 26, pp. 302-311.View/Download from: UTS OPUS or Publisher's site
© 2017 Elsevier B.V. Microalgal biomass has been used to produce biofuels, aquaculture feed, high-value chemicals such as pigments and antioxidants, and even human food. This study addresses one of the key bottlenecks to the commercialisation of microalgal bioproducts: the high energy and environmental cost of harvesting microalgal cells out of suspension. An innovative and sustainable autoflocculation procedure was developed to pre-concentrate microalgal biomass for easier har vesting. Microalgal cell agglomeration by autoflocculation at high pH was induced for the first time, without the addition of a chemical flocculant, in the commercially-relevant microalga Nannochloropsis oculata. Photosynthetic inorganic carbon uptake, in the absence of carbon dioxide supply by mass transfer, was used to raise the culture pH. Autoflocculation started at pH 9.5 and reached a maximum flocculation efficiency of 90% at pH 10.4. Microalgal surface charge-neutralisation by calcium cations, and sweep flocculation by calcium carbonate and calcium phosphate precipitates were identified as the dominant flocculation mechanisms. This was also the first study to measure changes in bacterial community composition under autoflocculation. There was a clear shift from free-living bacteria in suspension to attached bacteria during autoflocculation, with Flavobacteriales becoming the dominant order of bacteria. This highlights the influential role of attached bacteria and bacteria-produced extracellular polymeric substances in microalgal flocculation. This study shows that regulating carbon dioxide supply is a promising green alternative to traditional microalgal flocculation processes as it alleviates the requirement for costly and harmful chemical flocculants and brings us closer to sustainable microalgal bioproducts.
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.
Gribben, PE, Nielsen, S, Seymour, JR, Bradley, DJ, West, MN & Thomas, T 2017, 'Microbial communities in marine sediments modify success of an invasive macrophyte', Scientific Reports, vol. 7, no. 1, pp. 1-8.View/Download from: UTS OPUS or Publisher's site
© 2017 The Author(s). Invasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants. Whether sediment microbes modify the success of invasive macrophytes in marine ecosystems is untested, despite marin e sediment microbes controlling many ecological processes (e.g. nutrient cycling) comparable to those in terrestrial ecosystems. We first show that sediment bacterial communities differ between the native seagrass Zostera capricorni and the invasive alga Caulerpa taxifolia and that those differences relate to functional changes in sulfur cycling between the macrophytes. Second, by experimentally manipulating the microbial communities we show that intact microbial communities in Z. capricorni sediments provide biotic resistance by reducing C. taxifolia fragment growth 119% compared to when they are inactive, and intact microbial communities in C. taxifolia sediments have positive feedbacks by increasing fragment growth 200%. Thus, similar to terrestrial ecosystems, microorganisms appear to indirectly control the success of invasive macrophytes in marine ecosystems.
Lambert, BS, Raina, J-B, Fernandez, VI, Rinke, C, Siboni, N, Rubino, F, Hugenholtz, P, Tyson, GW, Seymour, JR & Stocker, R 2017, 'A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities.', Nature microbiology, vol. 2, pp. 1344-1349.View/Download from: UTS OPUS or Publisher's site
Microbial interactions influence the productivity and biogeochemistry of the ocean, yet they occur in miniscule volumes that cannot be sampled by traditional oceanographic techniques. To investigate the behaviours of marine microorganisms at spatially relevant scales, we engineered an in situ chemotaxis assay (ISCA) based on microfluidic technology. Here, we describe the fabrication, testing and first field results of the ISCA, demonstrating its value in accessing the microbial behaviours that shape marine ecosystems.A microfluidics-based assay for in situ chemotaxis experiments.
Messer, LF, Brown, MV, Furnas, MJ, Carney, RL, McKinnon, AD & Seymour, JR 2017, 'Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters.', Frontiers in Microbiology, vol. 8, pp. 1-16.View/Download from: UTS OPUS or Publisher's site
Discrepancies between bioavailable nitrogen (N) concentrations and phytoplankton growth rates in the oligotrophic waters of the Great Barrier Reef (GBR) suggest that undetermined N sources must play a significant role in supporting primary productivity. One such source could be biological dinitrogen (N2) fixation through the activity of "diazotrophic" bacterioplankton. Here, we investigated N2 fixation and diazotroph community composition over 10° S of latitude within GBR surface waters. Qualitative N2 fixation rates were found to be variable across the GBR but were relatively high in coastal, inner and outer GBR waters, reaching 68 nmol L(-1) d(-1). Diazotroph assemblages, identified by amplicon sequencing of the nifH gene, were dominated by the cyanobacterium Trichodesmium erythraeum, γ-proteobacteria from the Gamma A clade, and δ-proteobacterial phylotypes related to sulfate-reducing genera. However, diazotroph communities exhibited significant spatial heterogeneity, correlated with shifts in dissolved inorganic nutrient concentrations. Specifically, heterotrophic diazotrophs generally increased in relative abundance with increasing concentrations of phosphate and N, while Trichodesmium was proportionally more abundant when concentrations of these nutrients were low. This study provides the first in-depth characterization of diazotroph community composition and N2 fixation dynamics within the oligotrophic, N-limited surface waters of the GBR. Our observations highlight the need to re-evaluate N cycling dynamics within oligotrophic coral reef systems, to include diverse N2 fixing assemblages as a potentially significant source of dissolved N within the water column.
Raina, J-B, Clode, PL, Cheong, S, Bougoure, J, Kilburn, MR, Reeder, A, Forêt, S, Stat, M, Beltran, V, Thomas-Hall, P, Tapiolas, D, Motti, CM, Gong, B, Pernice, M, Marjo, CE, Seymour, JR, Willis, BL & Bourne, DG 2017, 'Subcellular tracking reveals the location of dimethylsulfoniopropionate in microalgae and visualises its uptake by marine bacteria.', eLife, vol. 6, pp. 1-17.View/Download from: UTS OPUS or Publisher's site
Phytoplankton-bacteria interactions drive the surface ocean sulfur cycle and local climatic processes through the production and exchange of a key compound: dimethylsulfoniopropionate (DMSP). Despite their large-scale implications, these interactions remain unquantified at the cellular-scale. Here we use secondary-ion mass spectrometry to provide the first visualization of DMSP at sub-cellular levels, tracking the fate of a stable sulfur isotope ((34)S) from its incorporation by microalgae as inorganic sulfate to its biosynthesis and exudation as DMSP, and finally its uptake and degradation by bacteria. Our results identify for the first time the storage locations of DMSP in microalgae, with high enrichments present in vacuoles, cytoplasm and chloroplasts. In addition, we quantify DMSP incorporation at the single-cell level, with DMSP-degrading bacteria containing seven times more (34)S than the control strain. This study provides an unprecedented methodology to label, retain, and image small diffusible molecules, which can be transposable to other symbiotic systems.
Seymour, JR, Amin, SA, Raina, J & Stocker, R 2017, 'Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships', Nature Microbiology, vol. 2, pp. 1-12.View/Download from: UTS OPUS or Publisher's site
By controlling nutrient cycling and biomass production at the base of the food web, interactions between phytoplankton and
bacteria represent a fundamental ecological relationship in aquatic environments. Although typically studied over large spatiotemporal
scales, emerging evidence indicates that this relationship is often governed by microscale interactions played out
within the region immediately surrounding individual phytoplankton cells. This microenvironment, known as the phycosphere,
is the planktonic analogue of the rhizosphere in plants. The exchange of metabolites and infochemicals at this interface governs
phytoplankton–bacteria relationships, which span mutualism, commensalism, antagonism, parasitism and competition. The
importance of the phycosphere has been postulated for four decades, yet only recently have new technological and conceptual
frameworks made it possible to start teasing apart the complex nature of this unique microbial habitat. It has subsequently
become apparent that the chemical exchanges and ecological interactions between phytoplankton and bacteria are far more
sophisticated than previously thought and often require close proximity of the two partners, which is facilitated by bacterial colonization
of the phycosphere. It is also becoming increasingly clear that while interactions taking place within the phycosphere
occur at the scale of individual microorganisms, they exert an ecosystem-scale influence on fundamental processes including
nutrient provision and regeneration, primary production, toxin biosynthesis and biogeochemical cycling. Here we review the
fundamental physical, chemical and ecological features of the phycosphere, with the goal of delivering a fresh perspective on
the nature and importance of phytoplankton–bacteria interactions in aquatic ecosystems.
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.
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.
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.
Labbate, M, Seymour, JR, Lauro, F & Brown, MV 2016, 'Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments', FRONTIERS IN MICROBIOLOGY, vol. 7.View/Download from: UTS OPUS or Publisher's site
Siboni, N, Balaraju, V, Carney, R, Labbate, M & Seymour, JR 2016, 'Spatiotemporal Dynamics of Vibrio spp. within the Sydny harbour Estuary', FRONTIERS IN MICROBIOLOGY, vol. 7.View/Download from: UTS OPUS or Publisher's site
Bibiloni-Isaksson, J, Seymour, JR, Ingleton, T, van de Kamp, J, Bodrossy, L & Brown, MV 2016, 'Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia', ENVIRONMENTAL MICROBIOLOGY, vol. 18, no. 12, pp. 4485-4500.View/Download from: UTS OPUS or Publisher's site
Carney, RL, Seymour, JR, Westhorpe, D & Mitrovic, SM 2016, 'Lotic bacterioplankton and phytoplankton community changes under dissolved organic-carbon amendment: evidence for competition for nutrients', MARINE AND FRESHWATER RESEARCH, vol. 67, no. 9, pp. 1362-1373.View/Download from: Publisher's site
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
Garren, M, Son, K, Tout, J, Seymour, JR & Stocker, R 2016, 'Temperature-induced behavioral switches in a bacterial coral pathogen.', The ISME journal, vol. 10, pp. 1363-1372.View/Download from: Publisher's site
Evidence to date indicates that elevated seawater temperatures increase the occurrence of coral disease, which is frequently microbial in origin. Microbial behaviors such as motility and chemotaxis are often implicated in coral colonization and infection, yet little is known about the effect of warming temperatures on these behaviors. Here we present data demonstrating that increasing water temperatures induce two behavioral switches in the coral pathogen Vibrio coralliilyticus that considerably augment the bacterium's performance in tracking the chemical signals of its coral host, Pocillopora damicornis. Coupling field-based heat-stress manipulations with laboratory-based observations in microfluidic devices, we recorded the swimming behavior of thousands of individual pathogen cells at different temperatures, associated with current and future climate scenarios. When temperature reached ⩾23 °C, we found that the pathogen's chemotactic ability toward coral mucus increased by >60%, denoting an enhanced capability to track host-derived chemical cues. Raising the temperature further, to 30 °C, increased the pathogen's chemokinetic ability by >57%, denoting an enhanced capability of cells to accelerate in favorable, mucus-rich chemical conditions. This work demonstrates that increasing temperature can have strong, multifarious effects that enhance the motile behaviors and host-seeking efficiency of a marine bacterial pathogen.The ISME Journal advance online publication, 4 December 2015; doi:10.1038/ismej.2015.216.
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...
Messer, LF, Mahaffey, C, Robinson, CM, Jeffries, TC, Baker, KG, Bibiloni Isaksson, J, Ostrowski, M, Doblin, MA, Brown, MV & Seymour, JR 2016, 'High levels of heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation.', The ISME journal, vol. 10, pp. 1499-1513.View/Download from: UTS OPUS or Publisher's site
Australia's tropical waters represent predicted 'hotspots' for nitrogen (N2) fixation based on empirical and modelled data. However, the identity, activity and ecology of diazotrophs within this region are virtually unknown. By coupling DNA and cDNA sequencing of nitrogenase genes (nifH) with size-fractionated N2 fixation rate measurements, we elucidated diazotroph dynamics across the shelf region of the Arafura and Timor Seas (ATS) and oceanic Coral Sea during Austral spring and winter. During spring, Trichodesmium dominated ATS assemblages, comprising 60% of nifH DNA sequences, while Candidatus Atelocyanobacterium thalassa (UCYN-A) comprised 42% in the Coral Sea. In contrast, during winter the relative abundance of heterotrophic unicellular diazotrophs (δ-proteobacteria and γ-24774A11) increased in both regions, concomitant with a marked decline in UCYN-A sequences, whereby this clade effectively disappeared in the Coral Sea. Conservative estimates of N2 fixation rates ranged from <1 to 91 nmol l(-1) day(-1), and size fractionation indicated that unicellular organisms dominated N2 fixation during both spring and winter, but average unicellular rates were up to 10-fold higher in winter than in spring. Relative abundances of UCYN-A1 and γ-24774A11 nifH transcripts negatively correlated to silicate and phosphate, suggesting an affinity for oligotrophy. Our results indicate that Australia's tropical waters are indeed hotspots for N2 fixation and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N2 fixation.The ISME Journal advance online publication, 27 November 2015; doi:10.1038/ismej.2015.205.
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.
Rinke, C, Low, S, Woodcroft, BJ, Raina, J, Skarshewski, A, Le, XH, Butler, MK, Stocker, R, Seymour, JR, Tyson, GW & Hugenholtz, P 2016, 'Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics', PeerJ, vol. 2016, no. 9.View/Download from: UTS OPUS or Publisher's site
High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.
Carney, RL, Mitrovic, SM, Jeffries, T, Westhorpe, D, Curlevski, N & Seymour, JR 2015, 'River bacterioplankton community responses to a high inflow event', Aquatic Microbial Ecology, vol. 75, no. 3, pp. 187-205.View/Download from: UTS OPUS or Publisher's site
© Inter-Research 2015. Microbes drive chemical cycling and productivity within river ecosystems, but their influence may shift when intense allochthonous inputs accompany high freshwater inflow (flood) events. Investigating how floods influence microbial processes is fundamentally important for our understanding of river ecology, but is generally overlooked. We analysed bacterioplankton community composition (BCC) and abundance over 4 mo following an enormous flood event in the Hunter River, Australia, that resulted in a major fish kill. Concentrations of dissolved organic carbon (DOC) and inorganic nutrients (N and P) were up to 3 times higher during the flood event compared to prior and subsequent months. Bacterial cell abundances were up to 10 times higher at impacted sites during the flood event. Using Automated Ribosomal Intergenic Spacer Analysis we found significant shifts in BCC between the flood impacted month and subsequent months (p < 0.05). Distance linear modelling indicated that DOC and dissolved N and P correlated most strongly with BCC patterns during the high inflow, whereas community dynamics correlated most strongly with nitrogen oxides and ammonium during the river's recovery phase. 16S rRNA amplicon pyrosequencing revealed that common soil-associated and facultative anaerobic genera of Proteobacteria were most dominant during the flood period, suggesting that a proportion of the bacterial community observed during this event were potentially inactive soil microbes transported into the river via terrestrial runoff. During the recovery period, Cyanobacteria and freshwater- associated genera of Actinobacteria and Proteobacteria became dominant in 16S rRNA pyrosequencing profiles. These observations indicate that allochthonous nutrients delivered via floods can significantly stimulate bacterial growth, underpinning substrate-controlled succession of bacterial communities and ultimately shaping the ecology within river ecosystems.
Macreadie, PI, Trevathan-Tackett, SM, Skilbeck, CG, Sanderman, J, Curlevski, N, Jacobsen, G & Seymour, JR 2015, 'Losses and recovery of organic carbon from a seagrass ecosystem following disturbance', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 282, no. 1817.View/Download from: Publisher's site
Messer, LF, Doubell, M, Jeffries, TC, Brown, MV & Seymour, JR 2015, 'Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary', AQUATIC MICROBIAL ECOLOGY, vol. 74, no. 1, pp. 1-15.View/Download from: UTS OPUS or Publisher's site
Tout, J, Jeffries, TC, Petrou, K, Tyson, GW, Webster, NS, Garren, M, Stocker, R, Ralph, PJ & Seymour, JR 2015, 'Chemotaxis by natural populations of coral reef bacteria', ISME JOURNAL, vol. 9, no. 8, pp. 1764-1777.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.
Laczka, OF, Labbate, M, Seymour, JR, Bourne, DG, Fielder, SS & Doblin, MA 2014, 'Surface Immuno-Functionalisation for the Capture and Detection of Vibrio Species in the Marine Environment: A New Management Tool for Industrial Facilities', PLOS ONE, vol. 9, no. 10.View/Download from: UTS OPUS or Publisher's site
Garren, M, Son, K, Raina, J, Rusconi, R, Menolascina, F, Shapiro, H, Tout, JA, Bourne, DG, Seymour, JR & Stocker, R 2014, 'A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals', The ISME Journal, vol. 8, pp. 999-1007.View/Download from: UTS OPUS or Publisher's site
Diseases are an emerging threat to ocean ecosystems. Coral reefs, in particular, are experiencing a worldwide decline because of disease and bleaching, which have been exacerbated by rising seawater temperatures. Yet, the ecological mechanisms behind most coral diseases remain unidentified. Here, we demonstrate that a coral pathogen, Vibrio coralliilyticus, uses chemotaxis and chemokinesis to target the mucus of its coral host, Pocillopora damicornis. A primary driver of this response is the host metabolite dimethylsulfoniopropionate (DMSP), a key element in the global sulfur cycle and a potent foraging cue throughout the marine food web. Coral mucus is rich in DMSP, and we found that DMSP alone elicits chemotactic responses of comparable intensity to whole mucus. Furthermore, in heat-stressed coral fragments, DMSP concentrations increased fivefold and the pathogens chemotactic response was correspondingly enhanced. Intriguingly, despite being a rich source of carbon and sulfur, DMSP is not metabolized by the pathogen, suggesting that it is used purely as an infochemical for host location. These results reveal a new role for DMSP in coral disease, demonstrate the importance of chemical signaling and swimming behavior in the recruitment of pathogens to corals and highlight the impact of increased seawater temperatures on disease pathways.
Lavery, TJ, Roudnew, B, Seymour, JR, Mitchell, JG, Smetacek, V & Nicol, S 2014, 'Whales sustain fisheries: Blue whales stimulate primary production in the Southern Ocean', Marine Mammal Science, vol. 30, no. 3, pp. 888-904.View/Download from: UTS OPUS or Publisher's site
It has previously been asserted that baleen whales compete with fisheries by consuming potentially harvestable marine resources. The regularly applied surplusyield model suggests that whale prey becomes available to fisheries if whales are removed, and has been presented as a justification for whaling. However, recent findings indicate that whales enhance ecosystem productivity by defecating iron that stimulates primary productivity in iron-limited waters. While juvenile whales and whales that are pregnant or lactating retain iron for growth and milk production, nonbreeding adult whales defecate most of the iron they consume. Here, we modify the surplus-yield model to incorporate iron defecation. After modeling a simplistic trajectory of blue whale recovery to historical abundances, the traditional surplusyield model predicts that 1011 kg of carbon yr1 would become unavailable to fisheries. However, this ignores the nutrient recycling role of whales. Our model suggests the population of blue whales would defecate 3 9 106 kg of iron yr1, which would stimulate primary production equivalent to that required to support prey consumption by the blue whale population. Thus, modifying the surplus-yield model to include iron defecation indicates that blue whales do not render marine resources unavailable to fisheries. By defecating iron-rich feces, blue whales promote Southern Ocean productivity, rather than reducing fishery yields.
Roudnew, B, Lavery, TJ, Seymour, JR, Jeffries, TC & Mitchell, JG 2014, 'Variability in Bacteria and Virus-Like Particle Abundances During Purging of Unconfined Aquifers', Groundwater, vol. 52, no. 1, pp. 118-124.View/Download from: UTS OPUS or Publisher's site
Standard methodologies for sampling the physicochemical conditions of groundwater recommend purging a bore for three bore volumes to avoid sampling the stagnant water within a bore and instead gain samples representative of the aquifer. However, there are currently no methodological standards addressing the amount of purging required to gain representative biological samples to assess groundwater bacterial and viral abundances. The objective of this study was to examine how bacterial and viral abundances change during the purging of bore volumes. Six bores infiltrating into unconfined aquifers were pumped for five or six bore volumes each and bacteria and virus-like particles (VLPs) were enumerated from each bore volume using flow cytometry. In examination of the individual bores trends in bacterial abundances were observed to increase, decrease, or remain constant with each purged bore volume. Furthermore, triplicates taken at each bore volume indicated substantial variations in VLP and bacterial abundances that are often larger than the differences between bore volumes. This indicates a high level of small scale heterogeneity in microbial community abundance in groundwater samples, and we suggest that this may be an intrinsic feature of bore biology. The heterogeneity observed may be driven by bottom up processes (variability in the distribution of organic and inorganic nutrients), top-down processes (grazing and viral lysis), physical heterogeneities in the bore, or technical artifacts associated with the purging process. We suggest that a more detailed understanding of the ecology underpinning this variability is required to adequately describe the microbiological characteristics of groundwater ecosystems.
Covering 70% of the earth's surface, with an average depth of 3.6 km, the ocean's total volume of 1.3 billion cubic kilometres represents perhaps the largest inhabitable space in the biosphere. Within this vast ecosystem, 90% of all living biomass is microbial. Indeed, seawater from all marine environments, ranging from the warm and sunlit upper ocean to the cold, dark and anoxic deep sea floor, and from the tropics to the arctic, is teeming with microbial life. A single teaspoon of seawater typically contains over 50 million viruses, 5 million Bacteria, 100,000 Archaea and 50,000 eukaryotic microbes. The numerical importance of these microbes is matched only by their ecological and biogeochemical significance. By performing the bulk of oceanic primary production and mediating key chemical transformation processes, planktonic microbes form the base of the marine food-web and are the engines that drive the ocean's major biogeochemical cycles (Figure 1). While marine microbes are the dominant biological feature throughout the entire water column and within ocean sediments, as well as being important symbionts and pathogens of marine animals and plants, this review will focus on the activity and diversity of microbes inhabiting seawater in the upper sun-lit depths of the global ocean.
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.
Dennis, PG, Seymour, JR, Kumbun, K & Tyson, G 2013, 'Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients', ISME Journal, vol. 7, no. 8, pp. 1661-1664.View/Download from: UTS OPUS or Publisher's site
Chemotaxis allows microorganisms to rapidly respond to different environmental stimuli; however, understanding of this process is limited by conventional assays, which typically focus on the response of single axenic cultures to given compounds. In this study, we used a modified capillary assay coupled with flow cytometry and 16S rRNA gene amplicon pyrosequencing to enumerate and identify populations within a lake water microbial community that exhibited chemotaxis towards ammonium, nitrate and phosphate. All compounds elicited chemotactic responses from populations within the lake water, with members of Sphingobacteriales exhibiting the strongest responses to nitrate and phosphate, and representatives of the Variovorax, Actinobacteria ACK-M1 and Methylophilaceae exhibiting the strongest responses to ammonium. Our results suggest that chemotaxis towards inorganic substrates may influence the rates of biogeochemical processes.
Mitchell, J, Seuront, L, Doubell, M, Losic, D, Voelcker, N, Seymour, JR & Lal, R 2013, 'The Role Of Diatom Nanostructures In Biasing Diffusion To Improve Uptake In A Patchy Nutrient Environment', PLoS One, vol. 8, no. 5, pp. 1-9.View/Download from: UTS OPUS or Publisher's site
Background Diatoms are important single-celled autotrophs that dominate most lit aquatic environments and are distinguished by surficial frustules with intricate designs of unknown function. Principal Findings We show that some frustule designs constrain diffusion to positively alter nutrient uptake. In nutrient gradients of 4 to 160 times over <5 cm, the screened-chambered morphology of Coscincodiscus sp. biases the nutrient diffusion towards the cell by at least 3.8 times the diffusion to the seawater. In contrast, the open-chambers of Thalassiosira eccentrica produce at least a 1.3 times diffusion advantage to the membrane over Coscincodiscus sp. when nutrients are homogeneous. Significance Diffusion constraint explains the success of particular diatom species at given times and the overall success of diatoms. The results help answer the unresolved question of how adjacent microplankton compete. Furthermore, diffusion constraint by supramembrane nanostructures to alter molecular diffusion suggests that microbes compete via supramembrane topology, a competitive mechanism not considered by the standard smooth-surface equations used for nutrient uptake nor in microbial ecology and cell physiology.
Roudnew, B, Lavery, T, Seymour, JR, Smith, R & Mitchell, J 2013, 'Spatially Varying Complexity Of Bacterial And Virus-like Particle Communities Within An Aquifer System', Aquatic Microbial Ecology, vol. 68, no. 3, pp. 259-266.View/Download from: UTS OPUS or Publisher's site
Hydrological and geological heterogeneity in the subsurface can isolate groundwater bodies in an aquifer system and create hydrologically distinct aquifers overlying each other with varying amounts of water exchange and unknown amounts of biological exchange. The heterogeneous nature of these subsurface waters likely drives changes in groundwater microbiological parameters. In the present study, flow cytometry was used to examine the abundance and cytometrically defined subpopulation structure of bacteria and virus-like particles (VLPs) in 3 distinct, vertically stratified aquifer layers consisting of an unconfined aquifer, a confining layer and a confined aquifer. Despite total microbial abundances remaining constant, the composition of bacterial and VLP communities varied among the aquifer layers. Cytometrically defined subpopulations were defined by nucleic acid content and size and ranged from 1 bacterial and VLP subpopulation in the unconfined aquifer to 4 bacterial and 3 VLP subpopulations in the confined aquifer. This variability in the subpopulation assemblages is likely driven by a combination of hydrological heterogeneity and biological interactions. The results presented here indicate complexity in microbial communities in discrete aquifer layers that may be overlooked when reporting general abundances. Groundwater bacteria and VLPs appear to be a sensitive indicator of the biological dynamics of aquifer systems and may be used to identify heterogeneous water bodies and help distinguish individual aquifer layers in an aquifer system.
Smith, R, Jeffries, TC, Roudnew, B, Seymour, JR, Fitch, AJ, Simons, KL, Speck, PG, Newton, K, Brown, MH & Mitchell, JG 2013, 'Confined aquifers as viral reservoirs', Environmental Microbiology Reports, vol. 5, no. 5, pp. 725-730.View/Download from: UTS OPUS or Publisher's site
Knowledge about viral diversity and abundance in deep groundwater reserves is limited. We found that the viral community inhabiting a deep confined aquifer in South Australia was more similar to reclaimed water communities than to the viral communities in the overlying unconfined aquifer community. This similarity was driven by high relative occurrence of the single-stranded DNA viral groups Circoviridae, Geminiviridae and Microviridae, which include many known plant and animal pathogens. These groups were present in a 1500-year-old water situated 80?m below the surface, which suggests the potential for long-term survival and spread of potentially pathogenic viruses in deep, confined groundwater. Obtaining a broader understanding of potentially pathogenic viral communities within aquifers is particularly important given the ability of viruses to spread within groundwater ecosystems.
Dongen-Vogels, V, Seymour, JR, Middleton, JF, Mitchell, JG & Seuront, L 2012, 'Shifts in picophytoplankton community structure influenced by changing upwelling conditions', Estuarine Coastal And Shelf Science, vol. 109, pp. 81-90.View/Download from: UTS OPUS or Publisher's site
The influence of upwelling events on the structure of picophytoplankton communities was assessed at the annual scale from a station within the South Australian shelf region. In this region, local (wind) and global (La Niña/El NiñoSouthern Oscillation) hydroclimatic conditions affect the development of upwelling over the austral summer. Using flow cytometry, changes in picophytoplankton community structure were investigated in relation to the properties of the water column when the nature and strength of upwelling event differed for the upwelling seasons of 2008, 2009, and 2010. In 2008, strong upwelling favorable southeasterlies were responsible for extensive upwelling and the dominance of picoeukaryotes. Alternatively, in 2009, the observed dominance of Prochlorococcus reflected the presence of oligotrophic conditions whilst southeasterlies were replaced by downwelling favorable north-westerlies that likely prohibited the full development of upwelling. In 2010, whilst southeasterlies remained relatively weak, particularly cold and low saline upwelled waters indicated enhanced upwelling events. This weak local wind field together with the occurrence of El Niño explained the observation of shallow upwelled waters below the warm surface layer and subsequent enhanced stratification. These conditions led to the dominance of Synechococcus in surface and fluorescence maximum depths, but of Prochlorococcus in bottom upwelled waters. The tight association between upwelling and stratification, i.e. whether upwelled waters reach shallower depths and/or mix with those of the surface as a result of variable climatic conditions, was suggested as the process driving the vertical heterogeneity of picophytoplankton populations. This study brings valuable information for changing picophytoplankton community structure with potential future changing hydroclimatic forcing.
Humphreys, W, Tetu, S, Elbourne, L, Gillings, M, Seymour, JR, Mitchell, J & Paulsen, I 2012, 'Geochemical and microbial diversity of Bundera Sinkhole, an anchialine system in the eastern Indian Ocean', Natura Croatica, vol. 21, no. S1, pp. 59-63.View/Download from: UTS OPUS
The anchialine system at Bundera sinkhole, Australia, exhibits pronounced hydrogeochemical structure through depth that is reflected in the composition and distribution of the fauna. It is a strongly structured microbial ecosystem the components of which also change with depth and which is dominated by sulfur bacteria and chemolithotrophic microbial classes.
Jeffries, TC, Seymour, JR, Newton, K, Smith, RJ, Seuront, L & Mitchell, JG 2012, 'Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient', Biogeosciences, vol. 9, no. 2, pp. 815-825.View/Download from: UTS OPUS or Publisher's site
Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes - organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem.
Lavery, TJ, Roudnew, B, Seymour, JR, Mitchell, JG & Jeffries, TC 2012, 'High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) Faeces', PLoS One, vol. 7, no. 5, pp. 1-9.View/Download from: UTS OPUS or Publisher's site
Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80%) were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80%) to Bacteriodetes (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production.
Roudnew, B, Seymour, JR, Jeffries, TC, Lavery, TJ, Smith, RJ & Mitchell, JG 2012, 'Bacterial and virus-like-particle abundances in purged and unpurged groundwater depth profiles', Ground Water Monitoring and Remediation, vol. 32, no. 4, pp. 72-77.View/Download from: UTS OPUS or Publisher's site
Bacteria and viruses are ubiquitous in subterranean aquatic habitats. Bacterial abundance is known to vary with depth in aquifers; however, whether viral abundance varies with depth is less well known. Here we use flow cytometry (FCM) to enumerate bacteria and virus-like particles (VLP) from groundwater depth profiles. Groundwater samples were obtained from a set of nested piezometers from depths of 15, 30, 45, 60, 80, and 90?m and bacteria and VLP abundances were determined in purged aquifer water and unpurged water at each slot depth. Mean bacterial abundance (cells?/?mL) was not significantly different in unpurged water (3.2?×?105) compared to purged water (1.4?×?105); however, mean VLP abundance (particles?/?mL) was significantly greater in unpurged water (4.4?×?105) compared to purged water (2.3?×?105). Purged water was used to investigate the aquifer depth profile and bacterial and VLP abundances were observed to vary significantly between depths. The virus-bacteria ratio was determined and was observed to steadily increase with depth. Overall, our data indicate the dynamic nature of bacterial and viral abundances in subsurface environments which should be considered when designing groundwater microbial sampling methodologies.
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
Smith, RJ, Jeffries, TC, Roudnew, B, Fitch, AJ, Seymour, JR, Delpin, MW, Newton, K, Brown, MH & Mitchell, JG 2012, 'Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems', Environmental Microbiology, vol. 14, no. 1 Special Issue, pp. 240-253.View/Download from: UTS OPUS or Publisher's site
A metagenomic analysis of two aquifer systems located under a dairy farming region was performed to examine to what extent the composition and function of microbial communities varies between confined and surface-influenced unconfined groundwater ecosystems. A fundamental shift in taxa was seen with an overrepresentation of Rhodospirillales, Rhodocyclales, Chlorobia and Circovirus in the unconfined aquifer, while Deltaproteobacteria and Clostridiales were overrepresented in the confined aquifer. A relative overrepresentation of metabolic processes including antibiotic resistance (beta-lactamase genes), lactose and glucose utilization and DNA replication were observed in the unconfined aquifer, while flagella production, phosphate metabolism and starch uptake pathways were all overrepresented in the confined aquifer. These differences were likely driven by differences in the nutrient status and extent of exposure to contaminants of the two groundwater systems. However, when compared with freshwater, ocean, sediment and animal gut metagenomes, the unconfined and confined aquifers were taxonomically and metabolically more similar to each other than to any other environment. This suggests that intrinsic features of groundwater ecosystems, including low oxygen levels and a lack of sunlight, have provided specific niches for evolution to create unique microbial communities. Obtaining a broader understanding of the structure and function of microbial communities inhabiting different groundwater systems is particularly important given the increased need for managing groundwater reserves of potable water.
Stocker, R & Seymour, JR 2012, 'Ecology and physics of bacterial chemotaxis in the ocean', Microbiology and Molecular Biology Reviews, vol. 76, no. 4, pp. 792-812.View/Download from: UTS OPUS or Publisher's site
Summary: Intuitively, it may seem that from the perspective of an individual bacterium the ocean is a vast, dilute, and largely homogeneous environment. Microbial oceanographers have typically considered the ocean from this point of view. In reality, marine bacteria inhabit a chemical seascape that is highly heterogeneous down to the microscale, owing to ubiquitous nutrient patches, plumes, and gradients. Exudation and excretion of dissolved matter by larger organisms, lysis events, particles, animal surfaces, and fluxes from the sediment-water interface all contribute to create strong and pervasive heterogeneity, where chemotaxis may provide a significant fitness advantage to bacteria. The dynamic nature of the ocean imposes strong selective pressures on bacterial foraging strategies, and many marine bacteria indeed display adaptations that characterize their chemotactic motility as high performance compared to that of enteric model organisms. Fast swimming speeds, strongly directional responses, and effective turning and steering strategies ensure that marine bacteria can successfully use chemotaxis to very rapidly respond to chemical gradients in the ocean.
Dongen-Vogels, V, Seymour, JR, Middleton, JF, Mitchell, JG & Seuront, L 2011, 'Influence of local physical events on picophytoplankton spatial and temporal dynamics in South Australian continental shelf waters', Journal of Plankton Research, vol. 33, no. 12, pp. 1825-1841.View/Download from: UTS OPUS or Publisher's site
We investigated the space-time dynamics of picophytoplankton in South Australian continental shelf waters from February 2008 to January 2009, focusing on localized physical events. We discriminated six picophytoplankton populations by flow cytometry, including Synechococcus (SYN1, SYN2), Prochlorococcus (PROC1, PROC2) and small and large picoeukaryotes (EUKS, EUKL). Local physical events observed included downwelling and dense waters outflowing from a nearby gulf in winter-early spring 2008, upwelling in summer and early spring 2008 and eddy formation in January 2009. Each population responded differently to these events, which resulted in up to four orders of magnitude changes in their abundances. Population-specific hotspots reflected a succession of distinct dominant communities associated with the strength of upwelling events, changes in fluorescence maximum depths and local downwelling and mixing processes. The unexpected high abundances and local dominance of Prochlorococcus in summer reflected the possible influence of eastward and westward current transports and the presence of a High-Light (PROC1)-and Low-Light (PROC2)-adapted ecotypes. This study highlights the role of localized physical events in the dominance of all three picophytoplankton groups that may be critical for the high productivity of the study region, and suggests the importance of hydroclimatic forcing for inter-annual changes in picophytoplankton communities.
Jeffries, TC, Seymour, JR, Gilbert, JA, Dinsdale, EA, Newton, K, Leterme, SS, Roudnew, B, Smith, RJ, Seuront, L & Mitchell, JG 2011, 'Substrate type determines metagenomic profiles from diverse chemical habitats', PLoS One, vol. 6, no. 9, pp. 1-9.View/Download from: UTS OPUS or Publisher's site
Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance.
Marcos, M, Seymour, JR, Luhar, M, Mitchell, JG, Durham, WM, Macke, A & Stocker, R 2011, 'Microbial Alignment In Flow Changes Ocean Light Climate', Proceedings Of The National Academy Of Sciences Of The United States Of America, vol. 108, no. 10, pp. 3860-3864.View/Download from: UTS OPUS or Publisher's site
The growth of microbial cultures in the laboratory often is assessed informally with a quick flick of the wrist: dense suspensions of microorganisms produce translucent
Lavery, TJ, Roudnew, B, Gill, P, Seymour, JR, Seuront, L, Johnson, G, Mitchell, J & Smetacek, V 2010, 'Iron Defecation By Sperm Whales Stimulates Carbon Export In The Southern Ocean', Proceedings Of The Royal Society B-Biological Sciences, vol. 277, no. 1699, pp. 3527-3531.View/Download from: UTS OPUS or Publisher's site
The iron-limited Southern Ocean plays an important role in regulating atmospheric CO2 levels. Marine mammal respiration has been proposed to decrease the efficiency of the Southern Ocean biological pump by returning photosynthetically fixed carbon to the
Seymour, JR, Ahmed, T, Durham, W & Stocker, R 2010, 'Chemotactic Response Of Marine Bacteria To The Extracellular Products Of Synechococcus And Prochlorococcus', Aquatic Microbial Ecology, vol. 59, no. 2, pp. 161-168.View/Download from: UTS OPUS or Publisher's site
The cyanobacterial genera Prochlorococcus and Synechococcus are key phototrophic organisms in the open ocean, and ecological interactions between these groups and heterotrophic bacteria have fundamental importance for marine carbon and nutrient cycling.
Seymour, JR, Simo, R, Ahmed, T & Stocker, R 2010, 'Chemoattraction to Dimethylsulfoniopropionate in the marine microbial food web', Science, vol. 329, no. 5989, pp. 342-345.View/Download from: UTS OPUS or Publisher's site
Phytoplankton-produced dimethylsulfoniopropionate (DMSP) provides underwater and atmospheric foraging cues for several species of marine invertebrates, fish, birds, and mammals. However, its role in the chemical ecology of marine planktonic microbes is largely unknown, and there is evidence for contradictory functions. By using microfluidics and image analysis of swimming behavior, we observed attraction toward microscale pulses of DMSP and related compounds among several motile strains of phytoplankton, heterotrophic bacteria, and bacterivore and herbivore microzooplankton. Because microbial DMSP cycling is the main natural source of cloud-forming sulfur aerosols, our results highlight how adaptations to microscale chemical seascapes shape planktonic food webs, while potentially influencing climate at the global scale.
Seuront, L, Leterme, SC, Seymour, JR, Mitchell, JG, Ashcroft, D, Noble, W, Thomson, PG, Davidson, AT, van den Enden, R, Scott, FJ, Wright, SW, Schapira, M, Chapperon, C & Cribb, N 2009, 'Role of microbial and phytoplanktonic communities in the control of seawater viscosity off East Antarctica (30-80Â° E)', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 57, no. 9-10, pp. 877-886.View/Download from: UTS OPUS or Publisher's site
Despite the long-standing belief that seawater viscosity is driven by temperature and salinity, biologically increased seawater viscosity has repeatedly been reported in relation to phytoplankton exudates in shallow, productive coastal waters. Here, seawater viscosity was investigated in relation to microbial and phytoplanktonic communities off the coast of East Antarctica along latitudinal transects located between 30°E and 80°E in sub-surface waters and at the deep chlorophyll maximum (DCM). The physical component of seawater viscosity observed along each transects ranged from 1.80 to 1.95 cP, while the actual seawater viscosity ranged from 1.85 to 3.69 cP. This resulted in biologically increased seawater viscosity reaching up to 84.9% in sub-surface waters and 77.6% at the DCM. Significant positive correlations were found between elevated seawater viscosity and (i) bacterial abundance in sub-surface waters and (ii) chlorophyll a concentration and the abundance of flow cytometrically-defined auto- and heterotrophic protists at the DCM. Among the 12 groups and 108 species of protists identified under light microscopy, dinoflagellates and more specifically Alexandrium tamarense and Prorocentrum sp. were the main contributors to the patterns observed for elevated seawater viscosity. Our observations, which generalised the link previously identified between seawater viscosity and phytoplankton composition and standing stock to the Southern Ocean, are the first demonstration of increases in seawater viscosity linked to marine bacterial communities, and suggest that the microbially-increased viscosity might quantitatively be at least as important as the one related to phytoplankton secretion.
Seymour, JR, Ahmed, T & Stocker, R 2009, 'Bacterial chemotaxis towards the extracellular products of the toxic phytoplankton Heterosigma akashiwo', Journal Of Plankton Research, vol. 31, no. 12, pp. 1557-1561.View/Download from: UTS OPUS or Publisher's site
Marine bacteria exhibit positive chemotactic responses to the extracellular exudates of the toxic phytoplankton Heterosigma akashiwo. In the environment, this will support bacteriaalgae associations with potential implications for harmful algal bloom dynamics.
Seymour, JR, Marcos & Stocker, R 2009, 'Resource Patch Formation and Exploitation throughout the Marine Microbial Food Web', AMERICAN NATURALIST, vol. 173, no. 1, pp. E15-E29.View/Download from: Publisher's site
Seymour, JR, Ahmed, T, Marcos, M & Stocker, R 2008, 'A microfluidic chemotaxis assay to study microbial behavior in diffusing nutrient patches', Limnology and Oceanography: Methods, vol. 6, pp. 477-488.View/Download from: UTS OPUS
The nutrient environment experienced by planktonic microorganisms is patchy at spatiotemporal scales commensurate with their motility and the efficiency with which chemotactic microbes can exploit this heterogeneous seascape influences trophodynamics and nutrient cycling rates in aquatic environments.
Seymour, JR, Seuront, L, Doubell, MJ & Mitchel, JG 2008, 'Mesoscale and microscale spatial variability of bacteria and viruses during a Phaeocystis globosa bloom in the Eastern English Channel', Estuarine, Coastal and Shelf Science, vol. 80, no. 4, pp. 589-597.View/Download from: UTS OPUS or Publisher's site
Sampling was conducted within inshore and offshore sites, characterized by highly dissimilar hydrodynamic and hydrobiological conditions, in the Eastern English Channel. The eutrophic inshore site was dominated by the influence of a dense bloom of the Prymnesiophyceae phytoplankton species Phaeocystis globosa, while the offshore site was characterized by more oceanic conditions. Within each site the microscale distributions of chlorophyll a and several flow cytometrically-defined subpopulations of heterotrophic bacteria and viruses were measured at a spatial resolution of 5 cm. The inshore site was characterized by comparatively high levels of microscale spatial variability, with concentrations of chlorophyll a, heterotrophic bacteria, and viruses varying by 8, 11 and 3.5-fold respectively across distances of several centimeters. Within the offshore site, microscale distributions of chlorophyll a and bacteria were markedly less variable than within the inshore site, although viruses exhibited slightly higher levels of heterogeneity. Significant mesoscale variability was also observed when mean microbial parameters were compared between the inshore and offshore sites. However, when the extent of change (max/min and coefficient of variation) was compared between meso- and microscales, the variability observed at the microscale, particularly in the inshore site, was substantially greater. This pattern suggests that microscale processes associated with Phaeocystis globosa bloom dynamics can generate heterogeneity amongst microbial communities to a greater degree than large scale oceanographic discontinuities.
Stocker, R, Seymour, JR, Samadani, A, Hunt, D & Polz, M 2008, 'Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches.', Proceedings of the National Academy of Sciences, vol. 105, no. 11, pp. 4209-4214.View/Download from: UTS OPUS or Publisher's site
Because ocean water is typically resource-poor, bacteria may gain significant growth advantages if they can exploit the ephemeral nutrient patches originating from numerous, small sources. Although this interaction has been proposed to enhance biogeochemical transformation rates in the ocean, it remains questionable whether bacteria are able to efficiently use patches before physical mechanisms dissipate them. Here we show that the rapid chemotactic response of the marine bacterium Pseudoalteromonas haloplanktis substantially enhances its ability to exploit nutrient patches before they dissipate. We investigated two types of patches important in the ocean: nutrient pulses and nutrient plumes, generated for example from lysed algae and sinking organic particles, respectively. We used microfluidic devices to create patches with environmentally realistic dimensions and dynamics. The accumulation of P. haloplanktis in response to a nutrient pulse led to formation of bacterial hot spots within tens of seconds, resulting in a 10-fold higher nutrient exposure for the fastest 20% of the population compared with nonmotile cells.
Seuront, L, Lacheze, C, Doubell, MJ, Seymour, JR, Dongen-Vogels, VV, Newton, K, Alderkamp, AC & Mitchell, JG 2007, 'The influence of Phaeocystis globosa on microscale spatial patterns of chlorophyll a and bulk-phase seawater viscosity', Biogeochemistry, vol. 83, no. 1-3, pp. 173-188.View/Download from: UTS OPUS or Publisher's site
A two-dimensional microscale (5 cm resolution) sampler was used over the course of a phytoplankton spring bloom dominated by Phaeocystis globosa to investigate the structural properties of chlorophyll a and seawater excess viscosity distributions. The microscale distribution patterns of chlorophyll a and excess viscosity were never uniform nor random. Instead they exhibited different types and levels of aggregated spatial patterns that were related to the dynamics of the bloom. The chlorophyll a and seawater viscosity correlation patterns were also controlled by the dynamics of the bloom with positive and negative correlations before and after the formation of foam in the turbulent surf zone. The ecological relevance and implications of the observed patchiness and biologically induced increase in seawater viscosity are discussed and the combination of the enlarged colonial form and mucus secretion is suggested as a competitive advantage of P. globosa in highly turbulent environments where this species flourishes.
Seymour, JR, Humphreys, WF & Mitchell, JG 2007, 'Stratification of the microbial community inhabiting an anchialine sinkhole', Aquatic Microbial Ecology, vol. 50, pp. 11-24.View/Download from: UTS OPUS or Publisher's site
Bundera Sinkhole in northwestern Australia is an anchialine ecosystem characterised by a highly stratified water column comprising a complex polymodal profile of several physico-chemical parameters. We studied the microscale and finescale dynamics of the resident microbial community within the sinkhole. Sub-millimetre scale distributions of phytoplankton abundance were measured in the top 8 m of the water column using a free-falling high resolution fluorometer. Depth profiles were characterised by a strong, 10 to 20 cm layer of elevated fluorescence, occurring at approximately 1 m depth, which despite changes in magnitude and width was found to persist during a 24 h sampling period. Near surface distributions of microbial populations were measured using a syringe sampling profiler, which allowed for collection of water samples at 5 cm resolution, and flow cytometric analysis. These samples revealed a complex microbial assemblage, with multiple sub-populations of viruses, bacteria and picophytoplankton present throughout the water column. Within 3 m profiles, the bacterial and virus populations showed marked shifts in relative abundance, with changes of over 35-fold observed across as little as 20 cm. Samples collected from the surface to a depth of 30 m by divers also revealed distinct peaks and layers in the relative abundance of the different bacteria and virus sub-populations, which often corresponded to heterogeneities in chemical and nutrient parameters, and at some depths indicated the prevalence of chemolithotrophic populations. The complex patterns described here represent the first comprehensive observations of microbial spatiotemporal dynamics throughout an anchialine ecosystem and reveal a highly structured microbial habitat consisting of discrete niches, each dominated by heterotrophic, phototrophic or chemoautotrophic microorganisms.
Seymour, JR, Marcos, M & Stocker, R 2007, 'Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers', Journal of Visualized Experiments, vol. 4, pp. 1-3.View/Download from: UTS OPUS
The degree to which planktonic microbes can exploit microscale resource patches will have considerable implications for oceanic trophodynamics and biogeochemical flux. However, to take advantage of nutrient patches in the ocean, swimming microbes must overcome the influences of physical forces including molecular diffusion and turbulent shear, which will limit the availability of patches and the ability of bacteria to locate them. Until recently, methodological limitations have precluded direct examinations of microbial behaviour within patchy habitats and realistic small-scale flow conditions. Hence, much of our current knowledge regarding microbial behaviour in the ocean has been procured from theoretical predictions. To obtain new information on microbial foraging behaviour in the ocean we have applied soft lithographic fabrication techniques to develop 2 microfluidic devices, which we have used to create (i) microscale nutrient patches with dimensions and diffusive characteristics relevant to oceanic processes and (ii) microscale vortices, with shear rates corresponding to those expected in the ocean. These microfluidic devices have permitted a first direct examination of microbial swimming and chemotactic behaviour within a heterogeneous and dynamic seascape. The combined use of epifluorescence and phase contrast microscopy allow direct examinations of the physical dimensions and diffusive characteristics of nutrient patches, while observing the population-level aggregative response, in addition to the swimming behaviour of individual microbes. These experiments have revealed that some species of phytoplankton, heterotrophic bacteria and phagotrophic protists are adept at locating and exploiting diffusing microscale resource patches within very short time frames.
Seymour, JR, Seuront, L & Mitchell, JG 2007, 'Microscale gradients of planktonic microbial communities above the sediment surface in a mangrove estuary', ESTUARINE, COASTAL AND SHELF SCIENCE, vol. 73, no. 3-4, pp. 651-666.View/Download from: UTS OPUS or Publisher's site
The microscale (1 and 4 cm sampling resolution) distributions of chemical (O2, NH3, NO3-, NO2-, PO43-) and biological (Chl a, phytoplankton, bacterioplankton, viruses) parameters were measured in the 16 cm of water immediately overlaying the sediment-water interface (SWI) within a temperate mangrove estuary in South Australia during December 2003 and March 2004. Shear velocities (u*) during the time of sampling were very low (<0.1 cm s-1), and we consequently predict that resuspension of organisms and materials was negligible. In December 2003, profiles were often characterised by strong gradients in nutrients and organisms, with the highest concentrations often observed within 0.5 cm of the SWI. Microscale patterns in O2, NH3, NO3- and NO2- indicated that a variety of anaerobic and aerobic transformation processes probably occurred at the SWI and within profiles. Strong gradients in PO43- were indicative of nutrient flux across the SWI as a consequence of degradation processes in the sediments. Pico- and nanophytoplankton concentrations were strongly correlated (p < 0.01) to PO43-, and exhibited 12- and 68-fold changes in abundance, respectively, with highest concentrations observed nearest to the SWI. Several bacterial subpopulations were discriminated using flow cytometry and significant shifts in the `cytometric structure of the bacterial community were observed within microscale profiles.
Doubell, MJ, Seuront, L, Seymour, JR, Patten, NL & Mitchell, JG 2006, 'High-Resolution Fluorometer for Mapping Microscale Phytoplankton Distributions', Applied and Environmental Microbiology, vol. 72, no. 6, pp. 4475-4478.View/Download from: UTS OPUS or Publisher's site
A new high-resolution, in situ profiling fluorometer maps fluorescence distributions with a spatial resolution of 0.5 to 1.5 mm to a depth of 70 m in the open ocean. We report centimeter-scale patterns for phytoplankton distributions associated with gradients exhibiting 10- to 30-fold changes in fluorescence in contrasting marine ecosystems.
Patten, NL, Seymour, JR & Mitchell, JG 2006, 'Flow cytometric analysis of virus-like particles and heterotrophic bacteria within coral-associated reef water', Journal of the Marine Biological Association of the United Kingdom, vol. 86, no. 3, pp. 563-566.View/Download from: UTS OPUS or Publisher's site
Using flow cytometry, two distinct populations of virus-like particles (VLP) and heterotrophic bacteria were defined within the 12 cm water layer immediately overlying healthy, diseased and dead acroporid corals. Bacterial abundances were similar in overlying water for all coral types, however, VLP were 30% higher above diseased corals than healthy or dead corals. Mean virus to bacteria ratios (VBR) were up to 30% higher above diseased corals than above healthy or dead coral or in distant water. Concomitant with increasing VLP concentrations within 5 cm of coral surfaces, VBR distributions were generally highest above healthy and diseased coral and depressed above dead coral. These results suggest fundamental shifts in the VLP and bacterial community in water associated with diseased corals.
Seymour, JR, Seuront, L, Doubell, MJ, Waters, RL & Mitchell, JG 2006, 'Microscale patchiness of virioplankton', Journal of the Marine Biological Association of the United Kingdom, vol. 86, no. 3, pp. 551-561.View/Download from: UTS OPUS or Publisher's site
The microscale spatial distributions of viruses were investigated in three contrasting environments including oligotrophic open ocean, eutrophic coastal and estuarine habitats. The abundances of two discrete populations of both viruses and heterotrophic bacteria were measured at spatial resolutions of between 1 and 5 cm using purpose-designed microscale sampling equipment and flow cytometric sample analysis. Within open water samples, virus distributions were characterized by non-normal distributions and by `hotspots' in abundance where concentrations varied by up to 17-fold. In contrast to patterns generally observed at larger spatiotemporal scales, there was no correlation between bacterial and viral abundance or correspondence between bacteria and virus hotspots within these samples. Consequently, strong hotspots and gradients in the virus:bacteria ratio (VBR) were also apparent within samples. Within vertical pro¢les taken from above the sediment water interface within a temperate mangrove estuary, distributions of planktonic viruses were characterized by gradients in abundance, with highest concentrations observed within the 1-2 cm immediately above the sediment surface, and virus distributions were correlated to bacterial abundance (P50.01). The patterns observed in these contrasting habitats indicate that microscale patchiness of virus abundance may be a common feature of the marine environment. This form of heterogeneity may have important implications for virus^host dynamics and subsequently in£uence microbial trophodynamics and nutrient cycling in the ocean.
Seymour, JR, Seuront, L & Mitchell, JG 2005, 'Microscale and small scale temporal dynamics of a coastal planktonic microbial community', Marine Ecology Progress Series, vol. 300, pp. 21-37.View/Download from: UTS OPUS or Publisher's site
The temporal dynamics of heterotrophic bacteria and Synechococcus-type cyanobacteria communities were studied in a coastal habitat characterised by strong hydrodynamic variability using 10 s (microscale) and 30 min (small-scale) sampling intervals. Flow cytometric analysis allowed for the discrimination of 3 populations of heterotrophic bacteria and the examination of the Synechococcus cell cycle. During the 11 h small-scale study, 2-fold changes in the total abundance of both the bacterial and Synechococcus communities were observed, and clear temporal patterns in the abundance, activity and cellular state of the 2 populations were evident. Cumulative sum analysis further revealed distinct periods and trends in the temporal dynamics of the bacterial and Synechococcus communities. Shifts in the abundance of all heterotrophic bacterial populations were significantly correlated to turbulent energy dissipation. No such correlation was evident for the Synechococcus population, which instead appeared to follow a diel cell cycle very similar in nature to patterns observed in other environments. In 2 microscale studies, conducted during dissimilar hydrodynamic conditions, approx. 2-fold shifts in the abundance of the bacterial and Synechococcus populations were also observed. Microscale temporal patterns were dominated by localised variability and the existence of hotspots in abundance and activity, although cumulative sum analysis also revealed more general trends, sometimes occurring over periods of several minutes.
Seymour, JR, Mitchell, JG & Seuront, L 2004, 'Microscale heterogeneity in the activity of coastal bacterioplankton communities', Aquatic Microbial Ecology, vol. 35, no. 1, pp. 1-16.View/Download from: Publisher's site
Microscale sampling techniques and flow cytometry were employed to measure the distribution patterns of 8 subpopulations of bacteria separated according to variations in cell fluorescence and light scatter properties. Subpopulations of bacteria defined on the basis of these parameters have recently been shown to represent cells exhibiting dissimilar activity levels, and we therefore assume that the subpopulations of bacteria identified here represent metabolically diverse groups. Microscale distribution patterns of these subpopulations were measured at a resolution of 4.5 and 12 mm, within 2 dissimilar coastal habitats, A mean 2-fold change in the abundance of the total bacterial community across sample sets was observed. However, levels of spatial heterogeneity were consistently higher for the cytometrically defined subpopulations than total counts. In most samples, the population of bacteria exhibiting the highest levels of green fluorescence, or DNA content, and hence assumed to represent the most active bacteria in the community, also showed the highest levels of microscale spatial variability, with a maximum change in abundance of 14.5-fold observed across a distance of 9 nun. Where Zipf rank-size analysis was conducted, the microscale distributions of subpopulations differed significantly (p < 0.05) in 79% of cases, implying that bacterial communities are made up of physiologically distinct compartments, perhaps influenced by different microscale features of the environment. We suggest that these results provide the first evidence for the existence of microscale heterogeneity in the metabolic activity of aquatic bacterial communities.
Waters, RL, Mitchell, JG & Seymour, JR 2003, 'Geostatistical characterisation of centimetre-scale spatial structure of in vivo fluorescence', Marine Ecology Progress Series, vol. 251.
Seymour, JR, Laverock, B, Nielsen, DA, Trevathan-Tackett, SM & Macreadie, PI 2018, 'The microbiology of seagrasses' in Seagrasses of Australia: Structure, Ecology and Conservation, pp. 343-392.View/Download from: Publisher's site
© Springer International Publishing AG, part of Springer Nature 2018. Like both terrestrial plants and other benthic marine organisms, seagrasses host abundant and diverse communities of microorganisms. These microbes fundamentally influence seagrass physiology and health, while also regulating the biogeochemical dynamics of entire seagrass meadows. Discrete populations of bacteria, fungi, microalgae, archaea and viruses inhabit seagrass leaves, roots and rhizomes and the surrounding sediments. The plethora of ecological interactions taking place between seagrasses and this microbiome span the continuum of symbiotic relationships from mutualism to parasitism. Indeed, the metabolic activities of some seagrass associated microbes, such as diazotrophic and sulphur oxidizing bacteria, govern the local chemical environment in ways that facilitate seagrass survival. On the other hand, pathogens, such as the protozoan parasite Labyrinthula cause disease outbreaks that can lead to mass seagrass die offs. While the role of the seagrass microbiome in defining the success of seagrass habitats is becoming increasingly apparent, there is still much to be learnt. For instance, the development of an understanding of how seagrass associated microbes may buffer or augment the negative impacts of growing environmental pressures will be valuable for informing decisions regarding the management and conservation of threatened seagrass habitats. In this chapter we will synthesise the current state of knowledge on the microbiology of seagrasses, with a goal of conveying the often overlooked importance of the seagrass microbiome in governing seagrass health and the biogeochemical stability of seagrass ecosystems.
Seuront, L, Lacheze, C, Doubell, MJ, Seymour, JR, Van Dongen-Vogels, V, Newton, K, Alderkamp, AC & Mitchell, JG 2007, 'The influence of Phaeocystis globosa on microscale spatial patterns of chlorophyll a and bulk-phase seawater viscosity' in Phaeocystis, Major Link in the Biogeochemical Cycling of Climate-Relevant Elements, pp. 173-188.View/Download from: Publisher's site
A two-dimensional microscale (5 cm resolution) sampler was used over the course of a phytoplankton spring bloom dominated by Phaeocystis globosa to investigate the structural properties of chlorophyll a and seawater excess viscosity distributions. The microscale distribution patterns of chlorophyll a and excess viscosity were never uniform nor random. Instead they exhibited different types and levels of aggregated spatial patterns that were related to the dynamics of the bloom. The chlorophyll a and seawater viscosity correlation patterns were also controlled by the dynamics of the bloom with positive and negative correlations before and after the formation of foam in the turbulent surf zone. The ecological relevance and implications of the observed patchiness and biologically induced increase in seawater viscosity are discussed and the combination of the enlarged colonial form and mucus secretion is suggested as a competitive advantage of P. globosa in highly turbulent environments where this species flourishes. © 2007 Springer Science+Business Media B.V.
Jeffries, TC, Newton, K, Leterme, S, Seymour, JR, Dinsdale, E, Gilbert, J, Roudnew, B, Smith, R, Seuront, L & Mitchell, J 2009, 'Taxonomic clustering of microbial metagenomes in the Coorong lagoon system', Adelaide, Australia.
Jeffries, TC, Newton, K, Leterme, S, Seymour, JR, Dinsdale, E, Roudnew, B, Smith, R, Seuront, L & Mitchell, JG 2009, 'Functional metagenomics of sediment microbial communities from a hypersaline coastal lagoon', Adelaide, Australia.
Lavery, TJ, Roudnew, B, Seymour, JR, Mitchell, JG, Seuront, L & Smetacek, V 2009, 'Whales: A net sink or source of carbon to the atmosphere?', Adelaide, Australia.
Newton, K, Jeffries, TC, Seymour, JR, Leterme, S, Mitchell, J & Seuront, L 2009, 'Impact of salinity on viral morphological diversity', Adelaide, Australia.
Seymour, JR 2009, 'Cascading resource patch exploitation in a heterogeneous microbial seascape', Adelaide, Australia.
Doubell, MJ, Seuront, L, Seymour, JR, Yamazaki, H & Mitchell, JG 2008, 'Microscale structure of a phytoplankton bloom.', Japan.
Hunt, DE, Seymour, JR, Wildschutte, HS, Stocker, R, Veneziano, D & Polz, ME 2008, 'Microscale clustering of bacteria around eukaryotes in the coastal ocean', United States.
Jeffries, TC, Newton, K, Leterme, S, Seymour, JR, Dinsdale, E, Roudnew, B, Smith, R, Seuront, L & Mitchell, JG 2008, 'Functional metagenomic profiling of microbial and viral communities in sediment along a naturally occurring salinity gradient', Cairns, Australia.
Newton, K, Jeffries, TC, Seymour, JR, Leterme, S, Mitchell, JG & Seuront, L 2008, 'Microbial abundance and diversity along a salinity gradient.', Cairns, Australia.
Patten, NL, Seymour, JR, Seuront, L, Harrison, P & Mitchell, JG 2008, 'Prokaryotic and viral abundances between different coral reef micro-habitats', Cairns, Australia.
Stocker, R & Seymour, JR 2008, 'Ecological implications of chemotactic motility', Lucca (Barga), Italy.
Stocker, R & Seymour, JR 2008, 'Patchiness in the microbial world: insights from microfluidic studies.', United States.
Stocker, R, Seymour, JR & Marcos, M 2008, 'Microbial life in the ocean.', New Orleans, LA.
Kamiya, E, Seymour, JR, Mitchell, JG, Nishimura, M, Hamasaki, K & Kogure, K 2007, 'Relationships between abundance of viral subpopulations, bacteria and picophytoplankton in coastal areas.', Japan.
Seymour, JR, Marcos, M & Stocker, R 2007, 'Using microfluidic channels to study microbial behaviour and ecology in a patchy seascape', Portugal.
Stocker, R & Seymour, JR 2007, 'Insights into the life of a microbe: a microfluidic approach', United Kingdom.
Humphreys, WF, Seymour, JR & Mitchell, JG 2006, 'Stratification of microbial communities in an anchialine sinkhole', Romania.
Seymour, JR & Stocker, R 2006, 'The causes and implications of microscale patchiness in the ocean studied using microfluidics.', United States.
Stocker, R, Seymour, JR & Marcos, M 2006, 'Microfluidics for studying microbial ecology', United States.
Seuront, L, Leterme, S, Seymour, JR & Mitchell, JG 2004, 'Sampling the sampling unit: A world in a bottle.', United States.
Seymour, JR & Mitchell, JG 2004, 'Microscale distributions of bacterioplankton and virus-like particles assessed using flow cytometry', United States.
Mitchell, JG, Hale, M, Seymour, JR & Barbara, G 2001, 'Early Glimpses of Submicrometer Biological Oceanography.', United States.
Mitchell, JG & Seymour, JR 2000, 'Water column microscale patchiness: Meeting of the tactic and turbulent length scales', Denmark.
Seymour, JR 2001, 'Spatial heterogeneity in bacterioplankton abundance', Australia.
Seymour, JR, Mitchell, JG & Waters, R 2000, 'Flow cytometric analysis allows for the measurement of marine microorganisms.', Australia.
Seymour, JR, Mitchell, JG, Waters, R & Pile, A 2000, 'High resolution small-scale sampling and flow cytometric analysis allows for the measurement of microdistributions of marine microorganisms', Australia.
Waters, R, Mitchell, JG, Seymour, JR & Pile, A 2000, 'The use of flow cytometry to characterise the marine planktonic microenvironment', Adelaide, Australia.
Waters, R, Seymour, JR, Pearson, L, Nelson, C, Bass, L & Mitchell, JG 1999, 'The role of small-scale turbulence in structuring the biological microenvironment.', United States.
Mitchell, JG, Barbara, G, Dillon, L, Pearson, L, Seymour, JR, Blackburn, N, Bergerson, B & Luchsinger, R 1998, 'Motility in marine bacteria', Australia.
Seymour, JR & Mitchell, JG 1998, 'Millimetre-scale distributions of marine bacteria.', Australia.
As the base of the marine food web, and the first step in the biological carbon pump, understanding changes in microbial community composition is essential for predicting changes in the marine nitrogen (N) cycle. Climate change projections suggest that oligotrophic waters will become more stratified with a concomitant shift in microbial community composition based on changes in N supply. In regions of strong boundary currents, eddies could reduce this limitation through nutrient uplift and other forms of eddy mixing. Understanding the preference for different forms of N by microbes is essential for understanding and predicting shifts in the microbial community. This study aims to understand the utilization of different N species within different microbial size fractions as well as understand the preferred source of N to these groups across varying mesoscale and sub-mesoscale features in the East Australian Current (EAC). In June 2015 we sampled microbial communities from three depths (surface, chlorophyll-a maximum and below the mixed layer), in three mesoscale and sub-mesoscale eddy features, as well as two end-point water masses (coastal and oligotrophic EAC water). Particulate matter was analysed for stable C and N isotopes, and seawater incubations with trace amounts of 15NO3, 15NH4, 15N2, 15Urea and 13C were undertaken. All samples were size fractionated into 0.3-2.0 µm, 2.0-10 µm, and >10 µm size classes, encompassing the majority of microbes in these waters. Microbial community composition was also assessed (pigments, flow cytometry, DNA), as well as physical and chemical parameters, to better understand the drivers of carbon fixation and nitrogen utilization across a diversity of water masses and microbial size classes. We observed that small, young features have a greater abundance of larger size classes. We therefore predict that these microbes will preferentially draw down the recently pulsed NO3. Ultimately, the size and age of a feature will determin...