I am a microbial ecologist studying bio-geochemical processes at the micro scale via electrochemical microsensors and molecular methods.
In 2010 I completed my PhD thesis on aerobic methane and ammonia transformation in the transient and extremely nutrient loaded environment of floating liquid manure crusts.
I am an Associate within the Plant Functional Biology and Climate Change Cluster (C3), thus bringing microsensor technology to UTS in collaboration with C3 member Professor Michael Kühl.
Initially my research will focus on microbially mediated nitrogen transformations in coral polyps with the aim to discover some of the mechanisms behind the suggested efficient nutrient recycling within coral reef ecosystems
- Micro scale analyses of respiratory and photosynthetic processes in the environment
- Processes controlling bio-geochemical cycling
- Interactions between microbes and higher organisms
- Environmental sustainability
- Technical application of microbes
Gardner, S.G., Raina, J.-.B., Nitschke, M.R., Nielsen, D.A., Stat, M., Motti, C.A., Ralph, P.J. & Petrou, K. 2017, 'A multi-trait systems approach reveals a response cascade to bleaching in corals.', BMC biology, vol. 15, no. 1, p. 117.View/Download from: UTS OPUS or Publisher's site
Climate change causes the breakdown of the symbiotic relationships between reef-building corals and their photosynthetic symbionts (genus Symbiodinium), with thermal anomalies in 2015-2016 triggering the most widespread mass coral bleaching on record and unprecedented mortality on the Great Barrier Reef. Targeted studies using specific coral stress indicators have highlighted the complexity of the physiological processes occurring during thermal stress, but have been unable to provide a clear mechanistic understanding of coral bleaching.Here, we present an extensive multi-trait-based study in which we compare the thermal stress responses of two phylogenetically distinct and widely distributed coral species, Acropora millepora and Stylophora pistillata, integrating 14 individual stress indicators over time across a simulated thermal anomaly. We found that key stress responses were conserved across both taxa, with the loss of symbionts and the activation of antioxidant mechanisms occurring well before collapse of the physiological parameters, including gross oxygen production and chlorophyll a. Our study also revealed species-specific traits, including differences in the timing of antioxidant regulation, as well as drastic differences in the production of the sulfur compound dimethylsulfoniopropionate during bleaching. Indeed, the concentration of this antioxidant increased two-fold in A. millepora after the corals started to bleach, while it decreased 70% in S. pistillata.We identify a well-defined cascading response to thermal stress, demarking clear pathophysiological reactions conserved across the two species, which might be central to fully understanding the mechanisms triggering thermally induced coral bleaching. These results highlight that bleaching is a conserved mechanism, but specific adaptations linked to the coral's antioxidant capacity drive differences in the sensitivity and thus tolerance of each coral species to thermal stress.
Macreadie, PI, Nielsen, DA, Kelleway, JJ, Atwood, TB, Seymour, JR, Petrou, K, Connolly, RM, Thomson, ACG, Trevathan-Tackett, SM & Ralph, PJ 2017, 'Can we manage coastal ecosystems to sequester more blue carbon?', Frontiers in Ecology and the Environment, vol. 15, no. 4, pp. 206-213.View/Download from: UTS OPUS or Publisher's site
© The Ecological Society of America To promote the sequestration of blue carbon, resource managers rely on best-management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment-level approaches. Drawing upon knowledge from a broad range of environmental variables that influence blue carbon sequestration, including warming, carbon dioxide levels, water depth, nutrients, runoff, bioturbation, physical disturbances, and tidal exchange, we discuss three potential management strategies that hold promise for optimizing coastal blue carbon sequestration: (1) reducing anthropogenic nutrient inputs, (2) reinstating top-down control of bioturbator populations, and (3) restoring hydrology. By means of case studies, we explore how these three strategies can minimize blue carbon losses and maximize gains. A key research priority is to more accurately quantify the impacts of these strategies on atmospheric greenhouse-gas emissions in different settings at landscape scales.
Petrou, K., Ralph, P.J. & Nielsen, D.A. 2017, 'A novel mechanism for host-mediated photoprotection in endosymbiotic foraminifera.', ISME Journal, vol. 11, no. 2, pp. 453-462.View/Download from: Publisher's site
Light underpins the health and function of coral reef ecosystems, where symbiotic partnerships with photosynthetic algae constitute the life support system of the reef. Decades of research have given us detailed knowledge of the photoprotective capacity of phototrophic organisms, yet little is known about the role of the host in providing photoprotection in symbiotic systems. Here we show that the intracellular symbionts within the large photosymbiotic foraminifera Marginopora vertebralis exhibit phototactic behaviour, and that the phototactic movement of the symbionts is accomplished by the host, through rapid actin-mediated relocation of the symbionts deeper into the cavities within the calcium carbonate test. Using a photosynthetic inhibitor, we identified that the infochemical signalling for host regulation is photosynthetically derived, highlighting the presence of an intimate communication between the symbiont and the host. Our results emphasise the central importance of the host in photosymbiotic photoprotection via a new mechanism in foraminifera that can serve as a platform for exploring host-symbiont communication in other photosymbiotic organisms.
Trevathan-Tackett, SM, Seymour, JR, Nielsen, DA, Macreadie, PI, Jeffries, TC, Sanderman, J, Baldock, J, Howes, JM, Steven, ADL & Ralph, PJ 2017, 'Sediment anoxia limits microbial-driven seagrass carbon remineralization under warming conditions.', FEMS Microbiology Ecology, vol. 93, no. 6.View/Download from: UTS OPUS or Publisher's site
Seagrass ecosystems are significant carbon sinks, and their resident microbial communities ultimately determine the quantity and quality of carbon sequestered. However, environmental perturbations have been predicted to affect microbial-driven seagrass decomposition and subsequent carbon sequestration. Utilizing techniques including 16S-rDNA sequencing, solid-state NMR and microsensor profiling, we tested the hypothesis that elevated seawater temperatures and eutrophication enhance the microbial decomposition of seagrass leaf detritus and rhizome/root tissues. Nutrient additions had a negligible effect on seagrass decomposition, indicating an absence of nutrient limitation. Elevated temperatures caused a 19% higher biomass loss for aerobically decaying leaf detritus, coinciding with changes in bacterial community structure and enhanced lignocellulose degradation. Although, community shifts and lignocellulose degradation were also observed for rhizome/root decomposition, anaerobic decay was unaffected by temperature. These observations suggest that oxygen availability constrains the stimulatory effects of temperature increases on bacterial carbon remineralization, possibly through differential temperature effects on bacterial functional groups, including putative aerobic heterotrophs (e.g. Erythrobacteraceae, Hyphomicrobiaceae) and sulfate reducers (e.g. Desulfobacteraceae). Consequently, under elevated seawater temperatures, carbon accumulation rates may diminish due to higher remineralization rates at the sediment surface. Nonetheless, the anoxic conditions ubiquitous to seagrass sediments can provide a degree of carbon protection under warming seawater temperatures.
Gardner, S.G., Nielsen, D.A., Laczka, O., Shimmon, R., Beltran, V.H., Ralph, P.J. & Petrou, K. 2016, 'Dimethylsulfoniopropionate, superoxide dismutase and glutathione as stress response indicators in three corals under short-term hyposalinity stress', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 283, no. 1824.View/Download from: UTS OPUS or Publisher's site
Brodersen, KE, Nielsen, DA, Ralph, PJ & Kuhl, M 2015, 'Oxic microshield and local pH enhancement protects Zostera muelleri from sediment derived hydrogen sulphide', NEW PHYTOLOGIST, vol. 205, no. 3, pp. 1264-1276.View/Download from: UTS OPUS or Publisher's site
Gardner, S.G., Nielsen, D.A., Petrou, K., Larkum, A.W.D. & Ralph, P.J. 2015, 'Characterisation of coral explants: a model organism for cnidarian-dinoflagellate studies', CORAL REEFS, vol. 34, no. 1, pp. 133-142.View/Download from: UTS OPUS or Publisher's site
Nielsen, D.A., Pernice, M., Schliep, M., Sablok, G., Jeffries, T.C., Kuehl, M., Wangpraseurt, D., Ralph, P.J. & Larkum, A.W.D. 2015, 'Microenvironment and phylogenetic diversity of Prochloron inhabiting the surface of crustose didemnid ascidians', ENVIRONMENTAL MICROBIOLOGY, vol. 17, no. 10, pp. 4121-4132.View/Download from: UTS OPUS or Publisher's site
Brodersen, K.E., Nielsen, D.A., Ralph, P.J. & Kuhl, M. 2014, 'A split flow chamber with artificial sediment to examine the below-ground microenvironment of aquatic macrophytes', MARINE BIOLOGY, vol. 161, no. 12, pp. 2921-2930.View/Download from: UTS OPUS or Publisher's site
Wangpraseurt, D, Polerecky, L, Larkum, A, Ralph, PJ, Nielsen, DA, Pernice, M & Kuhl, M 2014, 'The in situ light microenvironment of corals', Limnology and Oceanography, vol. 59, no. 3, pp. 917-926.View/Download from: UTS OPUS or Publisher's site
We used a novel diver-operated microsensor system to collect in situ spectrally resolved light fields on corals with a micrometer spatial resolution. The light microenvironment differed between polyp and coenosarc tissues with scalar irradiance (400700 nm) over polyp tissue, attenuating between 5.1- and 7.8-fold from top to base of small hemispherical coral colonies, whereas attenuation was at most 1.5-fold for coenosarc tissue. Fluctuations in ambient solar irradiance induced changes in light and oxygen microenvironments, which were more pronounced and faster in coenosarc compared with polyp tissue. Backscattered light from the surrounding benthos contributed . 20% of total scalar irradiance at the coral tissue surface and enhanced symbiont photosynthesis and the local O2 concentration, indicating an important role of benthos optics for coral ecophysiology. Light fields on corals are species and tissue specific and exhibit pronounced variation on scales from micrometers to decimeters. Consequently, the distribution, genetic diversity, and physiology of coral symbionts must be coupled with the measurements of their actual light microenvironment to achieve a more comprehensive understanding of coral ecophysiology.
Nielsen, DA, Schramm, A, Nielsen, LP & Revsbech, NP 2013, 'Seasonal methane oxidation potential in manure crusts', Applied and Environmental Microbiology, vol. 79, no. 1, pp. 407-410.View/Download from: UTS OPUS or Publisher's site
Organic crusts on liquid manure storage tanks harbor ammonia- and nitrite-resistant methane oxidizers and may significantly reduce methane emissions. Methane oxidation potential (0.6 mol CH4 m(-2) day(-1)) peaked during fall and winter, after 4 months of crust development. Consequences for methane mitigation potential of crusts are discussed.
Kofoed, M.V., Nielsen, D.A., Revsbech, N.P. & Schramm, A. 2012, 'Fluorescence in situ hybridization (FISH) detection of nitrite reductase transcripts (nirS mRNA) in Pseudomonas stutzeri biofilms relative to a microscale oxygen gradient', Systematic and Applied Microbiology, vol. 35, no. 8, pp. 513-517.View/Download from: UTS OPUS or Publisher's site
Microsensor measurements of oxygen were combined with mRNA-targeted ?uorescence in situ hybridization (FISH) to relate the expression of nitrite reductase (nirS) to oxygen concentrations in arti?- cial bio?lms of the denitri?er Pseudomonas stutzeri. A distinct zone of nirS transcript-containing cells was detected at the oxicanoxic transition zone, below an oxygen threshold concentration of 0.72.5 M, depending on incubation conditions. Although not a routine technique yet, the possibility of coupling microsensor and mRNA-targeted FISH analyses described here opens for studies addressing microenvironment, identity, and actual activity of microbes in strati?ed environments at single cell resolution
Jokic, T, Borisov, SM, Saf, R, Nielsen, DA, Kuhl, M & Klimant, I 2012, 'Highly photostable near-infrared fluorescent pH indicators and sensors based on BF2-chelated tetraarylazadipyrromethene dyes', Analytical Chemistry, vol. 84, pp. 6723-6730.View/Download from: UTS OPUS or Publisher's site
In this study, a series of new BF2-chelated tetraarylazadipyrromethane dyes are synthesized and are shown to be suitable for the preparation of on/off photoinduced electron transfer modulated fluorescent sensors. The new indicators are noncovalently entrapped in polyurethane hydrogel D4 and feature absorption maxima in the range 660â 710 nm and fluorescence emission maxima at 680â740 nm. Indicators have high molar absorption coefficients of â¼80 000 Mâ1 cmâ1, good quantum yields (up to 20%), excellent photostability and low cross-sensitivity to the ionic strength. pKa values of indicators are determined from absorbance and fluorescence measurements and range from 7 to 11, depending on the substitution pattern of electron-donating and -withdrawing functionalities. Therefore, the new indicators are suitable for exploitation and adaptation in a diverse range of analytical applications. Apparent pKa values in sensor films derived from fluorescence data show 0.5â1 pH units lower values in comparison with those derived from the absorption data due to FoÌrster resonance energy transfer from protonated to deprotonated form. A dual-lifetime referenced sensor is prepared, and application for monitoring of pH in corals is demonstrated.
Nielsen, D.A., Nielsen, L.P., Schramm, A. & Revsbech, N.P. 2010, 'Oxygen Distribution and Potential Ammonia Oxidation in Floating, Liquid Manure Crusts', Journal of Environmental Quality, vol. 39, no. 5, pp. 1813-1820.View/Download from: UTS OPUS or Publisher's site
Floating, organic crusts on liquid manure, stored as a result of animal production, reduce emission of ammonia (NH(3)) and other volatile compounds during storage. The occurrence of NO(2)(-) and NO(3)(-) in the crusts indicate the presence of actively metabolizing NH(3)-oxidizing bacteria (AOB) which may be partly responsible for this mitigation effect. Six manure tanks with organic covers (straw and natural) were surveyed to investigate the prevalence and potential activity of AOB and its dependence on the O(2) availability in the crust matrix as studied by electrochemical profiling. Oxygen penetration varied from <1 mm in young, poorly developed natural crusts and old straw crusts, to several centimeters in the old natural crusts. The AOB were ubiquitously present in all crusts investigated, but nitrifying activity could only be detected in old natural crusts and young straw crust with high O(2) availability. In old natural crusts, total potential NH(3) oxidation rates were similar to reported fluxes of NH(3) from slurry without surface crust. These results indicate that old, natural surface crusts may develop into a porous matrix with high O(2) availability that harbors an active population of aerobic microorganisms, including AOB. The microbial activity may thus contribute to a considerable reduction of ammonia emissions from slurry tanks with well-developed crusts.
Hansen, R.R., Nielsen, D.A., Schramm, A., Nielsen, L.P., Revsbech, N.P. & Hansen, M. 2009, 'Greenhouse Gas Microbiology in Wet and Dry Straw Crust Covering Pig Slurry', Journal of Environmental Quality, vol. 38, no. 3, pp. 1311-1319.View/Download from: UTS OPUS or Publisher's site
Liquid manure (Slurry) storages are sources of gases Such ammonia (NH(3)) and methane (CH(4)). Danish slurry storages are required to be covered to reduce NH(3) emissions and often a floating crust of straw is applied. This study investigated whether physical properties of the crust or crust microbiology had an effect oil the emission of the potent greenhouse gases CH(4) and nitrous oxide (N(2)O) when crust moisture was manipulated ("dry", "moderate", and "wet"). The dry crust had the deepest oxygen penetration (45 mm as compared to 20 mm in the wet treatment) as measured with microsensors, the highest amounts of nitrogen oxides (NO(2)(-) and NO(3)(-)) (up to 36 mu mol g(-1) wet weight) and the highest emissions of N(2)O and CH(4). Fluorescent in situ hybridization and gene-specific polymerase chain reaction (PCR) were used to detect occurrence of bacterial groups. Ammonia-oxidizing bacteria (AOB) were abundant in all three crust types, whereas nitrite-oxidizing bacteria (NOB) were undetectable and methane-oxidizing bacteria (MOB) were only sparsely present in the wet treatment. A change to anoxia did not affect the CH(4) emission indicating the virtual absence of aerobic methane oxidation in the investigated 2-mo old crusts. However, all increase in N(2)O emission was observed in all crusted treatments exposed to anoxia, and this was probably a result of denitrification based oil NO(x)(-) chat had accumulated in the crust during oxic conditions. To reduce overall greenhouse gas emissions, floating crust should be managed to optimize conditions for methanotrophs.
Ottosen, L., Poulsen, H., Nielsen, D.A., Finster, K., Nielsen, L.P. & Revsbech, N.P. 2009, 'Observations on microbial activity in acidified pig slurry', Biosystems Engineering, vol. 102, no. 3, pp. 291-297.View/Download from: UTS OPUS or Publisher's site
Acidification of pig slurry to pH 5.5 is used as a measure to reduce ammonia emission from pits and storages. The slurry is acidified with sulphuric acid in a process tank and pumped back to the slurry pits or to a storage tank. We investigated the effect of acidification on microbial activity. Oxygen consumption rate, methanogenesis and sulphate reduction were all reduced by more than 98% in the stored acidified slurry compared to untreated slurry. Despite higher sulphate concentration, the microbial metabolism was greatly compromised or absent in the acidified slurry. This could be explained by the high concentration of protonized short-chained volatile fatty acids in the acidified slurry (approximately 25 mM, compared to untreated slurry <0.1 mM), which act as an uncoupling agent of the cell membrane potential and thereby arrest microbial metabolism. In total the consequences of slurry acidification are greatly reduced production rates and loss of sulphide and methane, and eliminated loss of ammonia. On the other hand, increased volatilization and loss of smelly fatty acids is to be expected.