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Associate Professor Justin Seymour

Biography

I am an ARC Future Fellow and the leader of the Plant Functional Biology and Climate Change Cluster (C3) Ocean Microbes and Healthy Oceans research program at UTS.

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.

Professional

Image of Justin Seymour
Future Fellow and Associate Professor, Plant Functional Biology & Climate Change
Core Member, C3 - Plant Functional Biology and Climate Change
Ph D
 
Phone
+61 2 9514 1776

Research Interests

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).

Can supervise: Yes

Subject Coordinator and Chief Lecturer for Microbial Ecology (91170)

Guest Lecturer in Ecology (91154) and General Microbiology (91314)

Chapters

Seuront, L., Lacheze, C., Doubell, M.J., Seymour, J.R., Van Dongen-Vogels, V., Newton, K., Alderkamp, A.C. & Mitchell, J.G. 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.
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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.

Conferences

McInnes, A.S., Messer, L.F., Laiolo, L., Laverock, B., Laczka, O., Brown, M., Seymour, J.R. & Doblin, M.A. 2016, 'Microbial utilization of nitrogen in cold core eddies: size does matter', Association for Limnology & Oceanography (ASLO) Ocean Sciences Meeting,, New Orleans, USA.
Jeffries, T.C., Newton, K., Leterme, S., Seymour, J.R., 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.
Lavery, T.J., Roudnew, B., Seymour, J.R., Mitchell, J.G., Seuront, L. & Smetacek, V. 2009, 'Whales: A net sink or source of carbon to the atmosphere?', Adelaide, Australia.
Seymour, J.R. 2009, 'Cascading resource patch exploitation in a heterogeneous microbial seascape', Adelaide, Australia.
Jeffries, T.C., Newton, K., Leterme, S., Seymour, J.R., Dinsdale, E., Roudnew, B., Smith, R., Seuront, L. & Mitchell, J.G. 2009, 'Functional metagenomics of sediment microbial communities from a hypersaline coastal lagoon', Adelaide, Australia.
Newton, K., Jeffries, T.C., Seymour, J.R., Leterme, S., Mitchell, J. & Seuront, L. 2009, 'Impact of salinity on viral morphological diversity', Adelaide, Australia.
Patten, N.L., Seymour, J.R., Seuront, L., Harrison, P. & Mitchell, J.G. 2008, 'Prokaryotic and viral abundances between different coral reef micro-habitats', Cairns, Australia.
Jeffries, T.C., Newton, K., Leterme, S., Seymour, J.R., Dinsdale, E., Roudnew, B., Smith, R., Seuront, L. & Mitchell, J.G. 2008, 'Functional metagenomic profiling of microbial and viral communities in sediment along a naturally occurring salinity gradient', Cairns, Australia.
Stocker, R. & Seymour, J.R. 2008, 'Ecological implications of chemotactic motility', Lucca (Barga), Italy.
Hunt, D.E., Seymour, J.R., Wildschutte, H.S., Stocker, R., Veneziano, D. & Polz, M.E. 2008, 'Microscale clustering of bacteria around eukaryotes in the coastal ocean', United States.
Stocker, R. & Seymour, J.R. 2008, 'Patchiness in the microbial world: insights from microfluidic studies.', United States.
Doubell, M.J., Seuront, L., Seymour, J.R., Yamazaki, H. & Mitchell, J.G. 2008, 'Microscale structure of a phytoplankton bloom.', Japan.
Stocker, R., Seymour, J.R. & Marcos, M. 2008, 'Microbial life in the ocean.', New Orleans, LA.
Newton, K., Jeffries, T.C., Seymour, J.R., Leterme, S., Mitchell, J.G. & Seuront, L. 2008, 'Microbial abundance and diversity along a salinity gradient.', Cairns, Australia.
Kamiya, E., Seymour, J.R., Mitchell, J.G., Nishimura, M., Hamasaki, K. & Kogure, K. 2007, 'Relationships between abundance of viral subpopulations, bacteria and picophytoplankton in coastal areas.', Japan.
Seymour, J.R., Marcos, M. & Stocker, R. 2007, 'Using microfluidic channels to study microbial behaviour and ecology in a patchy seascape', Portugal.
Stocker, R. & Seymour, J.R. 2007, 'Insights into the life of a microbe: a microfluidic approach', United Kingdom.
Seymour, J.R. & Stocker, R. 2006, 'The causes and implications of microscale patchiness in the ocean studied using microfluidics.', United States.
Stocker, R., Seymour, J.R. & Marcos, M. 2006, 'Microfluidics for studying microbial ecology', United States.
Humphreys, W.F., Seymour, J.R. & Mitchell, J.G. 2006, 'Stratification of microbial communities in an anchialine sinkhole', Romania.
Seymour, J.R. & Mitchell, J.G. 2004, 'Microscale distributions of bacterioplankton and virus-like particles assessed using flow cytometry', United States.
Seuront, L., Leterme, S., Seymour, J.R. & Mitchell, J.G. 2004, 'Sampling the sampling unit: A world in a bottle.', United States.
Mitchell, J.G., Hale, M., Seymour, J.R. & Barbara, G. 2001, 'Early Glimpses of Submicrometer Biological Oceanography.', United States.
Seymour, J.R. 2001, 'Spatial heterogeneity in bacterioplankton abundance', Australia.
Seymour, J.R., Mitchell, J.G., Waters, R. & Pile, A. 2000, 'High resolution small-scale sampling and flow cytometric analysis allows for the measurement of microdistributions of marine microorganisms', Australia.
Mitchell, J.G. & Seymour, J.R. 2000, 'Water column microscale patchiness: Meeting of the tactic and turbulent length scales', Denmark.
Seymour, J.R., Mitchell, J.G. & Waters, R. 2000, 'Flow cytometric analysis allows for the measurement of marine microorganisms.', Australia.
Waters, R., Mitchell, J.G., Seymour, J.R. & Pile, A. 2000, 'The use of flow cytometry to characterise the marine planktonic microenvironment', Adelaide, Australia.
Waters, R., Seymour, J.R., Pearson, L., Nelson, C., Bass, L. & Mitchell, J.G. 1999, 'The role of small-scale turbulence in structuring the biological microenvironment.', United States.
Seymour, J.R. & Mitchell, J.G. 1998, 'Millimetre-scale distributions of marine bacteria.', Australia.
Mitchell, J.G., Barbara, G., Dillon, L., Pearson, L., Seymour, J.R., Blackburn, N., Bergerson, B. & Luchsinger, R. 1998, 'Motility in marine bacteria', Australia.

Journal articles

Messer, L.F., Mahaffey, C., M Robinson, C., Jeffries, T.C., Baker, K.G., Bibiloni Isaksson, J., Ostrowski, M., Doblin, M.A., Brown, M.V. & Seymour, J.R. 2016, 'High levels of heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation.', The ISME journal.
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 (-proteobacteria and -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 91nmoll(-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 -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.
Garren, M., Son, K., Tout, J., Seymour, J.R. & Stocker, R. 2016, 'Temperature-induced behavioral switches in a bacterial coral pathogen.', The ISME journal.
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&deg;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&deg;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, T.C., Curlevski, N.J., Brown, M.V., Harrison, D.P., Doblin, M.A., Petrou, K., Ralph, P.J. & Seymour, J.R. 2016, 'Partitioning of fungal assemblages across different marine habitats', ENVIRONMENTAL MICROBIOLOGY REPORTS, vol. 8, no. 2, pp. 235-238.
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Jeffries, T.C., Schmitz Fontes, M.L., Harrison, D.P., Van-Dongen-Vogels, V., Eyre, B.D., Ralph, P.J. & Seymour, J.R. 2016, 'Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary.', Frontiers in microbiology, vol. 6, pp. 1-17.
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The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide insights into the simultaneous influence of natural and anthropogenic drivers on the structure and...
Murray, S.A., Suggett, D.J., Seymour, J.R., Doblin, M., Kohli, G.S., Fabris, M. & Ralph, P.J. 2016, 'Unravelling the functional genetics of dinoflagellates: a review of approaches and opportunities', Perspectives in Phycology.
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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.
Doblin, M.A., Petrou, K., Sinutok, S., Seymour, J.R., Messer, L.F., Brown, M.V., Norman, L., Everett, J.D., McInnes, A.S., Ralph, P.J., Thompson, P.A. & Hassler, C.S. 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, p. e1973.
The intensification of western boundary currents in the global ocean will potentially influence meso-scale eddy generation, and redistribute microbes and their associated ecological and biogeochemical functions. To understand eddy-induced changes in microbial community composition as well as how they control growth, we targeted the East Australian Current (EAC) region to sample microbes in a cyclonic (cold-core) eddy (CCE) and the adjacent EAC. Phototrophic and diazotrophic microbes were more diverse (2-10 times greater Shannon index) in the CCE relative to the EAC, and the cell size distribution in the CCE was dominated (67%) by larger micro-plankton [Formula: see text], as opposed to pico- and nano-sized cells in the EAC. Nutrient addition experiments determined that nitrogen was the principal nutrient limiting growth in the EAC, while iron was a secondary limiting nutrient in the CCE. Among the diazotrophic community, heterotrophic NifH gene sequences dominated in the EAC and were attributable to members of the gamma-, beta-, and delta-proteobacteria, while the CCE contained both phototrophic and heterotrophic diazotrophs, including Trichodesmium, UCYN-A and gamma-proteobacteria. Daily sampling of incubation bottles following nutrient amendment captured a cascade of effects at the cellular, population and community level, indicating taxon-specific differences in the speed of response of microbes to nutrient supply. Nitrogen addition to the CCE community increased picoeukaryote chlorophyll a quotas within 24 h, suggesting that nutrient uplift by eddies causes a 'greening' effect as well as an increase in phytoplankton biomass. After three days in both the EAC and CCE, diatoms increased in abundance with macronutrient (N, P, Si) and iron amendment, whereas haptophytes and phototrophic dinoflagellates declined. Our results indicate that cyclonic eddies increase delivery of nitrogen to the upper ocean to potentially mitigate the negative consequences of increased ...
Siboni, N., Balaraju, V., Carney, R., Labbate, M. & Seymour, J.R. 2016, 'Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary.', Frontiers in microbiology, vol. 7, p. 460.
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Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for the presence of a spatiotemporally dynamic Vibrio community within...
Labbate, M., Seymour, J.R., Lauro, F. & Brown, M.V. 2016, 'Editorial: Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments.', Frontiers in microbiology, vol. 7, p. 1044.
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Messer, L.F., Doubell, M., Jeffries, T.C., Brown, M.V. & Seymour, J.R. 2015, 'Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary', Aquatic Microbial Ecology, vol. 74, no. 1, pp. 1-15.
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&copy; Inter-Research 2015 The ecology of microbial assemblages inhabiting classical (positive) estuaries has been well documented. However, we know relatively little about the microbial ecology of inverse (negative) estuaries, which exhibit different physical and hydrodynamic properties, including oligotrophy and hypersalinity. We investigated the dynamics of bacterioplankton communities in Spencer Gulf, an inverse estuary in temperate South Australia. We characterised patterns in the overall diversity and composition of the resident microbial assemblage, and tested the hypothesis that pelagic nitrogen-fixing bacteria (diazotrophs) could be an important functional group in the nutrient limited waters of the region. Prokaryotic and diazotrophic communities were evaluated using 16S ribosomal DNA and nifH amplicon tag pyrosequencing, respectively. Significant heterogeneity in microbial community composition and diazotrophic population structure was observed, which was driven by shifts in the relative importance of temperate vs. subtropical and oceanic vs. coastal ecotypes of Cyanobacteria throughout the inverse estuary. The globally significant unicellular cyanobacterium, UCYN-A 'Candidatus Atelocyano-bacterium thalassa', was the dominant diazotrophic phylotype. Temperature, chlorophyll a and nitrogen availability were all significant drivers of bacterioplankton dynamics within the gulf. These results demonstrate the heterogeneous microbiology of inverse estuaries, indicating that specific abiotic and biotic characteristics select for discrete microbial communities, and that pelagic nitrogen fixation may be important in this temperate oligotrophic system.
Tout, J., Jeffries, T.C., Petrou, K., Tyson, G.W., Webster, N.S., Garren, M., Stocker, R., Ralph, P.J. & Seymour, J.R. 2015, 'Chemotaxis by natural populations of coral reef bacteria', ISME JOURNAL, vol. 9, no. 8, pp. 1764-1777.
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Tout, J., Siboni, N., Messer, L.F., Garren, M., Stocker, R., Webster, N.S., Ralph, P.J. & Seymour, J.R. 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.
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Macreadie, P.I., Trevathan-Tackett, S.M., Skilbeck, C.G., Sanderman, J., Curlevski, N., Jacobsen, G. & Seymour, J.R. 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.
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Carney, R.L., Mitrovic, S.M., Jeffries, T., Westhorpe, D., Curlevski, N. & Seymour, J.R. 2015, 'River bacterioplankton community responses to a high inflow event', Aquatic Microbial Ecology, vol. 75, no. 3, pp. 187-205.
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&copy; 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.
Roudnew, B., Lavery, T.J., Seymour, J.R., Jeffries, T.C. & Mitchell, J.G. 2014, 'Variability in Bacteria and Virus-Like Particle Abundances During Purging of Unconfined Aquifers', Groundwater, vol. 52, no. 1, pp. 118-124.
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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.
Trevathan-Tackett, S.M., Macreadie, P.I., Ralph, P.J. & Seymour, J.R. 2014, 'Detachment and flow cytometric quantification of seagrass-associated bacteria', Journal of Microbiological Methods, vol. 102, pp. 23-25.
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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.
Garren, M., Son, K., Raina, J., Rusconi, R., Menolascina, F., Shapiro, H., Tout, J.A., Bourne, D.G., Seymour, J.R. & Stocker, R. 2014, 'A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals', The ISME Journal, vol. 8, pp. 999-1007.
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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, T.J., Roudnew, B., Seymour, J.R., Mitchell, J.G., 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.
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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.
Laczka, O.F., Labbate, M., Seymour, J.R., Bourne, D.G., Fielder, S.S. & Doblin, M.A. 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.
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Seymour, J.R. 2014, 'A sea of microbes: the diversity and activity of marine microorganisms', Microbiology Australia, vol. 35, no. 4, pp. 183-183.
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Mitchell, J., Seuront, L., Doubell, M., Losic, D., Voelcker, N., Seymour, J.R. & 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.
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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, J.R., 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.
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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, T.C., Roudnew, B., Seymour, J.R., Fitch, A.J., Simons, K.L., Speck, P.G., Newton, K., Brown, M.H. & Mitchell, J.G. 2013, 'Confined aquifers as viral reservoirs', Environmental Microbiology Reports, vol. 5, no. 5, pp. 725-730.
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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.
Dennis, P.G., Seymour, J.R., 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.
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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.
Lavery, T.J., Roudnew, B., Seymour, J.R., Mitchell, J.G. & Jeffries, T.C. 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.
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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.
Smith, R.J., Jeffries, T.C., Roudnew, B., Fitch, A.J., Seymour, J.R., Delpin, M.W., Newton, K., Brown, M.H. & Mitchell, J.G. 2012, 'Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems', Environmental Microbiology, vol. 14, no. 1 Special Issue, pp. 240-253.
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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.
Humphreys, W., Tetu, S., Elbourne, L., Gillings, M., Seymour, J.R., 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.
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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, T.C., Seymour, J.R., Newton, K., Smith, R.J., Seuront, L. & Mitchell, J.G. 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.
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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.
Stocker, R. & Seymour, J.R. 2012, 'Ecology and physics of bacterial chemotaxis in the ocean', Microbiology and Molecular Biology Reviews, vol. 76, no. 4, pp. 792-812.
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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.
Roudnew, B., Seymour, J.R., Jeffries, T.C., Lavery, T.J., Smith, R.J. & Mitchell, J.G. 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.
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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.
Dongen-Vogels, V., Seymour, J.R., Middleton, J.F., Mitchell, J.G. & Seuront, L. 2012, 'Shifts in picophytoplankton community structure influenced by changing upwelling conditions', Estuarine Coastal And Shelf Science, vol. 109, pp. 81-90.
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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 Ni&ntilde;a/El Ni&ntilde;oSouthern 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 Ni&ntilde;o 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.
Seymour, J.R., Doblin, M.A., Jeffries, T.C., Brown, M.V., Newton, K., Ralph, P.J., Baird, M.E. & Mitchell, J.G. 2012, 'Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current', Environmental Microbiology Reports, vol. 4, pp. 548-555.
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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
Humphreys, W., Tetu, S., Elbourne, L., Gillings, M., Seymour, J., 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. SUPPL.1, pp. 59-63.
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.
Marcos, M., Seymour, J.R., Luhar, M., Mitchell, J.G., Durham, W.M., 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.
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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
Jeffries, T.C., Seymour, J.R., Gilbert, J.A., Dinsdale, E.A., Newton, K., Leterme, S.S., Roudnew, B., Smith, R.J., Seuront, L. & Mitchell, J.G. 2011, 'Substrate type determines metagenomic profiles from diverse chemical habitats', PLoS One, vol. 6, no. 9, pp. 1-9.
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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.
Dongen-Vogels, V., Seymour, J.R., Middleton, J.F., Mitchell, J.G. & 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.
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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.
Lavery, T.J., Roudnew, B., Gill, P., Seymour, J.R., 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.
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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, J.R., 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.
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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, J.R., Simo, R., Ahmed, T. & Stocker, R. 2010, 'Chemoattraction to Dimethylsulfoniopropionate in the marine microbial food web', Science, vol. 329, no. 5989, pp. 342-345.
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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.
Seymour, J.R., 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.
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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.
Seuront, L., Leterme, S.C., Seymour, J.R., Mitchell, J.G., Ashcroft, D., Noble, W., Thomson, P.G., Davidson, A.T., van den Enden, R., Scott, F.J., Wright, S.W., Schapira, M., Chapperon, C. & Cribb, N. 2009, 'Role of microbial and phytoplanktonic communities in the control of seawater viscosity off East Antarctica (30-80° E)', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 57, no. 9-10, pp. 877-886.
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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&deg;E and 80&deg;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, J.R., Marcos & Stocker, R. 2009, 'Resource Patch Formation and Exploitation throughout the Marine Microbial Food Web', AMERICAN NATURALIST, vol. 173, no. 1, pp. E15-E29.
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Seymour, J.R., 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.
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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.
Stocker, R., Seymour, J.R., 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.
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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.
Seymour, J.R., Seuront, L., Doubell, M.J. & Mitchel, J.G. 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.
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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.
Seymour, J.R., Seuront, L. & Mitchell, J.G. 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.
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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.
Seymour, J.R., 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.
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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, J.R., Humphreys, W.F. & Mitchell, J.G. 2007, 'Stratification of the microbial community inhabiting an anchialine sinkhole', Aquatic Microbial Ecology, vol. 50, pp. 11-24.
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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.
Seuront, L., Lacheze, C., Doubell, M.J., Seymour, J.R., Dongen-Vogels, V.V., Newton, K., Alderkamp, A.C. & Mitchell, J.G. 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.
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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, J.R., Seuront, L., Doubell, M.J., Waters, R.L. & Mitchell, J.G. 2006, 'Microscale patchiness of virioplankton', Journal of the Marine Biological Association of the United Kingdom, vol. 86, no. 3, pp. 551-561.
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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&cent;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&pound;uence microbial trophodynamics and nutrient cycling in the ocean.
Patten, N.L., Seymour, J.R. & Mitchell, J.G. 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.
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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.
Doubell, M.J., Seuront, L., Seymour, J.R., Patten, N.L. & Mitchell, J.G. 2006, 'High-Resolution Fluorometer for Mapping Microscale Phytoplankton Distributions', Applied and Environmental Microbiology, vol. 72, no. 6, pp. 4475-4478.
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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.
Seymour, J.R., Seuront, L. & Mitchell, J.G. 2005, 'Microscale and small scale temporal dynamics of a coastal planktonic microbial community', Marine Ecology Progress Series, vol. 300, pp. 21-37.
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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, J.R., Mitchell, J.G. & Seuront, L. 2004, 'Microscale heterogeneity in the activity of coastal bacterioplankton communities', Aquatic Microbial Ecology, vol. 35, no. 1, pp. 1-16.
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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, R.L., Mitchell, J.G. & Seymour, J.R. 2003, 'Geostatistical characterisation of centimetre-scale spatial structure of in vivo fluorescence', Marine Ecology Progress Series, vol. 251.