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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 Microbiology Group 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, Plant Functional Biology & Climate Change
Ph D
 
Phone
+61 2 9514 1776
Room
CB07.06.30

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, Springer Netherlands, 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

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'.
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?'.
Seymour, J.R. 2009, 'Cascading resource patch exploitation in a heterogeneous microbial seascape'.
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'.
Newton, K., Jeffries, T.C., Seymour, J.R., Leterme, S., Mitchell, J. & Seuront, L. 2009, 'Impact of salinity on viral morphological diversity'.
Patten, N.L., Seymour, J.R., Seuront, L., Harrison, P. & Mitchell, J.G. 2008, 'Prokaryotic and viral abundances between different coral reef micro-habitats'.
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'.
Stocker, R. & Seymour, J.R. 2008, 'Ecological implications of chemotactic motility'.
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'.
Stocker, R. & Seymour, J.R. 2008, 'Patchiness in the microbial world: insights from microfluidic studies.'.
Doubell, M.J., Seuront, L., Seymour, J.R., Yamazaki, H. & Mitchell, J.G. 2008, 'Microscale structure of a phytoplankton bloom.'.
Stocker, R., Seymour, J.R. & Marcos, M. 2008, 'Microbial life in the ocean.'.
Newton, K., Jeffries, T.C., Seymour, J.R., Leterme, S., Mitchell, J.G. & Seuront, L. 2008, 'Microbial abundance and diversity along a salinity gradient.'.
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.'.
Seymour, J.R., Marcos, M. & Stocker, R. 2007, 'Using microfluidic channels to study microbial behaviour and ecology in a patchy seascape'.
Stocker, R. & Seymour, J.R. 2007, 'Insights into the life of a microbe: a microfluidic approach'.
Seymour, J.R. & Stocker, R. 2006, 'The causes and implications of microscale patchiness in the ocean studied using microfluidics.'.
Stocker, R., Seymour, J.R. & Marcos, M. 2006, 'Microfluidics for studying microbial ecology'.
Humphreys, W.F., Seymour, J.R. & Mitchell, J.G. 2006, 'Stratification of microbial communities in an anchialine sinkhole'.
Seymour, J.R. & Mitchell, J.G. 2004, 'Microscale distributions of bacterioplankton and virus-like particles assessed using flow cytometry'.
Seuront, L., Leterme, S., Seymour, J.R. & Mitchell, J.G. 2004, 'Sampling the sampling unit: A world in a bottle.'.
Mitchell, J.G., Hale, M., Seymour, J.R. & Barbara, G. 2001, 'Early Glimpses of Submicrometer Biological Oceanography.'.
Seymour, J.R. 2000, 'Spatial heterogeneity in bacterioplankton abundance'.
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'.
Mitchell, J.G. & Seymour, J.R. 2000, 'Water column microscale patchiness: Meeting of the tactic and turbulent length scales'.
Seymour, J.R., Mitchell, J.G. & Waters, R. 2000, 'Flow cytometric analysis allows for the measurement of marine microorganisms.'.
Waters, R., Mitchell, J.G., Seymour, J.R. & Pile, A. 2000, 'The use of flow cytometry to characterise the marine planktonic microenvironment'.
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.'.
Seymour, J.R. & Mitchell, J.G. 1998, 'Millimetre-scale distributions of marine bacteria.'.
Mitchell, J.G., Barbara, G., Dillon, L., Pearson, L., Seymour, J.R., Blackburn, N., Bergerson, B. & Luchsinger, R. 1998, 'Motility in marine bacteria'.

Journal articles

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. 2013, National Ground Water Association.
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.
Tout, J., Jeffries, T.C., Webster, N.S., Stocker, R., Ralph, P.J. & Seymour, J.R. 2014, 'Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef', Microbial Ecology, pp. 1-13.
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To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions. 2014 Springer Science+Business Media New York.
Garren, M., Son, K., Raina, J.-.B., Rusconi, R., Menolascina, F., Shapiro, O.H., Tout, J., Bourne, D.G., Seymour, J.R. & Stocker, R. 2014, 'A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals', ISME Journal, vol. 8, no. 5, 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 pathogen's 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. 2014 International Society for Microbial Ecology All rights reserved.
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. *.
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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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Bacteria from the genus Vibrio are a common and environmentally important group of bacteria within coastal environments and include species pathogenic to aquaculture organisms. Their distribution and abundance are linked to specific environmental parameters, including temperature, salinity and nutrient enrichment. Accurate and efficient detection of Vibrios in environmental samples provides a potential important indicator of overall ecosystem health while also allowing rapid management responses for species pathogenic to humans or species implicated in disease of economically important aquacultured fish and invertebrates. In this study, we developed a surface immuno-functionalisation protocol, based on an avidin-biotin type covalent binding strategy, allowing specific sandwich-type detection of bacteria from the Vibrio genus. The assay was optimized on 12 diverse Vibrio strains, including species that have implications for aquaculture industries, reaching detection limits between 7103 to 3104 cells mL-1. Current techniques for the detection of total Vibrios rely on laborious or inefficient analyses resulting in delayed management decisions. This work represents a novel approach for a rapid, accurate, sensitive and robust tool for quantifying Vibrios directly in industrial systems and in the environment, thereby facilitating rapid management responses.
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.J., Seymour, J.R., Smith, R.J. & Mitchell, J.G. 2013, 'Spatially varying complexity of bacterial and viruslike 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 ground - water 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 hetero geneous 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. Copyright Inter-Research 2013.
Smith, R.J., 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 80m 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. 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.
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, 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 (?-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. 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
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.
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. 2012 Author(s).
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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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 90m 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 (3.2105) compared to purged water (1.4105); however, mean VLP abundance (particles/mL) was significantly greater in unpurged water (4.4105) compared to purged water (2.3105). 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. Ground Water Monitoring & Remediation. 2012, National Ground Water Association.
van 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 Nia/El Nio-Southern 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 Nio 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. 2012 Elsevier Ltd.
Seymour, J.R., Doblin, M.A., Jeffries, T.C., Brown, M.V., Newton, K., Ralph, P.J., Baird, M. & Mitchell, J.G. 2012, 'Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current', Environmental Microbiology Reports, vol. 4, no. 5, 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. 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.
Marcos, Seymour, J.R., Luhar, M., Durham, W.M., Mitchell, J.G., 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 "swirls" when agitated. Here, we rationalize the mechanism behind this phenomenon and show that the same process may affect the propagation of light through the upper ocean. Analogous to the shaken test tubes, the ocean can be characterized by intense fluid motion and abundant microorganisms. We demonstrate that the swirl patterns arise when elongated microorganisms align preferentially in the direction of fluid flow and alter light scattering. Using a combination of experiments and mathematical modeling, we find that this phenomenon can be recurrent under typical marine conditions. Moderate shear rates (0.1 s-1) can increase optical backscattering of natural microbial assemblages by more than 20%, and even small shear rates (0.001 s-1) can increase backscattering from blooms of large phytoplankton by more than 30%. These results imply that fluid flow, currently neglected in models of marine optics, may exert an important control on light propagation, influencing rates of global carbon fixation and how we estimate these rates via remote sensing.
Jeffries, T.C., Seymour, J.R., Gilbert, J.A., Dinsdale, E.A., Newton, K., Leterme, S.S.C., 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.
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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. 2011 Jeffries et al.
Van 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 spacetime 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 winterearly 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. The Author 2011.
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, p. e25173.
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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.
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. 2010, '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 30E and 80E 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. 2009 Elsevier Ltd.
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.M. & 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. We applied a microfluidic chemotaxis assay to study the chemotactic response of 3 marine bacterial isolates (Pseudoalteromonas haloplanktis, Vibrio alginolyticus and Silicibacter sp. TM1040) to the chemical products of Synechococcus elongatus and Prochlorococcus marinus MED 4Ax. In the ocean, chemical products from these cyanobacteria may be released into the water column via extracellular exudation or cell lysis. Strong and rapid chemotactic responses by all 3 bacterial strains occurred in reaction to the Synechococcus products. P. haloplanktis cells exhibited the strongest attraction, accumulating within the chemoattractant band in concentrations of up to 9-fold above background levels. Positive chemotaxis to Prochlorococcus chemical products also occurred, with P. haloplanktis and Silicibacter sp. TM1040 exhibiting the strongest responses. These observations indicate that marine bacteria can exhibit behavioural responses to the chemical products of Synechococcus and Prochlorococcus, which may support ecological associations between these important populations of marine prokaryotes in the environment. Inter-Research 2010.
Seymour, J.R., Sim, R., Ahmed, T. & Stocker, R. 2010, 'Chemoattraction to dimethylsulfoniopropionate throughout 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 bacteria-algae associations with potential implications for harmful algal bloom dynamics.
Seymour, J.R., Marcos & Stocker, R. 2009, 'Resource patch formation and exploitation throughout the marine microbial food web', American Naturalist, vol. 173, no. 1.
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Exploitation of microscale (?m-mm) resource patches by planktonic microorganisms may influence oceanic trophodynamics and nutrient cycling. However, examinations of microbial behavior within patchy microhabitats have been precluded by methodological limitations. We developed a microfluidic device to generate microscale resource patches at environmentally realistic spatiotemporal scales, and we examined the exploitation of these patches by marine microorganisms. We studied the foraging response of three sequential levels of the microbial food web: a phytoplankton (Dunaliella tertiolecta), a heterotrophic bacterium (Pseudoalteromonas haloplanktis), and a phagotrophic protist (Neobodo designis). Population-level chemotactic responses and single-cell swimming behaviors were quantified. Dunaliella tertiolecta accumulated within a patch of NH4+, simulating a zooplankton excretion, within 1 min of its formation. Pseudoalteromonas haloplanktis cells also exhibited a chemotactic response to patches of D. tertiolecta exudates within 30 s, whereas N. designis shifted swimming behavior in response to bacterial prey patches. Although they relied on different swimming strategies, all three organisms exhibited behaviors that permitted efficient and rapid exploitation of resource patches. These observations imply that microscale nutrient patchiness may subsequently trigger the sequential formation of patches of phytoplankton, heterotrophic bacteria, and protozoan predators in the ocean. Enhanced uptake and predation rates driven by patch exploitation could accelerate carbon flux through the microbial loop. 2009 by The University of Chicago. All rights reserved.
Seymour, J.R., Ahmed, T., Marcos & Stocker, R. 2008, 'A microfluidic chemotaxis assay to study microbial behavior in diffusing nutrient patches', Limnology and Oceanography: Methods, vol. 6, no. SEPTEMBER, pp. 477-488.
The nutrient environment experienced by planktonic microorganisms is patchy at spatiotemporal scales commensurate with their motility (?m - cm), and the efficiency with which chemotactic microbes can exploit this heterogeneous seascape influences trophodynamics and nutrient cycling rates in aquatic environments. Yet, methodological limitations have largely prevented direct examinations of microbial behavior within heterogeneous microenvironments. We used soft lithography to fabricate a microfluidic-based chemotaxis assay to study the foraging response of aquatic microbes to diffusing microscale nutrient patches. The transparency, biocompatibility, and simplicity of microfluidic devices make them ideally suited for microbial ecology studies. A microinjector was used to create a 300 ?m-wide nutrient band, simulating a pulse release of solutes. The chemotactic response of microbes to the diffusing patch was measured at the population and single-cell level. In contrast to traditional chemotaxis assays, this technique permits the assessment and quantification of chemotaxis toward a potential attractant in real time, enabling rapid screening of multiple chemicals. Furthermore, detailed information on chemotactic behavior can be obtained by tracking individual organisms. Here, we applied this microassay to study the chemotactic behavior of a range of aquatic microorganisms, including three marine bacterial isolates, a species of phagotrophic flagellate, and a species of phytoplankton. Each organism exhibited a rapid chemotactic response to a variety of chemical compounds, suggesting that many marine microbes are adapted to life within patchy microenvironments. The chemotaxis assay described here was found to be a flexible platform for studying both the specific case of microbes foraging within patchy habitats and as a broadly applicable tool for rapidly assessing and quantifying microbial chemotaxis. 2008, by the American Society of Limnology and Oceanography, Inc.
Stocker, R., Seymour, J.R., Samadani, A., Hunt, D.E. & Polz, M.F. 2008, 'Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches', Proceedings of the National Academy of Sciences of the United States of America, 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. Moreover, the chemotactic response of P. haloplanktis was >10 times faster than the classic chemotaxis model Escherichia coli, leading to twice the nutrient exposure. We demonstrate that such rapid response allows P. haloplanktis to colonize nutrient plumes for realistic particle sinking speeds, with up to a 4-fold nutrient exposure compared with nonmotile cells. These results suggest that chemotactic swimming strategies of marine bacteria in patchy nutrient seascapes exert strong influence on carbon turnover rates by triggering the formation of microscale hot spots of bacterial productivity. 2008 by The National Academy of Sciences of the USA.
Seymour, J.R., Seuront, L., Doubell, M.J. & Mitchell, 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. 2008 Elsevier Ltd. All rights reserved.
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. Two populations of viruses were correlated to the phytoplankton and low DNA (LDNA) bacteria, and each exhibited elevated concentrations within 0.5 cm of the SWI. In March 2004, microscale distributions of O2 and nutrients were more homogenous than in December 2003, and dissimilar microbial community structure and patterns were observed above the SWI. The patterns observed here support the prediction that benthic processes can strongly influence the ecology of planktonic communities in the overlaying water, and provide further evidence for the existence of microscale variability amongst communities of aquatic microorganisms. 2007 Elsevier Ltd. All rights reserved.
Seymour, J.R., Marcos & Stocker, R. 2007, 'Chemotactic response of marine micro-organisms to micro-scale nutrient layers', Journal of Visualized Experiments, no. 4.
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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. We have also shown that up to moderate shear rates, marine bacteria are able to fight the flow and swim through their environment at their own accord. However, beyond a threshold high shear level, bacteria are aligned in the shear flow and are less capable of swimming without disturbance from the flow. Microfluidics represents a novel and inexpensive approach for studying aquatic microbial ecology, and due to its suitability for accurately creating realistic flow fields and substrate gradients at the microscale, is ideally applicable to examinations of microbial behaviour at the smallest scales of interaction. We therefore suggest that microfluidics represents a valuable tool for obtaining a better understanding of the ecology of microorganisms in the ocean. 2007 Journal of Visualized Experiments.
Seymour, J.R., Humphreys, W.F. & Mitchell, J.G. 2007, 'Stratification of the microbial community inhabiting an anchialine sinkhole', Aquatic Microbial Ecology, vol. 50, no. 1, 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 subpopulations 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. Inter-Research 2007.
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', 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. 2007 Springer Science+Business Media, Inc.
Seymour, J.R., Marcos & Stocker, R. 2007, 'Chemotactic response of marine micro-organisms to micro-scale nutrient layers.', J Vis Exp, no. 4, p. 203.
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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. We have also shown that up to moderate shear rates, marine bacteria are able to fight the flow and swim through their environment at their own accord. However, beyond a threshold high shear level, bacteria are aligned in the shear flow and are less capable of swimming without disturbance from the flow. Microfluidics represents a novel and inexpensive approach for studying aquatic microbial ecology, and due to its suitability for accurately creating realistic flow fields and substrate gradients at the microscale, is ideally applicable to examinations of microbial behaviour at the smallest scales of interaction. We therefore suggest that microfluidics represents a valuable tool for obtaining a better understanding of the ecology of microorganisms in the ocean.
Seymour, J.R., Seuront, L., Doubell, M., 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 profiles 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 (P<0.01). 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 influence 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. Copyright 2006, American Society for Microbiology. All Rights Reserved.
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.
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. Fundamentally different patterns, in the extent of temporal variability and coupling between the different microbial populations, were observed between the microscale and small-scale studies, suggesting that intrinsically different mechanisms and responses occurred independently and simultaneously at the different temporal scales. Furthermore, the variability in microbial parameters observed over these short temporal scales indicates the profound importance of microscale and small-scale processes in the ecology of communities of marine microorganisms. Inter-Research 2005.
Seymour, J.R., Patten, N.L., Bourne, D.G. & Mitchell, J.G. 2005, 'Spatial dynamics of virus-like particles and heterotrophic bacteria within a shallow coral reef system', Marine Ecology Progress Series, vol. 288, no. 1, p. 8.
Variations in the abundance and community characteristics of virus-like particles (VLP) and heterotrophic bacteria within a shallow, near-shore coral reef were determined using flow cytometric analysis. Mean concentrations of 6.5 105 and 1.3 105 ml1 were observed for VLP and bacterioplankton, respectively, although concentrations of both populations varied significantly (p < 0.05) between 4 distinct reef water types. Significant (p < 0.05) variability in the percentage of high DNA (HDNA) bacteria, applied here as an estimate of the proportion of active bacterial cells, and the virus:bacteria ratio (VBR) was also observed between different reef water types. Microscale profiles were taken in the 12 cm layer of water directly above the surface of coral colonies to determine the small-scale spatial relationships between coral colonies and planktonic microbial communities. Across these profiles, mean changes of 2- and 3.5-fold were observed for bacterioplankton and VLP communities, respectively, with VLP abundance positively correlated to bacteria in 75% of profiles. Bacterial and VLP abundance, percentage of HDNA bacteria, and VBR all generally exhibited increasing trends with proximity to the coral surface. VLP abundance was significantly higher (p < 0.05) in the 4 cm closest to the coral surface, and the VBR was higher at the coral surface than in any other zone. The patterns observed here indicate that VLP represent an abundant and dynamic community within coral reefs, are apparently coupled to the spatial dynamics of the bacterioplankton community, and may consequently significantly influence nutrient cycling rates and food-web structure within coral reef ecosystems.
Seymour, J.R., Patten, N., Bourne, D.G. & Mitchell, J.G. 2005, 'Spatial dynamics of virus-like particles and heterotrophic bacteria within a shallow coral reef system', Marine Ecology Progress Series, vol. 288, pp. 1-8.
Variations in the abundance and community characteristics of virus-like particles (VLP) and heterotrophic bacteria within a shallow, near-shore coral reef were determined using flow cytometric analysis. Mean concentrations of 6.5 105 and 1.3 105 ml-1 were observed for VLP and bacterioplankton, respectively, although concentrations of both populations varied significantly (p < 0.05) between 4 distinct reef water types. Significant (p < 0.05) variability in the percentage of high DNA (HDNA) bacteria, applied here as an estimate of the proportion of active bacterial cells, and the virus:bacteria ratio (VBR) was also observed between different reef water types. Microscale profiles were taken in the 12 cm layer of water directly above the surface of coral colonies to determine the small-scale spatial relationships between coral colonies and planktonic microbial communities. Across these profiles, mean changes of 2- and 3.5-fold were observed for bacterioplankton and VLP communities, respectively, with VLP abundance positively correlated to bacteria in 75% of profiles. Bacterial and VLP abundance, percentage of HDNA bacteria, and VBR all generally exhibited increasing trends with proximity to the coral surface. VLP abundance was significantly higher (p < 0.05) in the 4 cm closest to the coral surface, and the VBR was higher at the coral surface than in any other zone. The patterns observed here indicate that VLP represent an abundant and dynamic community within coral reefs, are apparently coupled to the spatial dynamics of the bacterioplankton community, and may consequently significantly influence nutrient cycling rates and food-web structure within coral reef ecosystems. Inter-Research 2005.
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.
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 mm. 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.
Seymour, J.R., Mitchell, J.G., Pearson, L. & Waters, R.L. 2000, 'Heterogeneity in bacterioplankton abundance from 4.5 millimetre resolution sampling', Aquatic Microbial Ecology, vol. 22, no. NA, pp. 143-153.
A suite of pneumatically operated sampling devices was employed to investigate distributional patterns of marine bacteria at the millimetre scale.
Seymour, J.R., Mitchell, J.G., Pearson, L. & Waters, R.L. 2000, 'Heterogeneity in bacterioplankton abundance from 4.5 millimetre resolution sampling', Aquatic Microbial Ecology, vol. 22, no. 2, pp. 143-153.
A suite of pneumatically operated sampling devices was employed to investigate distributional patterns of marine bacteria at the millimetre scale. Spatial heterogeneity in bacterial abundance, or patchiness, was expressed as a coefficient of variation, and ranged from 5.5 to 75 %. Discrete regions of enhanced bacterial abundance, as well as clear gradients in abundance across entire sample arrays were observed, with changes in bacterial abundance of up to 16-fold observed across a distance of 32 mm. The role of turbulence in influencing bacterial distribution patterns was examined in a series of laboratory experiments. Levels of heterogeneity were found to be up to 6.5 times higher in stirred than unstirred water samples under laboratory conditions. The gradients in bacterial abundance observed here suggest that small-scale processes operate within the marine microenvironment to create and maintain spatial structure in the bacterioplankton community. We suggest that previously hypothesised nanoscale 'hot spots' and microzones exist only as maxima within a continuously variable distribution of bacteria within the marine environment.