Estuarine Microbial Community Research Articles

Flooding promotes the coalescence of microbial community in estuarine habitats

Microbial community coalescence describes the mixing of microbial communities and their integration with the surrounding environment, which is common in natural ecosystems and has potential impacts on ecological processes. However, few studies have focused on microbial community coalescence between different habitats in estuarine regions. In this study, we comprehensively investigated the environmental characteristics and bacterial community changes of different habitats (water body (Water), subtidal sediments (SS) and intertidal salt marsh sediments (SM)) in Luanhe estuary during flood and normal flow periods. The results showed that flood event significantly reduced the salinity of the estuarine habitats, changed the nutrient structure and intensified the eutrophication of estuarine water. By calculating the proportion of overlapping groups and applying the ‘FEAST’ algorithm, we revealed that flood event facilitated the migration of bacterial communities along alternative pathways across habitats, markedly enhanced the cross-habitat mobility of bacterial communities, which underscores the pivotal role of flood event in driving bacterial community coalescence. Flood-induced community coalescence not only increased the α-diversity of bacterial communities within habitats, but also increased the proportion of overlapped species between habitats, ultimately leading to homogenization between habitats. Canonical correlation analysis combined co-occurrence network analysis revealed that flood event attenuated the role of environmental filtration in microbial assembly, while increased the impact of dispersal processes and intensified interspecific competition among microorganisms, led to the change of keystone species and reduced the complexity and stability of bacterial communities. In conclusion, this study demonstrates the complex effects of flood events on estuarine microbial communities from the perspective of multi-habitat interactions in the estuary, and emphasizes the key role of river hydrodynamic conditions in facilitating the coalescence of estuarine microbial communities. We look forward to further attention and research on estuarine microbial coalescence, which will provide new insights into assessing the stability and resilience of estuarine ecosystems under flood challenges and the sustainable management of estuarine wetlands.

Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary

BackgroundMicrobial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the “salt-in” strategy, involving inorganic ion uptake, or the “salt-out” strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem.ResultsHere, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline—specific to low-, intermediate-, or high-salinity—based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the “inorganic ion transport and metabolism” COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the “salt-in” strategy, three to the “salt-out” strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K+ transporter related to the “salt-in” strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla.ConclusionsWe demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the “salt-in” strategy mediated by Trk-type K+ transporters for microorganisms thriving under osmotic stress in the short residence-time estuary.22YT9hkSS5Zn-gk-qyndrEVideo

Microbial community assembly responses to polycyclic aromatic hydrocarbon contamination across water and sediment habitats in the Pearl River Estuary

Along with rapid urbanization and intensive human activities, polycyclic aromatic hydrocarbon (PAH) pollution in the Pearl River Estuary (PRE) and its effects on the microbial community have attracted extensive attention. However, the potential and mechanism of microbial degradation of PAHs across water and sediment habitats remain obscure. Herein, the estuarine microbial community structure, function, assembly process and co-occurrence patterns impacted by PAHs were comprehensively analyzed using environmental DNA-based approaches. The contamination and distribution of PAHs were jointly affected by anthropogenic and natural factors. Some of the keystone taxa were identified as PAH-degrading bacteria (i.e., genera Defluviimonas, Mycobacterium, families 67–14, Rhodobacteraceae, Microbacteriaceae and order Gaiellales in water) or biomarkers (i.e., Gaiellales in sediment) that were significantly correlated with PAH levels. The proportion of deterministic process in the high PAH-polluted water (76%) was much higher than that in the low pollution area (7%), confirming the significant effect of PAHs on the microbial community assembly. In sediment, the communities with high phylogenetic diversity demonstrated a great extent of niche differentiation, exhibited a stronger response to environmental variables and were strongly influenced by deterministic processes (40%). Overall, deterministic and stochastic processes are closely related to the distribution and mass transfer of pollutants, and substantially affect the biological aggregation and interspecies interaction within communities in the habitats.

Network and machine learning analyses of estuarine microbial communities along a freshwater-marine mixed gradient

Microbial communities are important elements in the marine environment, contributing to nutrient cycling and biogeochemical processes. Estuaries comprise environments exhibiting characteristics from freshwater to marine, leading to distinct microbial communities across this environmental gradient. Here, we examine the spatial dynamics of microbial communities in Macquarie Harbour, an estuarine system on the West coast of Tasmania, Australia. Water was sampled along the estuary to explore the structure and composition of the microbial communities using 16S/18S rRNA gene amplicon sequencing. Multivariate analyses showed environmental variables and community compositions varying along a longitudinal (river to adjacent ocean) gradient at the surface. In the Harbour, differences in the microbial community were observed between surface (0–1 m) and intermediate depths (4.5–11 m depth). The results of differential abundance, network and Partial Least Square analyses suggest that Macquarie Harbour is a mixing zone, where the distributions of archaeal, bacterial and eukaryotic communities are influenced by oceanic and riverine inputs. These results provide critical insights into the Macquarie Harbour environment and the importance of understanding the role of microbial communities for similar systems elsewhere.

Ecological Impacts of Aged Freshwater Biofilms on Estuarine Microbial Communities Elucidated Through Microcosm Experiments: A Microbial Invasion Perspective.

Inadvertent introductions of alien species via biofilms as a vector released through ballast water are of environmental importance, yet their consequences are not much known. In the present study, biofilm communities developed in an inland freshwater port under in situ and dark conditions were subjected to long-term dark incubations. Subsequently, the impact of these aged biofilms as vectors on estuarine water column communities were evaluated using microcosm experiments in the laboratory. Variations in biofilm and planktonic microbial communities were quantified using quantitative PCR.Upon prolonged dark incubation, a shift in bacterial diversity with an increase in tolerant bacterial communities better adapted to stress was observed. Actinobacteria were the dominant taxa in both aged biofilms upon dark incubations. The laboratory studies indicated that on exposure of these biofilms to estuarine water, resuscitation of Vibrio alginolyticus, V. parahaemolyticus, and V. cholerae from a dormant state existing in these biofilms to culturable form was observed. Moreover, the results revealed that both the biofilm types can pose a threat to the environment, but the degree of risk can be attributed to the imbalance caused by significant changes in the surrounding estuarine microbial communities. Consequently, this may result in either proliferation or decline of some genera with different metabolic potential and resuscitation of pathogenic forms not present earlier, thereby influencing the ecology of the environment. Quantifying these effects in the field using biofilm metagenomes with an emphasis on virulent species and understanding traits that enable them to adapt to changing environments is a way forward.

Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary

Microbes (e.g., bacteria and archaea) are indispensable components for the key biological processes of estuarine ecosystems and three main habitats (sediment, particle, and water) are harboring diverse estuarine microbes. However, we still know little about how the microbial community structures, potential keystone species, and network properties change among these three habitats in estuarine ecosystems. In this study, we collected size-fractioned water and sediment samples from the Pearl River Estuary to reveal their microbial diversity, community structures, network properties, and potential keystone taxa. We found that the sediment microbial community was remarkably more diverse than particle-attached (PA) and free-living (FL) communities, whereas its ecological network was less complex in terms of node distance and connectivity. TOC was determined as the main driver of sediment community, while the PA and FL communities were predominantly shaped by NO2−, non-ionic ammonia (NH) and pH. Among the bulk water, there were no significant differences between PA and FL communities in diversity, community structure, and network complexity. However, the PA community was more susceptible to metal elements, suggesting their higher level of involvement in physiological metabolism. Potential keystone taxa among community networks were taxonomically divergent in three habitats. Specifically, Synechococcales (Cyanobacteria) and Actinomarinales (Actinobacteria) exclusively served as the module-hubs in FL network, while members from phylum Proteobacteria and Bacteroidetes were the module-hubs and connectors in PA network. Potential keystone taxa in sediment network were more diverse and covered 9 phyla, including the only archaeal lineage Bathyarchaeia (Crenarchaeota). Overall, our study provided more detailed information about estuarine microbial communities in three habitats, especially the potential keystone species, which provided new perspectives on evaluating further effects of anthropogenic disturbances on estuarine microbes and facilitated the environment monitoring based on microbial community.

Study of Heavy Metals and Microbial Communities in Contaminated Sediments Along an Urban Estuary

Estuarine sediments are increasingly contaminated by heavy metals as a result of urbanization and human activities. Continuous multi-heavy metal accumulation in the ecosystem can provoke new effects on top of the complex environmental interactions already present in estuarine ecosystems. It is important to study their integrated influence on imperative microbial communities to reflect on the environmental and ecological risks they may impose. Inductively coupled plasma optical emission spectroscopy analysis for five metals Cd, Cr, Cu, Pb, and Zn showed that Cr and Cu concentrations in intertidal sediments of the urbanized Yangtze River estuary in China have consistently exceeded respective threshold effect concentration (TEC) levels. The geo-accumulation and potential ecological risk index results of the five metals showed that all sampling sites were weakly to moderately polluted, and at considerable to high ecological risk, respectively. Redundancy and correlation analyses showed that Zn followed by Cr in the ecosystem were explanatory of the shifts in recorded microbial community structures. However, the spatial variation in metal concentrations did not correspond to the selection of metal resistance genes (MRGs). Unlike many other dominant bacterial taxa, most of the sulfate-reducing bacteria (SRB) and associated sulfate respiration as the dominant microbially contributed ecological function were found to negatively correlate with Zn and total heavy metal pollution. Zn concentration was proposed to be a potent indicator for heavy metal pollution-associated microbial community compositional shifts under urbanized estuarine conditions. The associations between heavy metals and estuarine microbial communities in this study demonstrate the influence of heavy metals on microbial community structure and adaptations that is often overshadowed by environmental factors (i.e., salinity and nutrients).

Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance.

Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2 O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2 O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.

Keystone species of coastal ecosystems from the Bay of Biscay

Estuarine and coastal ecosystems play a fundamental role in human activities. Since millions of people depend on the numerous resources they offer (i.e., fisheries, transportation, and recreational activities), these ecosystems are also exposed to a high anthropogenic pressure. In order to better monitor and regulate such pressures, it is critical to improve our understanding of the functioning of these ecosystems. This is especially important for microorganisms, considering, for instance, their important roles in biogeochemical cycles. In this study we investigate estuarine and coastal microbial communities along the coast of the Basque Country using eDNA metabarcoding of bacterioplankton and microbenthos samples along a time series, from locations that present different degrees of disturbance. Metabarcoding of the 16S and 18S rRNA gene was carried out, and the OTU and taxa tables generated were used to reconstruct ecological networks, representing potential biological interactions. These ecological networks were used to identify on one hand the species that play a major role in the maintenance of the whole community structure (keystones), and on the other, complex network modules affected by environmental impacts. Here, we define keystone taxa as those that presented the highest ratio between the degree of connectivity (number of associations they established within the network) and their relative abundance. The underlying aim of this study is to develop novel “bioindicators” based on taxa that are both sensitive to impacts and important for community structure. Results of two seawater communities, one from offshore waters and the other from the coast, showed similar bacterial composition at family level, dominated by Flavobacteraceae and Rhodobacteraceae. Nevertheless, their ecological network properties differed strongly: for a similar number of taxa that established associations, the conectance was similar in both communities, but the number of associations in the coastal community was twice as high as for the offshore one, resulting in a higher modularity. Identified keystone taxa were taxonomically different between both communities: those from the coastal community belonged to Protobacteria, Bacteroidetes, Firmicutes, and Fusobacteria phyla, while the keystones from the offshore community belonged to Proteobacteria, Actinobacteria, Chloroflexi, Thaumarchaeota, PAUC34f and Verrucomicrobia. Moreover, we identified “connector” taxa that presented the highest values of betweenness centrality. These taxa, without having a high degree of connectivity, may be important for the interaction structure because they connect modules, i.e., highly connected subnetworks within the whole network. Further, hierarchical clustering was performed to identify seasonal trends and to better understand the associations retrieved. Taxa with different seasonal preference often grouped together in the same modules, which indicates that modularity was not caused primarily by seasonality.

Community, Distribution, and Ecological Roles of Estuarine Archaea.

Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.

Evidence of Mercury Methylation and Demethylation by the Estuarine Microbial Communities Obtained in Stable Hg Isotope Studies

Microbial activity is a critical factor controlling methylmercury formation in aquatic environments. Microbial communities were isolated from sediments of two highly mercury-polluted areas of the Tagus Estuary (Barreiro and Cala do Norte) and differentiated according to their dependence on oxygen into three groups: aerobic, anaerobic, and sulphate-reducing microbial communities. Their potential to methylate mercury and demethylate methylmercury was evaluated through incubation with isotope-enriched Hg species (199HgCl and CH3201HgCl). The results showed that the isolated microbial communities are actively involved in methylation and demethylation processes. The production of CH3199Hg was positively correlated with sulphate-reducing microbial communities, methylating up to 0.07% of the added 199Hg within 48 h of incubation. A high rate of CH3201Hg degradation was observed and >20% of CH3201Hg was transformed. Mercury removal of inorganic forms was also observed. The results prove the simultaneous occurrence of microbial methylation and demethylation processes and indicate that microorganisms are mainly responsible for methylmercury formation and accumulation in the polluted Tagus Estuary.

The Effect of Increased Loads of Dissolved Organic Matter on Estuarine Microbial Community Composition and Function.

Increased river loads are projected as one of the major consequences of climate change in the northern hemisphere, leading to elevated inputs of riverine dissolved organic matter (DOM) and inorganic nutrients to coastal ecosystems. The objective of this study was to investigate the effects of elevated DOM on a coastal pelagic food web from the coastal northern Baltic Sea, in a 32-day mesocosm experiment. In particular, the study addresses the response of bacterioplankton to differences in character and composition of supplied DOM. The supplied DOM differed in stoichiometry and quality and had pronounced effects on the recipient bacterioplankton, driving compositional changes in response to DOM type. The shifts in bacterioplankton community composition were especially driven by the proliferation of Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Alpha- and Betaproteobacteria populations. The DOM additions stimulated protease activity and a release of inorganic nutrients, suggesting that DOM was actively processed. However, no difference between DOM types was detected in these functions despite different community compositions. Extensive release of re-mineralized carbon, nitrogen and phosphorus was associated with the bacterial processing, corresponding to 25–85% of the supplied DOM. The DOM additions had a negative effect on phytoplankton with decreased Chl a and biomass, particularly during the first half of the experiment. However, the accumulating nutrients likely stimulated phytoplankton biomass which was observed to increase towards the end of the experiment. This suggests that the nutrient access partially outweighed the negative effect of increased light attenuation by accumulating DOM. Taken together, our experimental data suggest that parts of the future elevated riverine DOM supply to the Baltic Sea will be efficiently mineralized by microbes. This will have consequences for bacterioplankton and phytoplankton community composition and function, and significantly affect nutrient biogeochemistry.

Effects of the invasive clam Corbicula fluminea (Müller, 1774) on an estuarine microbial community

The Asian clam Corbicula fluminea (Müller, 1774) is well recognized for its invasive behavior and high ecological and economic impacts, being classified as one of the 100 worst invasive alien species (IAS) in Europe. In this study, we performed a manipulative experiment under natural conditions to assess the effects of C. fluminea on sediments biochemistry and on the structure of an estuarine microbial (fungi and bacteria) community. We placed 5 treatments (control, rock, closed, live and open) for 2months in the Minho estuary (NW Iberian Peninsula). No differences were detected between treatments regarding the values of carbon (C), nitrite (NO2−), ammonium (NH4+), phosphate (PO43−) and calcium (Ca) in the sediments; however, potassium (K) had higher values in the open treatment. Furthermore, we found that the presence of live C. fluminea stimulated fungal biomass (but not diversity) and bacterial diversity. Bioturbation activities by C. fluminea are possibly the main mechanism explaining these results; however, other factors such as the presence of other macroinvertebrate species and/or production of feces and pseudofeces by C. fluminea cannot be excluded. To our knowledge, this is the first manipulative experiment under natural conditions that clearly shows the effects of C. fluminea on an estuarine microbial community. Given the widespread distribution of this IAS and the paucity of quantitative assessments of invasive bivalves' effects on microbial communities, it will be important that future studies further investigate these processes.

The Role of Heterotrophic Microbial Communities in Estuarine C Budgets and the Biogeochemical C Cycle with Implications for Global Warming: Research Opportunities and Challenges.

Estuaries are among the most productive and economically important marine ecosystems at the land-ocean interface and contribute significantly to exchange of CO2 with the atmosphere. Estuarine microbial communities are major links in the biogeochemical C cycle and flow of C in food webs from primary producers to higher consumers. Considerable attention has been given to bacteria and autotrophic eukaryotes in estuarine ecosystems, but less research has been devoted to the role of heterotrophic eukaryotic microbes. Current research is reviewed here on the role of heterotrophic eukaryotic microbes in C biogeochemistry and ecology of estuaries, with particular attention to C budgets, trophodynamics, and the metabolic fate of C in microbial communities. Some attention is given to the importance of these processes in climate change and global warming, especially in relation to sources and sinks of atmospheric CO2 , while also documenting the current paucity of research on the role of eukaryotic microbes that contribute to this larger question of C biogeochemistry and the environment. Some recommendations are made for future directions of research and opportunities of applying newer technologies and analytical approaches to a more refined analysis of the role of C in estuarine microbial community processes and the biogeochemical C cycle.

Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment

Little knowledge is available about the potential impact of commercial silver nanoparticles (Ag-NPs) on estuarine microbial communities. The Hugli river estuary, India, is susceptible to heavy metals pollution through boat traffic, and there is the potential for Ag-NP exposure via effluent discharged from ongoing municipal and industrial activities located in close proximity. This study investigated the effects of commercial Ag-NPs on native microbial communities in estuarine sediments collected from five stations, using terminal restriction fragment length polymorphism (T-RFLP) technique. An increase in the number of bacteria in consortium in sediments was observed following exposure to Ag-NPs. In general microbial communities may be resistant in estuarine systems to the antimicrobial effects of commercial Ag-NPs, but key microorganisms, such as Pelobacter propionicus, disappeared following exposure to Ag-NPs. In conclusion, the T-RFLP analysis indicated that Ag-NPs have the potential to shape estuarine sediment bacterial community structure.

Shifts in the metabolic function of a benthic estuarine microbial community following a single pulse exposure to silver nanoparticles

The increasing use of silver nanoparticles (AgNPs) as a biocidal agent and their potential accumulation in sediments may threaten non-target natural environmental bacterial communities. In this study a microcosm approach was established to investigate the effects of well characterized OECD AgNPs (NM-300) on the function of the bacterial community inhabiting marine estuarine sediments (salinity 31‰). The results showed that a single pulse of NM-300 AgNPs (1 mg L−1) that led to sediment concentrations below 6 mg Ag kg−1 dry weight inhibited the bacterial utilization of environmentally relevant carbon substrates. As a result, the functional diversity changed, but recovered after 120 h under the experimental conditions. This microcosm study suggests that AgNPs under environmentally relevant experimental conditions can negatively affect bacterial function and provides an insight into the understanding of the bacterial community response and resilience to AgNPs exposure, important for informing relevant regulatory measures.

Estuarine sediment hydrocarbon-degrading microbial communities demonstrate resilience to nanosilver

Little is currently known about the potential impact of silver nanoparticles (AgNPs) on estuarine microbial communities. The Colne estuary, UK, is susceptible to oil pollution through boat traffic, and there is the potential for AgNP exposure via effluent discharged from a sewage treatment works located in close proximity. This study examined the effects of uncapped AgNPs (uAgNPs), capped AgNPs (cAgNPs) and dissolved Ag2SO4, on hydrocarbon-degrading microbial communities in estuarine sediments. The uAgNPs, cAgNPs and Ag2SO4 (up to 50 mg L−1) had no significant impact on hydrocarbon biodegradation (80–92% hydrocarbons were biodegraded by day 7 in all samples). Although total and active cell counts in oil-amended sediments were unaffected by silver exposure; total cell counts in non-oiled sediments decreased from 1.66 to 0.84 × 107 g−1 dry weight sediment (dws) with 50 mg L−1 cAgNPs and from 1.66 to 0.66 × 107 g−1 dws with 0.5 mg L−1 Ag2SO4 by day 14. All silver-exposed sediments also underwent significant shifts in bacterial community structure, and one DGGE band corresponding to a member of Bacteroidetes was more prominent in non-oiled microcosms exposed to 50 mg L−1 Ag2SO4 compared to non-silver controls. In conclusion, AgNPs do not appear to affect microbial hydrocarbon-degradation but do impact on bacterial community diversity, which may have potential implications for other important microbial-mediated processes in estuaries.

Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay.

Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders of magnitude, followed by taxon-specific quantitation of isotopic incorporation using NanoSIMS analysis of high-density microarrays. The resulting data revealed that trophic response to AA availability falls along a continuum between copiotrophy and oligotrophy, and high and low activity. To illustrate strategies along this continuum more simply, we statistically categorized microbial taxa among three trophic types, based on their incorporation responses to increasing resource concentration. The data indicated that taxa with copiotrophic-like resource use were not necessarily the most active, and taxa with oligotrophic-like resource use were not always the least active. Two of the trophic strategies were not randomly distributed throughout a 16S rDNA phylogeny, suggesting they are under selective pressure in this ecosystem and that a link exists between evolutionary relatedness and substrate affinity. The diversity of strategies to adapt to differences in resource availability highlights the need to expand our understanding of microbial interactions with organic matter in order to better predict microbial responses to a changing environment.

Metabolic Responses of Estuarine Microbial Communities to Discharge of Surface Runoff and Groundwater from Contrasting Landscapes

Groundwater discharge is increasingly recognized as a significant source of nutrient input to coastal waters, relative to surface water inputs. There remains limited information, however, on the extent to which nutrients and organic matter from each of these two flowpaths influence the functional responses of coastal microbial communities. As such, this study determined dissolved organic carbon (DOC) and nutrient concentrations of surface water runoff and groundwater from both an urbanized and a relatively pristine forested drainage basin near Myrtle Beach, South Carolina, and quantified the changes in production rates and biomass of phytoplankton and bacterioplankton in response to these inputs during two microcosm incubation experiments (August and October, 2011). Rainwater in the urbanized basin that would otherwise enter the groundwater appeared to be largely rerouted into the surface flowpath by impervious surfaces, bypassing ecosystem buffers and filtration mechanisms. Surface runoff from the developed basin was most enriched in nutrients and DOC and yielded the highest production rates of the various source waters upon addition to coastal waters. The metabolic responses of phytoplankton and bacterioplankton were generally well predicted as a function of initial chemical composition of the various source waters, though more so with bacterial production. Primary and bacterial productivities often correlated at reciprocal time points (24-h measurement of one with the 72-h measurement of the other). These results suggest human modification of coastal watersheds enhances the magnitude of dissolved constituents delivered to coastal waters as well as alters their distributions between surface and groundwater flowpaths, with significant implications for microbial community structure and function in coastal receiving waters.

Impact of Alexandrium tamarense allelochemicals on DOM dynamics in an estuarine microbial community

Plankton and dissolved organic carbon (DOC) dynamics in fractionated estuarine microbial communities (<150 μm, <60 μm and <20 μm), incubated with allelopathic (lytic) or non allelopathic (non-lytic) Alexandrium tamarense filtrates were investigated over a period of 48 h. Additionally, the amount of dissolved organic matter (DOM) available for bacterial growth in the treatments was measured via bacterial seawater culture experiments immediately and 6 h after addition of A. tamarense filtrates. The lack of effect on DOC concentrations and plankton community composition in lytic treatments indicated that allelochemicals did not inhibit the growth of the microbial community. Nevertheless, bacterial seawater culture experiments provided evidence that lytic filtrate addition provoked the release of bioavailable DOM from the microbial community. Since DOM was only released from the largest seawater fraction, microorganisms >60 μm were probably most sensitive towards allelochemicals.