The Complexity of the Holobiont in the Red Sea Coral Euphyllia paradivisa under Heat Stress.

The recognition of the microbiota complexity and their role in the evolution of their host is leading to the popularization of the holobiont concept. However, the coral holobiont (host and its microbiota) is still enigmatic and unclear. Here, we explore the complex relations between different holobiont members of a mesophotic coral Euphyllia paradivisa. We subjected two lines of the coral-with photosymbionts, and without photosymbionts (apo-symbiotic)-to increasing temperatures and to antibiotics. The different symbiotic states were characterized using transcriptomics, microbiology and physiology techniques. The bacterial community's composition is dominated by bacteroidetes, alphaproteobacteria, and gammaproteobacteria, but is dependent upon the symbiont state, colony, temperature treatment, and antibiotic exposure. Overall, the most important parameter determining the response was whether the coral was a symbiont/apo-symbiotic, while the colony and bacterial composition were secondary factors. Enrichment Gene Ontology analysis of coral host's differentially expressed genes demonstrated the cellular differences between symbiotic and apo-symbiotic samples. Our results demonstrate the significance of each component of the holobiont consortium and imply a coherent link between them, which dramatically impacts the molecular and cellular processes of the coral host, which possibly affect its fitness, particularly under environmental stress.

The effect of coagulants and antiscalants discharged with seawater desalination brines on coastal microbial communities: A laboratory and in situ study from the southeastern Mediterranean.

Desalination outflows frequently discharge brine containing coagulants and antiscalants (e.g. Iron-hydroxides and polyphosphonates) to the coastal environment. Here we examined changes in composition and productivity of natural microbial coastal communities in experimental mesocosms treated with either iron-hydroxide (Fe), polyphosphonate (Pn), or a combination of high salinities with both chemicals (All). Within 2 h of addition Fe already altered the microbial community composition, enhanced the bacterial production (BP) and cell specific production (BP/BA), and decreased primary production. Addition of Pn, relieved phosphorus stress as demonstrated by the immediate (within 2 h) and significant reduction in the ecto-enzyme alkaline phosphatase activity (APA). Synergistic effects were observed in the All treatment, reflected by increased production of both primary and bacterial producers as P-stress was relieved. After 10 days of incubation, the microbial community composition changed significantly only in the All treatment. The Fe-only treatment caused a significant decline in autotrophic biomass and in the assimilation number (AN), while in both the Pn and the All treatments the BP/BA increased with the added P. We also examined the microbial community responses in a natural impacted environment at the Ashkelon seawater desalination plant brine discharge site during summer and winter. The community composition differed in elevated-salinity compared with non-impacted stations with higher AN and bacterial efficiencies (BP/BA) measured in summer in the elevated-salinity stations. The seasonal differences in responses may reflect both biotic (i.e. initial community composition) and abiotic factors (currents and residence time of salinity gradients). Our results emphasize that desalination brine discharges that include chemicals such as iron-hydroxide and polyphosphonates can induce physiological and compositional changes in the microbial community. With the expansion of desalination facilities worldwide such shifts in composition and function of the microbial communities may destabilize and change local aquatic food webs and should thus be monitored.

Microbial metatranscriptomes from the thermally stratified Gulf of Aqaba/Eilat during summer.

The water column in the oligotrophic Gulf of Aqaba/Eilat experiences distinct seasonal cycles with the cooling air and water temperatures of late fall and winter destabilizing the thermocline and forming mixed layer depths reaching 300 to 700m. As air temperatures warm thermal re-stratification results in a stable thermocline throughout the summer which physically separates a photic, nutrient-poor surface layer from an aphotic, nutrient-rich deep layer. Here we present the first metatranscriptome dataset, and its taxonomic assignments, sampled from three depths of the 700m deep Station A in the Gulf of Aqaba during the summer stratification (surface - 10m, deep chlorophyll maximum (DCM) - 85m, deep aphotic zone -500m). Intensive transcriptional activity was attributed to Prochlorococcus - the most abundant photosynthetic organism in the RNA-seq dataset - both at the surface and at the DCM. In contrast, cDNA reads related to picoeukaryotic algae were detected almost exclusively at the DCM. The metatranscriptomes presented here provide a basis for examining the seasonal differences in microbial gene expression by comparison with the published metatranscriptomes sampled during the winter deep-mixing from the same station.

Enhanced salinities, as a proxy of seawater desalination discharges, impact coastal microbial communities of the eastern Mediterranean Sea.

Seawater desalination plants increase local coastal salinities by discharging concentrated brine back to the sea with ∼ 50% higher than ambient salinities. The impacts of high salinities on microbial coastal populations of the eastern Mediterranean Sea (EMS) were examined in two mesocosm experiments; first, during the mixed-spring and second, during the stratified-summer periods with average salinity of ∼ 39. Ambient salinities were increased by 5% and 15%. Higher salinity (15%) mesocosms induced rapid (within 2 h) declines in both primary productivity (PP) and algal biomass parallel to an increase in bacterial productivity. Subsequently, for the duration of the experiments (11-12 days), both Chlorophyll a and PP rates increased (2 to 5 and 1.5 to 2.5-fold, respectively) relative to unamended controls. The initial assemblages of the ambient microbial populations and intensity of salinity enrichments influenced the community responses. During the mixed-spring experiment, the composition of prokaryotic and eukaryotic populations shifted only slightly, suggesting high functional plasticity of the initial populations. While during the stratified-summer experiment, high salinity changed the composition and reduced the biodiversity of the microbial communities. In an ultra-oligotrophic environment such as the EMS, salinity induced declines in microbial diversity may provide a tipping point destabilizing the local aquatic food web.

Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in TMF-/- mice.

Tata Element Modulatory Factor (TMF/ARA160) is a multifunctional Golgi-associated protein, which accumulates in colonic enterocytes and goblet cells. Mice lacking TMF/ARA160 (TMF(-/-)) produce thick and uniform colonic mucus that resists adherent bacterial colonization and diminishes susceptibility of these mice to induced acute colitis, through a mechanism that is not fully understood. Here, we show that mucus secretion by goblet cells is altered in the colon of TMF(-/-) mice, resulting in the formation of a highly oligomerized colonic gel-forming mucin, MUC2. Microbiome analysis revealed a shift in the microbiota of TMF(-/-) mice leading to predominance of the Firmicutes phylum and a significantly higher abundance of probiotic beneficial bacterial species. Notably, this trait was transmissible, and when cohoused with wild-type animals, TMF(-/-) mice influenced the microbiota and diminished the susceptibility of wild-type mice to chemically induced dextran sulfate sodium colitis. Thus, altered mucus secretion in TMF(-/-) mouse colons is accompanied by a reprogrammed intestinal microbiota, leading to a transmissible reduced sensitivity to induced colitis.

Automatic microfiber filtration (AMF) of surface water: impact on water quality and biofouling evolution.

In the current study we examined the impact of thread filtration using an automatic microfiber filter on Lake Kinneret water quality and as a new application to control biofouling over time. We found that automatic microfiber filtration (AMF) reduced total iron and aluminum in water by over 80%. Particle analysis (>2 µm) revealed a total particle removal efficiency of ≈ 90%, with AMF removal efficiency increasing with increasing particle size and decreasing particle circularity. Regarding microbiological parameters, AMF did not affect bacterial counts or composition in the water. However, it did control biofilm evolution and affected its microbial community composition. AMF controlled biofilm over time by maintaining premature biofilms of less than 10 µm mean thickness compared to biofilms of unfiltered water (up to 60 µm mean thickness). In addition, biofilms developing in AMF filtered water contained relatively low levels of extracellular polymeric substances. While biofilms of unfiltered water were dominated by Proteobacteria (≤ 50%) followed by Bacteroidetes (20-30%) during all 4 weeks of the experiment, biofilms of AMF filtered water were dominated by Proteobacteria (≤ 90%) and especially Alphaproteobacteria after 2 weeks, and Chloroflexi (≈ 60%) after 4 weeks. The decrease in Bacteroidetes might originate from removal of transparent exopolymer particles, which are occasionally colonized by Bacteroidetes. The increase in Alphaproteobacteria and Chloroflexi was explained by these robust groups' ability to adjust to different environments.

Dinitrogen fixation in aphotic oxygenated marine environments.

We measured N2 fixation rates from oceanic zones that have traditionally been ignored as sources of biological N2 fixation; the aphotic, fully oxygenated, nitrate (NO(-) 3)-rich, waters of the oligotrophic Levantine Basin (LB) and the Gulf of Aqaba (GA). N2 fixation rates measured from pelagic aphotic waters to depths up to 720 m, during the mixed and stratified periods, ranged from 0.01 nmol N L(-1) d(-1) to 0.38 nmol N L(-1) d(-1). N2 fixation rates correlated significantly with bacterial productivity and heterotrophic diazotrophs were identified from aphotic as well as photic depths. Dissolved free amino acid amendments to whole water from the GA enhanced bacterial productivity by 2-3.5 fold and N2 fixation rates by ~2-fold in samples collected from aphotic depths while in amendments to water from photic depths bacterial productivity increased 2-6 fold while N2 fixation rates increased by a factor of 2 to 4 illustrating that both BP and heterotrophic N2 fixation were carbon limited. Experimental manipulations of aphotic waters from the LB demonstrated a significant positive correlation between transparent exopolymeric particle (TEP) concentrations and N2 fixation rates. This suggests that sinking organic material and high carbon (C): nitrogen (N) micro-environments (such as TEP-based aggregates or marine snow) could support high heterotrophic N2 fixation rates in oxygenated surface waters and in the aphotic zones. Indeed, our calculations show that aphotic N2 fixation accounted for 37 to 75% of the total daily integrated N2 fixation rates at both locations in the Mediterranean and Red Seas with rates equal or greater to those measured from the photic layers. Moreover, our results indicate that that while N2 fixation may be limited in the surface waters, aphotic, pelagic N2 fixation may contribute significantly to new N inputs in other oligotrophic basins, yet it is currently not included in regional or global N budgets.

Rhodobacteraceae are the key members of the microbial community of the initial biofilm formed in Eastern Mediterranean coastal seawater.

The formation of biofilms and biofouling is a common feature in aquatic environments. The aim of this study was to identify the primary colonizers of biofilm formed in Eastern Mediterranean Coastal water at different seasons and follow early dynamics of biofilm community development. Pre-treated coastal seawater and biofilm samples were collected from six different sampling events of 2 weeks' duration each during 1 year. The microbial community composition and specific abundance were estimated by 16S rRNA gene clone libraries and fluorescence in situ hybridization-confocal laser scanning microscopy (FISH-CLSM), respectively. The biofilm formed over the course of the year was fairly consistent in terms of community composition and overall abundance with the exception of spring season. Alphaproteobacteria (30-70% of total bacteria), in particular Rhodobacteraceae, were the dominant bacteria in the biofilm, regardless of season, followed by Bacteroidetes (5-35%) and Gammaproteobacteria (6-35%). There was a decrease in relative abundance of Alphaproteobacteria and an increase in the abundance of Bacteroidetes between the initial and 2-week-old biofilm. This observation may aid man-made facilities that have to deal with biofilm formation and help the development of appropriate strategies to control those biofilms.

Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific).

The Clipperton lagoon in the North Pacific Ocean has been isolated from the surrounding sea for c. 160 years. It has a stratified water column that comprises an oxic and brackish upper water layer (mixolimnion) and a deep sulfuric anoxic saline layer (monimolimnion), separated by a steep pycnocline. Here, we test whether the Clipperton lagoon with its distinctive physico-chemical features, geographic isolation, recent water column stratification, and large nutrient input harbors original microbial communities. The combination of capillary electrophoresis single-strand polymorphism (CE-SSCP) fingerprinting and sequencing of cloned bacterial and archaeal 16S rRNA genes, and functional genes for methanogenesis (mcrA), methanotrophy (pmoA), and sulfate reduction (dsrAB), revealed that microbial communities and pathways were highly stratified down the water column. The mixolimnion contained ubiquitous freshwater clades of Alpha- and Betaproteobacteria, while the pycnocline contained mostly green sulfur bacteria (phylum Chlorobi). Sequences of the upper layers were closely related to sequences found in other aquatic ecosystems, suggesting that they have a strong potential for dispersal and colonization. In contrast, the monimolimnion contained new deeply branching bacterial divisions within the OP11 cluster and the Bacteroidetes, and was the most diverse of the layers. The unique environmental conditions characterizing the deep layers of the lagoon may explain the novelty of the microbial communities found at the Clipperton atoll.

Microbial activity and organic matter dynamics during 4 years of irrigation with treated wastewater.

The global changes in rainfall frequency and quantity have subjected arid and semi-arid regions to long periods of drought. As this phenomenon corresponds to increasing trend of water shortage, the use of treated wastewater (TWW) has been suggested as an alternative for irrigation of agricultural crops in these areas. The aim of the study was to investigate the short- and middle-term effects of TWW irrigation on the soil microbial activities and organic carbon content. The microbial community activity was measured every 1-3 months for 4 years in a persimmon (Diospyros kaki) orchard. These activities were used here as an indicator for the soil health. The hydrolysis activity (detected by fluorescein diacetate hydrolysis (FDA) assay) increased during the irrigation season and was significantly higher in soils irrigated with TWW compared to those irrigated with freshwater (FW). This activity was also negatively correlated with dissolved organic carbon (DOC) concentrations during the irrigation season, suggesting that the community degraded the DOC in the soils regardless of its origin. The irrigation season was also characterized by an increase in nitrification potential in both TWW- and FW-irrigated soils, which coincided with high concentrations of nitrate (50 mg kg(-1) soil). Overall, there was an increase in all measured activities during the irrigation season, and they were higher in the TWW soils. However, it appears that after each irrigation season, the potential activity of the community returned to levels similar to or even slightly lower than those of FW-irrigated soil during the wet season, suggesting that the periodic irrigation did not significantly change the soil microbial activity.

The impact of reduced pH on the microbial community of the coral Acropora eurystoma.

Rising concentrations of atmospheric carbon dioxide are acidifying the world's oceans. Surface seawater pH is 0.1 units lower than pre-industrial values and is predicted to decrease by up to 0.4 units by the end of the century. This change in pH may result in changes in the physiology of ocean organisms, in particular, organisms that build their skeletons/shells from calcium carbonate, such as corals. This physiological change may also affect other members of the coral holobiont, for example, the microbial communities associated with the coral, which in turn may affect the coral physiology and health. In the present study, we examined changes in bacterial communities in the coral mucus, tissue and skeleton following exposure of the coral Acropora eurystoma to two different pH conditions: 7.3 and 8.2 (ambient seawater). The microbial community was different at the two pH values, as determined by denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis. Further analysis of the community in the corals maintained at the lower pH revealed an increase in bacteria associated with diseased and stressed corals, such as Vibrionaceae and Alteromonadaceae. In addition, an increase in the number of potential antibacterial activity was recorded among the bacteria isolated from the coral maintained at pH 7.3. Taken together, our findings highlight the impact that changes in the pH may have on the coral-associated bacterial community and their potential contribution to the coral host.

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles.

Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or "pseudo-metagenomes", for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.

Expression of acetate permease-like (apl ) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations.

The addition of acetate to uranium-contaminated aquifers in order to stimulate the growth and activity of Geobacter species that reduce uranium is a promising in situ bioremediation option. Optimizing this bioremediation strategy requires that sufficient acetate be added to promote Geobacter species growth. We hypothesized that under acetate-limiting conditions, subsurface Geobacter species would increase the expression of either putative acetate symporters genes (aplI and aplII). Acetate was added to a uranium-contaminated aquifer (Rifle, CO) in two continuous amendments separated by 5 days of groundwater flush to create changing acetate concentrations. While the expression of aplI in monitoring well D04 (high acetate) weakly correlated with the acetate concentration over time, the transcript levels for this gene were relatively constant in well D08 (low acetate). At the lowest acetate concentrations during the groundwater flush, the transcript levels of aplII were the highest. The expression of aplII decreased 2-10-fold upon acetate reintroduction. However, the overall instability of acetate concentrations throughout the experiment could not support a robust conclusion regarding the role of apl genes in response to acetate limitation under field conditions, in contrast to previous chemostat studies, suggesting that the function of a microbial community cannot be inferred based on lab experiments alone.

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer.

Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphate-limitation were identified by microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high-affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU upregulated the most. Quantitative PCR analysis of pstB and phoU transcript levels in G. sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium-bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve because of the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.

Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.

Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater.

The influence of ammonium availability on bacterial community structure and the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by 2 orders of magnitude (< 4 to 400 microM) across th study site. Analysis of 16S rRNA sequences suggested that ammonium may have been one factor influencing the community composition prior to acetate amendment with Rhodoferax species predominating over Geobacter species with higher ammonium and Dechloromonas species dominating at the site with lowest ammonium. However, once acetate was added and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to acetate concentrations rather than ammonium levels. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium transporter gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during uranium reduction. The abundance of amtB was inversely correlated to ammonium levels, whereas nifD transcript levels were similar across all sites examined. These results suggest that nifD and amtB expression are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB transcript expression appears to be a useful approach for monitoring the nitrogen-related physiological status of subsurface Geobacter species. This study also emphasizes the need for more detailed analysis of geochemical and physiological interactions at the field scale in order to adequately model subsurface microbial processes during bioremediation.

Highly conserved genes in Geobacter species with expression patterns indicative of acetate limitation.

Analysis of the genome of Geobacter sulfurreducens revealed four genes encoding putative symporters with homology to ActP, an acetate transporter in Escherichia coli. Three of these genes, aplA, aplB and aplC, are highly similar (over 90 % identical) and fell within a tight phylogenetic cluster (Group I) consisting entirely of Geobacter homologues. Transcript levels for all three genes increased in response to acetate limitation. The fourth gene, aplD, is phylogenetically distinct (Group II) and its expression was not influenced by acetate availability. Deletion of any one of the three genes in Group I did not significantly affect acetate-dependent growth, suggesting functional redundancy. Attempts to recover mutants in which various combinations of two of these genes were deleted were unsuccessful, suggesting that at least two of these three transporter genes are required to support growth. Closely related Group I apl genes were found in the genomes of other Geobacter species whose genome sequences are available. Furthermore, related genes could be detected in genomic DNA extracted from a subsurface environment undergoing in situ uranium bioremediation. The transporter genes recovered from the subsurface were most closely related to Group I apl genes found in the genomes of cultured Geobacter species that were isolated from contaminated subsurface environments. The increased expression of these genes in response to acetate limitation, their high degree of conservation among Geobacter species and the ease with which they can be detected in environmental samples suggest that Group I apl genes of the Geobacteraceae may be suitable biomarkers for acetate limitation. Monitoring the expression of these genes could aid in the design of strategies for acetate-mediated in situ bioremediation of uranium-contaminated groundwater.

Diversity and abundance of glycosyl hydrolase family 5 in the North Atlantic Ocean.

The diversity and abundance of glycosyl hydrolase family 5 (GH5) were studied in the North Atlantic Ocean. This family was chosen because of the large number of available sequences from cultured bacteria, the variety of substrates it targets, and the high number of similar sequences in the Sargasso Sea environmental genome database. Three clone libraries of a GH5 subcluster were constructed from the Mid-Atlantic Bight and the eastern and western North Atlantic Ocean. The two North Atlantic Ocean libraries did not differ from each other but both were significantly less diverse than the Mid-Atlantic Bight library. The abundance of GH5 genes estimated by quantitative PCR was positively correlated with chlorophyll concentrations in the eastern part of a transect from Fort Pierce, Florida, to the Azores and in a depth profile, suggesting that the supply of labile organic material selects for GH5-bearing bacteria in these waters. However, the data suggest that only <1% of all bacteria harbor the GH5 subcluster. These and other data suggest that the hydrolysis of polysaccharides requires complicated multi-enzyme systems.

Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware Estuary.

The contribution of major bacterial groups to the assimilation of extracellular polymeric substances (EPS) and glucose in the Delaware Estuary was assessed using microautoradiography and fluorescence in situ hybridization. Bacterial groups contributed to EPS and glucose assimilation in part according to their distribution in the estuary. Abundance of the phylogenetic groups explained 35% and 55% of the variation in EPS and glucose assimilation, respectively. Actinobacteria contributed 70% to glucose assimilation in freshwater, while Alphaproteobacteria assimilated 60% of this compound in saline water. In contrast, various bacterial groups dominated the assimilation of EPS. Actinobacteria and Betaproteobacteria contributed the most in the freshwater section, whereas Cytophaga-like bacteria and Alpha- and Gammaproteobacteria participated in EPS assimilation in the lower part of the estuary. In addition, we examined the fraction of bacteria in each group that assimilated glucose or EPS. Overall, the fraction of bacteria in all groups that assimilated glucose was higher than the fraction that assimilated EPS (15 to 30% versus 5 to 20%, respectively). We found no correlation between the relative abundance of a group in the estuary and the fraction of bacteria actively assimilating glucose or EPS; the more active groups were often less abundant. Our results imply that the bacterial community in the Delaware Estuary is not controlled solely by "bottom-up" factors such as dissolved organic matter.

Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean.

Members of the SAR11 clade often dominate the composition of marine microbial communities, yet their contribution to biomass production and the flux of dissolved organic matter (DOM) is unclear. In addition, little is known about the specific components of the DOM pool utilized by SAR11 bacteria. To better understand the role of SAR11 bacteria in the flux of DOM, we examined the assimilation of leucine (a measure of biomass production), as well as free amino acids, protein, and glucose, by SAR11 bacteria in the Northwest Atlantic Ocean. We found that when SAR11 bacteria were >25% of total prokaryotes, they accounted for about 30 to 50% of leucine incorporation, suggesting that SAR11 bacteria were major contributors to bacterial biomass production and the DOM flux. Specific growth rates of SAR11 bacteria either equaled or exceeded growth rates for the total prokaryotic community. In addition, SAR11 bacteria were typically responsible for a greater portion of amino acid assimilation (34 to 61%) and glucose assimilation (45 to 57%) than of protein assimilation (< or = 34%). These data suggest that SAR11 bacteria do not utilize various components of the DOM pool equally and may be more important to the flux of low-molecular-weight monomers than to that of high-molecular-weight polymers.