Within- and between-Lake Variability in the Composition of Bacterioplankton Communities: Investigations Using Multiple Spatial Scales

This study examined the similarity of epilimnetic bacterial community composition (BCC) across several within- and among-lake spatial scales, and the environmental factors giving rise to similar bacterial communities in different lakes were also explored. Samples were collected from 13 northern and southern Wisconsin lakes representing gradients in lake size, productivity, dissolved organic carbon and humic acid contents, and pH. Hypotheses regarding patchy distribution of bacterial communities in lakes were tested by comparing samples collected from nearby (tens of meters) and distant (hundreds of meters) sampling sites in the same lake. BCC was characterized by using a molecular fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA). Overall, samples collected at the 10-m, 100-m, and between-lake scales differed by 13, 17, and 75%, respectively. Variation at these last two scales was significant. The development of within-lake variation in BCC appeared to depend on the isolation of water by lake shoreline features such as bays or narrow constrictions. ARISA profiles from northern lakes had fewer peaks and were less similar to each other than were those of the southern lakes, suggesting that regional features do not necessarily lead to the development of similar bacterial communities. Lakes at similar positions on productivity and dissolved organic carbon concentration gradients had similar bacterial communities, and bacterial diversity was positively correlated with lake productivity and water temperature. Factorial studies taking into account these gradients, as well as regional spatial scales, should provide much insight into the nature of aquatic bacterial biogeography.     

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by pyrosequencing 16S rRNA V4‐region gene fragments obtained by PCR amplification of community genomic DNA with bacterial‐ or archaeal‐specific primers. Duplicate LCS sediment cores collected during hypoxia had higher concentrations of Fe(II), and dissolved inorganic carbon, phosphate, and ammonium than cores collected when overlying water oxygen concentrations were normal. Pyrosequencing yielded 158 686 bacterial and 225 591 archaeal sequences from 20 sediment samples, representing five 2‐cm depth intervals in the duplicate cores. Bacterial communities grouped by sampling date and sediment depth in a neighbor‐joining analysis using Chao–Jaccard shared species values. Redundancy analysis indicated that variance in bacterial communities was mainly associated with differences in sediment chemistry between oxic and hypoxic water column conditions. Gammaproteobacteria (26.5%) were most prominent among bacterial sequences, followed by Firmicutes (9.6%), and Alphaproteobacteria (5.6%). Crenarchaeotal, thaumarchaeotal, and euryarchaeotal lineages accounted for 57%, 27%, and 16% of archaeal sequences, respectively. In Thaumarchaeota Marine Group I, sequences were 96–99% identical to the Nitrosopumilus maritimus SCM1 sequence, were highest in surficial sediments, and accounted for 31% of archaeal sequences when waters were normoxic vs. 13% of archaeal sequences when waters were hypoxic. Redundancy analysis showed Nitrosopumilus‐related sequence abundance was correlated with high solid‐phase Fe(III) concentrations, whereas most of the remaining archaeal clusters were not. In contrast, crenarchaeotal sequences were from phylogenetically diverse lineages, differed little in relative abundance between sampling times, and increased to high relative abundance with sediment depth. These results provide further evidence that marine sediment microbial community composition can be structured according to sediment chemistry and suggest the expansion of hypoxia in coastal waters may alter sediment microbial communities involved in carbon and nitrogen cycling.     

Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structure

The phylogenetic composition of bacterioplankton communities in the water column of four shallow eutrophic lakes was analyzed by partially sequencing cloned 16S rRNA genes and by PCR-DGGE analysis. The four lakes differed in nutrient load and food web structure: two were in a clearwater state and had dense stands of submerged macrophytes, while two others were in a turbid state characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had very high nutrient levels (total phosphorus > 100 microg/l), while the other lakes were less nutrient rich (total phosphorus < 100 microg/l). Cluster analysis, multidimensional scaling and ANOSIM (analysis of similarity) were used to investigate differences among the bacterial community composition in the four lakes. Our results show that each lake has its own distinct bacterioplankton community. The samples of lake Blankaart differed substantially from those of the other lakes; this pattern was consistent throughout the year of study. The bacterioplankton community composition in lake Blankaart seems to be less diverse and less stable than in the other three lakes. Clone library results reveal that Actinobacteria strongly dominated the bacterial community in lake Blankaart. The relative abundance of Betaproteobacteria was low, whereas this group was dominant in the other three lakes. Turbid lakes had a higher representation of Cyanobacteria, while clearwater lakes were characterized by more representatives of the Bacteroidetes. Correlating our DGGE data with environmental parameters, using the BIOENV procedure, suggests that differences are partly related to the equilibrium state of the lake.     

Within- and between-lake variability in the composition of bacterioplankton communities: investigations using multiple spatial scales

This study examined the similarity of epilimnetic bacterial community composition (BCC) across several within- and among-lake spatial scales, and the environmental factors giving rise to similar bacterial communities in different lakes were also explored. Samples were collected from 13 northern and southern Wisconsin lakes representing gradients in lake size, productivity, dissolved organic carbon and humic acid contents, and pH. Hypotheses regarding patchy distribution of bacterial communities in lakes were tested by comparing samples collected from nearby (tens of meters) and distant (hundreds of meters) sampling sites in the same lake. BCC was characterized by using a molecular fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA). Overall, samples collected at the 10-m, 100-m, and between-lake scales differed by 13, 17, and 75%, respectively. Variation at these last two scales was significant. The development of within-lake variation in BCC appeared to depend on the isolation of water by lake shoreline features such as bays or narrow constrictions. ARISA profiles from northern lakes had fewer peaks and were less similar to each other than were those of the southern lakes, suggesting that regional features do not necessarily lead to the development of similar bacterial communities. Lakes at similar positions on productivity and dissolved organic carbon concentration gradients had similar bacterial communities, and bacterial diversity was positively correlated with lake productivity and water temperature. Factorial studies taking into account these gradients, as well as regional spatial scales, should provide much insight into the nature of aquatic bacterial biogeography.     

Bacterial and archaeal communities inhabiting mussels,sediment and water in Indonesian anchialine lakes

Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding ‘open water’ marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.     

Direct and indirect effects of hypoxia on benthos in Corpus Christi Bay, Texas, U.S.A.

Hypoxia (low oxygen conditions) has been found in the southeastern region of Corpus Christi Bay, Texas, U.S.A. every summer since 1988. The objectives of the current study were to determine direct and indirect effects of hypoxia on macrofauna. Direct physiological effects of hypoxia include reduction of benthic abundance, biomass, diversity, species richness and species evenness because of physiological intolerance. Indirect ecological effects of hypoxia include predation of emerging benthic fauna from the sediment. Macrofaunal community characteristics were compared vertically within sediments in caged and uncaged sediment samples in hypoxic and normoxic areas. Cage effects were determined with partial cages, which had reduced flow and no predator exclusion. Dissolved oxygen concentrations during the experiment was monitored in water column profiles and continuous measurement of bottom water in the hypoxic and normoxic areas. Hypoxia in Corpus Christi Bay in 1999 occurred as transient events, many of which were of short duration (less than 1 h) and moderate intensity (around 2 mg l^− 1). The macrobenthic community characteristics (i.e., abundance, biomass, species richness, diversity, and evenness) were directly affected by hypoxia as indicated by depressed levels and few deeper-dwelling organisms in the hypoxic area. Community structure was also different between the hypoxic and normoxic areas because of loss of species (presumably due to intolerance to low oxygen) in the hypoxic areas. Benthic invertebrates were found primarily in the surface in the hypoxic area, but there was no significant indication of indirect effects, i.e., increased predation pressure in the hypoxic area. The increased exposure to predation risk may be mitigated by predator avoidance of hypoxic areas. In conclusion, hypoxia in Corpus Christi Bay has negative direct effects on benthic organisms, but no indirect effects, such as increased predation pressure. The most significant finding is the interaction between hypoxia and vertical distributions of infauna, which drive hypoxia intolerant organisms to the surface and out of sediments.     

Bacterial Inhibitors in Lake Water

The populations of six bacterial genera fell rapidly after their addition to sterile lake water but not after their addition to buffer. The decline in numbers of two species that were studied further, Klebsiella pneumoniae and Micrococcus flavus, occurred even when the buffer was added to sterile lake water. The inhibition of K. pneumoniae by substances in lake water varied with the season of the year, and the rate and extent of decline of both species were different in sterile samples of different lakes. The extent of reduction in the density of K. pneumoniae was independent of initial population size and was diminished by the addition of 10 μg of glucose per ml of lake water. The toxin was removed from lake water by dialysis and by a cation-exchange resin but not by an anion-exchange resin, and it was destroyed by heating. The inhibition of K. pneumoniae was not evident in lake water buffered at a pH value above 8.0. We suggest that toxins may be important in determining the composition of the bacterial community of lakes.     

Summer sedimentation in six shallow arctic lakes

The movement of sediment between the lake bottom and water column of shallow lakes can be sizeable due to the large potential for resuspension in these systems. Resuspended sediments have been shown to alter phytoplankton community composition and elevate water column production and nutrient concentrations. We measured the summer sedimentation rates of two lakes in 2003 and six lakes in 2004. All lakes were shallow and located in the Alaskan Arctic. In 2004, turbidity, light attenuation, total sediment:chlorophyll a mass in the sediment traps, and thermal stratification were also measured in each of the lakes. The sediment:chlorophyll a mass was much greater than if the sediment was derived from phytoplankton production in all of the lakes, indicating that the source of the sedimenting material was resuspension and allochthonous inputs. Consistent with these findings, the temporal variation in sedimentation rate was synchronous between most lakes, and sedimentation rate was positively related to wind speed and rainfall suggesting that sedimentation rate was strongly influenced by landscape-scale factors (e.g., wind and rain events). Two of the lakes are located on deposits of loess that accumulated during past glacial periods. These two lakes had sedimentation rates that were significantly greater and more variable than any of the other lakes in the study, as well as high turbidity and light attenuation. Our results indicate that sedimentation in these shallow arctic lakes is supported primarily by allochthonous inputs and resuspension and that landscape-scale factors (e.g., weather and geology) impact on the transport of materials between the lake bottom and water column. Handling editor: J. Saros     

Spatiotemporal changes in the structure and composition of a less-abundant bacterial phylum (Planctomycetes) in two perialpine lakes

We used fingerprinting and cloning-sequencing to study the spatiotemporal dynamics and diversity of Planctomycetes in two perialpine lakes with contrasting environmental conditions. Planctomycetes, which are less-abundant bacteria in freshwater ecosystems, appeared to be structured in the same way as the entire bacterial community in these ecosystems. They were more diversified and displayed fewer temporal variations in the hypolimnia than in the epilimnia. Like the more-abundant bacterial groups in aquatic systems, Planctomycetes communities seem to be composed of a very small number of abundant and widespread operational taxonomic units (OTUs) and a large number of OTUs that are present at low abundance. This indicates that the concept of "abundant or core" and "rare" bacterial phylotypes could also be applied to less-abundant freshwater bacterial phyla. The richness and diversity of Planctomycetes were mainly driven by pH and were similar in both of the lakes studied, whereas the composition of the Planctomycetes community seemed to be determined by a combination of factors including temperature, pH, and nutrients. The relative abundances of the dominant OTUs varied over time and were differently associated with abiotic factors. Our findings demonstrate that less-abundant bacterial phyla, such as Planctomycetes, can display strong spatial and seasonal variations linked to environmental conditions and suggest that their functional role in the lakes studied might be attributable mainly to a small number of phylotypes and vary over space and time in the water column.     

Spatial variability in the abundance and composition of the free-living bacterioplankton community in the pelagic zone of Lake Bourget (France)

Spatial variations in the abundance and diversity of the free-living bacterioplankton community of a large Alpine lake, Lake Bourget (France), were investigated in the pelagic zone by means of two two-dimensional samplings taken in 2003. Lake-water samples were collected in winter during water mixing, and in early summer during stratification. The population abundance in each sample was determined by flow cytometry. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments from organisms measuring less than 2 mum was used to assess eubacterioplankton community composition. In winter, no obvious differences were observed in either the abundance or the diversity of the bacterial community, on either the horizontal or the vertical scales. The only influence detected was that of river water input, but this was at a very minor scale relative to the surface area of the lake. In early summer, changes were found in the community composition on the vertical scale related to the thermal stratification of the water column. There were also marked differences on the horizontal scale at 15 m depth due to internal waves. The implications of these findings for sampling strategies are very important from the perspective of comparative studies of free-living bacterial community diversity and functioning in large and deep lakes.     

Global distribution and diversity of marine Verrucomicrobia

Verrucomicrobia is a bacterial phylum that is commonly detected in soil, but little is known about the distribution and diversity of this phylum in the marine environment. To address this, we analyzed the marine microbial community composition in 506 samples from the International Census of Marine Microbes as well as 11 coastal samples taken from the California Current. These samples from both the water column and sediments covered a wide range of environmental conditions. Verrucomicrobia were present in 98% of the analyzed samples, and thus appeared nearly ubiquitous in the ocean. Based on the occurrence of amplified 16S ribosomal RNA sequences, Verrucomicrobia constituted on average 2% of the water column and 1.4% of the sediment bacterial communities. The diversity of Verrucomicrobia displayed a biogeography at multiple taxonomic levels and thus, specific lineages appeared to have clear habitat preference. We found that subdivision 1 and 4 generally dominated marine bacterial communities, whereas subdivision 2 was more frequent in low salinity waters. Within the subdivisions, Verrucomicrobia community composition were significantly different in the water column compared with sediment as well as within the water column along gradients of salinity, temperature, nitrate, depth and overall water column depth. Although we still know little about the ecophysiology of Verrucomicrobia lineages, the ubiquity of this phylum suggests that it may be important for the biogeochemical cycle of carbon in the ocean.     

Microbiology and chemistry of acid lakes in Florida: I. Effects of drought and post-drought conditions

Short term changes in acid loading and dissolved organic carbon (DOC) content were studied in relation to water column bacteria of ten acid lakes on the Katharine Ordway Preserve, Florida. Five clear oligotrophic lakes and five dark dystrophic lakes were sampled during and after a drought period in July and September, 1985. Water column bacterial densities, light extinction, chlorophyll a, DOC, pH, dissolved oxygen, nutrients, and other chemical variables were measured. Significant positive correlations existed among DOC, chlorophyll a, pH, and water column bacterial densities during the drought period.There were no significant changes in water column bacterial densities or pH of clear lakes in the post-drought period, despite a 4.6 fold increase in acid loading from rainfall. A 3 fold increase of DOC, a decline in pH, and decreased bacterial densities in dark lakes suggested inhibition of bacteria by DOC and pH. A decrease in the relationship of DOC to bacterial numbers in all lakes was also noted. The correlations among DOC, chlorophyll a, and pH were no longer significant.Using data from both time periods significant polynomial regressions were observed between DOC and bacterial density and DOC and chlorophyll a. Maximum bacterial numbers occurred at 20 mg C 1^–1 of DOC. Above this bacterial numbers decreased also suggesting an inhibitory effect of DOC. Because pH was lower after DOC had increased in the dark lakes, the increase in acid conditions may have enhanced this inhibitory effect. The short term effects of DOC on the dark-lake bacteria greatly exceeded the influence of acid loading on clear-lake bacteria.     

Chitinase gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions

Chitin is an abundant biopolymer whose degradation is mediated primarily by bacterial chitinases. We developed a degenerate PCR primer set to amplify a approximately 900-bp fragment of family 18, group I chitinase genes and used it to retrieve these gene fragments from environmental samples. Clone libraries of presumptive chitinase genes were created for nine water and six sediment samples from 10 aquatic environments including freshwater and saline lakes, estuarine water and sediments, and the central Arctic Ocean. Putative chitinase sequences were also retrieved from the Sargasso Sea metagenome sequence database. We were unable to obtain PCR product with these primers from an alkaline, hypersaline lake (Mono Lake, California). In total, 108 partial chitinase gene sequences were analyzed, with a minimum of 5 and a maximum of 13 chitinase sequences obtained from each library. All chitinase sequences were novel compared to previously identified sequences. Intralibrary sequence diversity was low, while we found significant differences between libraries from different water column samples and between water column and sediment samples. However, identical sequences were retrieved from samples collected at widely distributed locations that did not necessarily represent similar environments, suggesting homogeneity of chitinoclastic communities between some environments.     

Chitinase Gene Sequences Retrieved from Diverse Aquatic Habitats Reveal Environment-Specific Distributions

Chitin is an abundant biopolymer whose degradation is mediated primarily by bacterial chitinases. We developed a degenerate PCR primer set to amplify a ~900-bp fragment of family 18, group I chitinase genes and used it to retrieve these gene fragments from environmental samples. Clone libraries of presumptive chitinase genes were created for nine water and six sediment samples from 10 aquatic environments including freshwater and saline lakes, estuarine water and sediments, and the central Arctic Ocean. Putative chitinase sequences were also retrieved from the Sargasso Sea metagenome sequence database. We were unable to obtain PCR product with these primers from an alkaline, hypersaline lake (Mono Lake, California). In total, 108 partial chitinase gene sequences were analyzed, with a minimum of 5 and a maximum of 13 chitinase sequences obtained from each library. All chitinase sequences were novel compared to previously identified sequences. Intralibrary sequence diversity was low, while we found significant differences between libraries from different water column samples and between water column and sediment samples. However, identical sequences were retrieved from samples collected at widely distributed locations that did not necessarily represent similar environments, suggesting homogeneity of chitinoclastic communities between some environments.     

High Bacterial Diversity in Epilithic Biofilms of Oligotrophic Mountain Lakes

Benthic microbial biofilms attached to rocks (epilithic) are major sites of carbon cycling and can dominate ecosystem primary production in oligotrophic lakes. We studied the bacterial community composition of littoral epilithic biofilms in five connected oligotrophic high mountain lakes located at different altitudes by genetic fingerprinting and clone libraries of the 16S rRNA gene. Different intra-lake samples were analyzed, and consistent changes in community structure (chlorophyll a and organic matter contents, and bacterial community composition) were observed along the altitudinal gradient, particularly related with the location of the lake above or below the treeline. Epilithic biofilm genetic fingerprints were both more diverse among lakes than within lakes and significantly different between montane (below the tree line) and alpine lakes (above the tree line). The genetic richness in the epilithic biofilm was much higher than in the plankton of the same lacustrine area studied in previous works, with significantly idiosyncratic phylogenetic composition (specifically distinct from lake plankton or mountain soils). Data suggest the coexistence of aerobic, anaerobic, phototrophic, and chemotrophic microorganisms in the biofilm, Bacteroidetes and Cyanobacteria being the most important bacterial taxa, followed by Alpha-, Beta-, Gamma-, and Deltaproteobacteria, Chlorobi, Planctomycetes, and Verrucomicrobia. The degree of novelty was especially high for epilithic Bacteroidetes, and up to 50?% of the sequences formed monophyletic clusters distantly related to any previously reported sequence. More than 35?% of the total sequences matched at <95?% identity to any previously reported 16S rRNA gene, indicating that alpine epilithic biofilms are unexplored habitats that contain a substantial degree of novelty within a short geographical distance. Further research is needed to determine whether these communities are involved in more biogeochemical pathways than previously thought.     

Bacterial diversity and hydrography of Etoliko,an anoxic semi-enclosed coastal basin in Western Greece

Etoliko, an anoxic semi-enclosed basin, is part of a complex wetland in Western Greece extremely rich in biodiversity. It covers an area of 1,700 ha with an atypical orientation that has been formed tectonically. In order to identify the main factors influencing the bacterial profile at the Etoliko basin, 48 samples were collected, representing seasonal variation at four sampling stations. Physico-chemical analysis of the samples indicates the presence of three layers in the Etoliko basin: (1) low-density surface layer, (2) a layer with a steep density gradient, and (3) dense water below a depth of 20 m. A permanent halocline, whose thickness is varying seasonally, has been identified in the Etoliko basin water column, while the spatiotemporal salinity distribution was highly affected by the basin’s interaction with the nearby Messolonghi lagoon. The anoxic zone extends from 20 m below the surface to the bottom of the Etoliko basin in summer, while the bottom layer was hypoxic during winter. Bacterial populations were analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial richness and diversity were calculated and compared across samples. Hierarchical analysis showed that ARISA clustered the surface water samples according to seasonal variation, while sediment and near-to-bottom water samples appear to be stable and to cluster together. Non-metric multidimensional scaling (MDS) indicates that bacterial composition depends on dissolved oxygen and salinity. Increase in salinity of the ecosystem leads to a significant reduction of the microbial diversity.     

Intra- and inter-specific variation in metabolic gene expression in relationship to environmental hypoxia

In this study, we explored how environmental oxygen levels affect the metabolic phenotype of sympatric sunfish known to differ in their hypoxia tolerance. We examined bluegill (Lepomis macrochirus) and pumpkinseed (Lepomis gibbosus), two species commonly found in the same water bodies, though pumpkinseed are considered more hypoxia tolerant, and survive in hypoxic lakes that exclude bluegill. Freshly caught Lake Opinicon pumpkinseed possessed significantly higher glycolytic enzyme activities (PGI, ALD, GAPDH, ENO, and LDH) than bluegill, but after holding the fish in an oxygenated environment for 7days, pumpkinseed glycolytic enzymes (PGI, ALD, and LDH) and mRNA (LDHA and HIF1α) declined to bluegill's levels. When glycolytic enzymes and mRNA were compared in pumpkinseed populations from seven lakes, only Penyck Lake pumpkinseed had significantly elevated glycolytic enzyme activity that did not diminish with normoxic holding. The levels of mRNA for LDHA and HIF1α did not differ between lakes and did not change in response to normoxic holding in the Penyck Lake fish. Collectively, these studies on sunfish show that hypoxia tolerance contributes to ecological niche specialization between species, and provides an example of a population that has adapted chronically elevated glycolytic enzyme activity independent of current dissolved oxygen in the water.     

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary

Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA−a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O₂ L^-1. This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O₂ L^-1), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems.     

Novel and Unexpected Prokaryotic Diversity in Water and Sediments of the Alkaline,Hypersaline Lakes of the Wadi An Natrun,Egypt

The phylogenetic diversity of the bacterial and archaeal community in the water and sediments of three large lakes of the Wadi An Natrun was investigated using 16S rRNA clone libraries. The bacterial community was diverse: 769 clones formed 345 operational taxonomic units (OTUs) defined at 99% 16S rRNA sequence identity. The bacterial community in both the water and sediments of the lakes was dominated by clones affiliated with the low G + C Gram-type-positive group, alpha-proteobacteria, and Bacteroidetes, (11-39, 11-30, and 10-37% of OTUs observed, respectively), patterns that have been observed in previously described alkaline, athalassohaline systems. However, a relatively high proportion of Firmicutess-related clones in the water of the lakes and alpha-proteobacteria in the sediments was observed. The bacterial community composition of the water and sediment of the same lake and of different lakes was significantly different (p < 0.05). Operational taxonomic units related to the gamma-proteobacteria were more abundant in the sediment of Lake Fazda, whereas the sediment of Lake UmRisha was dominated by members of the delta-proteobacteria. The proportion of gamma-proteobacterial and Bacteroidetes-affiliated OTUs were predominant in the water of Lake UmRisha and differed significantly from other lake waters (chi-squared analysis, p < or = 0.01). The more oxygenated and dilute nature of Lake Hamra was reflected in its microbial community composition, with the abundance of Bacillales sequences in the water, the absence of Halanaerobiales, Clostridiales, and Archaea in the water, and the presence of representatives of more phyla such as the Actinobacteria, Spirochaetes, and Verrucomicrobia. The archaeal community composition appeared less diverse: 589 clones resulted in 198 OTUs defined at 99% 16S rRNA sequence identity, and all sequences fell into the phylum Euryarchaeota. Phylogenetic analysis showed that many of the sequences were distantly related (83-90% 16S rRNA sequence identity) to cultured and uncultured archaea, with many clones forming clusters that branched deeply within the Euryarchaeota. Forty-two and 53% of the bacterial and archaeal clones had less than 90% 16S rRNA sequence identity to previously described sequences. This indicates that the water and sediments of the Wadi An Natrun harbor a unique and novel prokaryotic diversity that is different from what has been described among other alkaline, athalassohaline lakes.     

Are the landscape‐level drivers of water column and surface sediment diatoms different?

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