Structure Of Microbial Assemblages Research Articles

Catchment characteristics and seasonality control the composition of microbial assemblages exported from three outlet glaciers of the Greenland Ice Sheet.

Glacial meltwater drains into proglacial rivers where it interacts with the surrounding landscape, collecting microbial cells as it travels downstream. Characterizing the composition of the resulting microbial assemblages in transport can inform us about intra-annual changes in meltwater flowpaths beneath the glacier as well as hydrological connectivity with proglacial areas. Here, we investigated how the structure of suspended microbial assemblages evolves over the course of a melt season for three proglacial catchments of the Greenland Ice Sheet (GrIS), reasoning that differences in glacier size and the proportion of glacierized versus non-glacierized catchment areas will influence both the identity and relative abundance of microbial taxa in transport. Streamwater samples were taken at the same time each day over a period of 3 weeks (summer 2018) to identify temporal patterns in microbial assemblages for three outlet glaciers of the GrIS, which differed in glacier size (smallest to largest; Russell, Leverett, and Isunnguata Sermia [IS]) and their glacierized: proglacial catchment area ratio (Leverett, 76; Isunnguata Sermia, 25; Russell, 2). DNA was extracted from samples, and 16S rRNA gene amplicons sequenced to characterize the structure of assemblages. We found that microbial diversity was significantly greater in Isunnguata Sermia and Russell Glacier rivers compared to Leverett Glacier, the latter of which having the smallest relative proglacial catchment area. Furthermore, the microbial diversity of the former two catchments continued to increase over monitored period, presumably due to increasing hydrologic connectivity with proglacial habitats. Meanwhile, diversity decreased over the monitored period in Leverett, which may have resulted from the evolution of an efficient subglacial drainage system. Linear discriminant analysis further revealed that bacteria characteristic to soils were disproportionately represented in the Isunnguata Sermia river, while putative methylotrophs were disproportionately abundant in Russell Glacier. Meanwhile, taxa typical for glacierized habitats (i.e., Rhodoferax and Polaromonas) dominated in the Leverett Glacier river. Our findings suggest that the proportion of deglaciated catchment area is more influential to suspended microbial assemblage structure than absolute glacier size, and improve our understanding of hydrological flowpaths, particulate entrainment, and transport.

Effects of Ocean Acidification on Resident and Active Microbial Communities of Stylophora pistillata.

Ocean warming and ocean acidification (OA) are direct consequences of climate change and affect coral reefs worldwide. While the effect of ocean warming manifests itself in increased frequency and severity of coral bleaching, the effects of ocean acidification on corals are less clear. In particular, long-term effects of OA on the bacterial communities associated with corals are largely unknown. In this study, we investigated the effects of ocean acidification on the resident and active microbiome of long-term aquaria-maintained Stylophora pistillata colonies by assessing 16S rRNA gene diversity on the DNA (resident community) and RNA level (active community). Coral colony fragments of S. pistillata were kept in aquaria for 2 years at four different pCO2 levels ranging from current pH conditions to increased acidification scenarios (i.e., pH 7.2, 7.4, 7.8, and 8). We identified 154 bacterial families encompassing 2,047 taxa (OTUs) in the resident and 89 bacterial families including 1,659 OTUs in the active communities. Resident communities were dominated by members of Alteromonadaceae, Flavobacteriaceae, and Colwelliaceae, while active communities were dominated by families Cyclobacteriacea and Amoebophilaceae. Besides the overall differences between resident and active community composition, significant differences were seen between the control (pH 8) and the two lower pH treatments (7.2 and 7.4) in the active community, but only between pH 8 and 7.2 in the resident community. Our analyses revealed profound differences between the resident and active microbial communities, and we found that OA exerted stronger effects on the active community. Further, our results suggest that rDNA- and rRNA-based sequencing should be considered complementary tools to investigate the effects of environmental change on microbial assemblage structure and activity.

Spatial variation in the gastrointestinal microbiome, diet, and nutritional condition of a juvenile flatfish among coastal habitats

Gut microbiota are important for the health, fitness and development of animal hosts, but little is known about these assemblages in wild populations of fish. Such knowledge is particularly important for juvenile life stages where nutritional intake critically determines early development, growth, and ultimately recruitment. We characterise the microbiome inhabiting the gut of young-of-the-year European plaice (‘YOY plaice’) on sandy beaches, their key juvenile habitat, and examine how these microbial communities vary spatially in relation to diet and nutritional condition of their plaice hosts. Body size, diet (stomach fullness and eukaryotic 18S ribosomal sequencing), nutritional condition (RNA:DNA) and gut microbiota (16S prokaryotic ribosomal sequencing) were compared in fish at two spatial scales: between beaches separated by 10s of kilometres and between sites at different depths on the same beach, separated by 10s of metres. The main microbial phyla in YOY plaice guts were Proteobacteria, Spirochaetes, Tenericutes and Verrucomicrobiae. Within the Proteobacteria there was an unusual dominance of Alphaproteobacteria. Differences in body size, diet and nutritional condition of YOY plaice between beaches were accompanied by differences in gut microbial assemblage structure. Notably, substantially reduced nutritional condition and size at one of the beaches was associated with lower stomach fullness, reduced consumption of annelids and differences in the abundance and presence of specific microbial taxa. Differences were also detected in microbial assemblages, body size, and diet between depths within the same nursery beach, although stomach fullness and nutritional condition did not vary significantly. The functional links between the environment, gut microbiota, and their hosts are potentially important mediators of the development of young fish through critical life stages. Our study indicates that these links need to be addressed at 10 km and even 10 m scales to capture the variability observed in wild populations of juvenile fish.

Microbial tropicalization driven by a strengthening western ocean boundary current.

Western boundary currents (WBCs) redistribute heat and oligotrophic seawater from the tropics to temperate latitudes, with several displaying substantial climate change-driven intensification over the last century. Strengthening WBCs have been implicated in the poleward range expansion of marine macroflora and fauna, however, the impacts on the structure and function of temperate microbial communities are largely unknown. Here we show that the major subtropical WBC of the South Pacific Ocean, the East Australian Current (EAC), transports microbial assemblages that maintain tropical and oligotrophic (k-strategist) signatures, to seasonally displace more copiotrophic (r-strategist) temperate microbial populations within temperate latitudes of the Tasman Sea. We identified specific characteristics of EAC microbial assemblages compared with non-EAC assemblages, including strain transitions within the SAR11 clade, enrichment of Prochlorococcus, predicted smaller genome sizes and shifts in the importance of several functional genes, including those associated with cyanobacterial photosynthesis, secondary metabolism and fatty acid and lipid transport. At a temperate time-series site in the Tasman Sea, we observed significant reductions in standing stocks of total carbon and chlorophyll a, and a shift towards smaller phytoplankton and carnivorous copepods, associated with the seasonal impact of the EAC microbial assemblage. In light of the substantial shifts in microbial assemblage structure and function associated with the EAC, we conclude that climate-driven expansions of WBCs will expand the range of tropical oligotrophic microbes, and potentially profoundly impact the trophic status of temperate waters.

Timescales of variation in diversity and production of bacterioplankton assemblages in the Lower Mississippi River.

Rivers are characterized by rapid and continuous one-way directional fluxes of flowing, aqueous habitat, chemicals, suspended particles, and resident plankton. Therefore, at any particular location in such systems there is the potential for continuous, and possibly abrupt, changes in diversity and metabolic activities of suspended biota. As microorganisms are the principal catalysts of organic matter degradation and nutrient cycling in rivers, examination of their assemblage dynamics is fundamental to understanding system-level biogeochemical patterns and processes. However, there is little known of the dynamics of microbial assemblage composition or production of large rivers along a time interval gradient. We quantified variation in alpha and beta diversity and production of particle-associated and free-living bacterioplankton assemblages collected at a single site on the Lower Mississippi River (LMR), the final segment of the largest river system in North America. Samples were collected at timescales ranging from days to weeks to months up to a year. For both alpha and beta diversity, there were similar patterns of temporal variation in particle-associated and free-living assemblages. Alpha diversity, while always higher on particles, varied as much at a daily as at a monthly timescale. Beta diversity, in contrast, gradually increased with time interval of sampling, peaking between samples collected 180 days apart, before gradually declining between samples collected up to one year apart. The primary environmental driver of the temporal pattern in beta diversity was temperature, followed by dissolved nitrogen and chlorophyll a concentrations. Particle-associated bacterial production corresponded strongly to temperature, while free-living production was much lower and constant over time. We conclude that particle-associated and free-living bacterioplankton assemblages of the LMR vary in richness, composition, and production at distinct timescales in response to differing sets of environmental factors. This is the first temporal longitudinal study of microbial assemblage structure and dynamics in the LMR.

Microcosm on a bottle: experimental tests on the colonization of plastic and glass substrates in a retention reservoir

The last few decades have seen a dramatic increase in water pollution due to various types of waste generated by human activity. These include plastic and glass accumulating in the shore area of lakes and oceans. These substrates may be colonized by various groups of aquatic organisms. Little is known of the trophic interrelationships between micro- and macroorganisms colonizing plastic (PB) and glass bottles (GB). Therefore, the main objective of the present study was to determine the taxonomic composition and abundance of micro- and macroorganisms colonizing artificial, anthropogenic substrates, the trophic relationships between the organisms colonizing these substrates, and the influence of the physicochemical properties of the water on the formation of such assemblages. Studies of micro- and macroorganisms were carried out on the surface of PB and GB in a eutrophic retention basin. Both the species richness and abundance of microorganisms and metazoa were found to be determined by the type of substrate colonized as well as by the physicochemical properties of the water (primarily the content of total organic carbon and biogenic compounds). Furthermore, the trophic structure of microbial assemblages demonstrated seasonal variability. In spring, the substrates were colonized by typical bacterivorous ciliates, whereas in the following seasons there was a larger share of omnivorous species (ciliates and rotifers). This may indicate that the accumulation of various types of anthropogenic waste, in the present case GB and PB, may contribute to changes in the matter and energy cycle, including the carbon cycle, in various microhabitats of aquatic ecosystems.

Impact of euxinic holomictic conditions on prokaryotic assemblages in a marine meromictic lake

The water column of marine Rogoznica Lake (Croatia) is stratified throughout the year. However, on rare occasions, the lake exhibits complete mixing, primarily driven by meteorological conditions. On such occasions, anoxic, sulfide-rich bottom water mixes with the oxic surface layer, triggering both the oxidation of sulfide predominantly to colloidal sulfur and the establishment of euxinic conditions throughout the water column. We investigated prokaryotic communities during euxinic holomictic conditions. High-throughput sequencing of the 16S rRNA gene showed that these sulfur-driven communities were dominated by Planctomycetales, chemolithotrophic Epsilonbactereota (mainly Arcobacteraceae) and Gammaproteobacteria (Thioglobaceae), followed by Alpha- (Rhodobacteraceae) and Deltaproteobacteria (Desulfobulbaceae and Desulfobacteraceae). The majority of archaeal sequences belonged to Nanoarchaeota, all of which were designated as Woesearchaeia. This class has not been recorded in other meromictic lakes. Both bacterial and archaeal 16S rRNA gene abundance did not vary significantly across the vertical profile of the lake, as shown by quantitative PCR. However, hierarchical clustering showed a significant difference between the microbial assemblage structure in stratified periods and during a holomictic event. Besides the structure, this stressful event had a manifold effect on bacterial and archaeal assemblages by decreasing their diversity and abundance when compared to the usual stratified conditions.

Sediment microbial assemblage structure is modified by marine polychaete gut passage.

Invertebrate activities in sediments, predominantly the redistribution of particles and porewater, are well-known to regulate the structure of associated microbial assemblages; however, relatively little attention has been given to the effects of sediment ingestion, gut passage and excretion by deposit-feeding invertebrates. Here, we use high-throughput sequencing and quantitative PCR to examine how passage through the gut of the marine polychaete Hediste diversicolor affects the structure of bacterial and archaeal assemblages and the abundance of nitrogen cycling taxa. We show that the digestive tract of H. diversicolor contains unique transitory microbial assemblages that, during gut passage, become more like the surrounding sediment assemblages. Enrichment of similar microbial taxa in both the hindgut and the burrow wall suggest that these transitory gut assemblages may influence the composition of the local sediment community. The hindgut of H. diversicolor also forms a reservoir for unique ammonia-oxidising archaeal taxa. Furthermore, distinct microbial assemblages on external polychaete surfaces suggest that deposit-feeding invertebrates act as vectors that transport microbes between sediment patches. Collectively, these findings suggest that the passage of sediment and associated microbial assemblages through the gut of deposit feeding invertebrates is likely to play a significant role in regulating sediment microbial assemblages and biogeochemical functioning.

Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources.

Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH4) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH4-producing organisms (methanogens) would reflect the distribution of CH4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH4-cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH4-producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.

A modified high-throughput analysis of PLFAs in soil

Microbial community profiling via phospholipid fatty-acid (PLFA) analysis is an insightful technique which elucidates the phenotypic structure of microbial assemblages within soil. Previous iterations of PLFA analysis have used large quantities of chemicals and can take extended periods of time to perform. Another barrier to the implementation of this method is the cost and availability of specialised machinery. We report on a high-throughput method which reduces both the time to extract PLFAs from soil and reduces the quantity of chemicals required.

Microbial decomposition is highly sensitive to leaf litter emersion in a permanent temperate stream

Drought frequency and intensity in some temperate regions are forecasted to increase under the ongoing global change, which might expose permanent streams to intermittence and have severe repercussions on stream communities and ecosystem processes. In this study, we investigated the effect of drought duration on microbial decomposition of Populus nigra leaf litter in a temperate permanent stream (Oliveira, NW Portugal). Specifically, we measured the response of the structural (assemblage composition, bacterial and fungal biomass) and functional (leaf litter decomposition, extracellular enzyme activities (EEA), and fungal sporulation) parameters of fungal and bacterial communities on leaf litter exposed to emersion during different time periods (7, 14 and 21d). Emersion time affected microbial assemblages and litter decomposition, but the response differed among variables. Leaf decomposition rates and the activity of β-glucosidase, cellobiohydrolase and phosphatase were gradually reduced with increasing emersion time, while β-xylosidase reduction was similar when emersion last for 7 or more days, and the phenol oxidase reduction was similar at 14 and 21days of leaf emersion. Microbial biomass and fungal sporulation were reduced after 21days of emersion. The structure of microbial assemblages was affected by the duration of the emersion period. The shifts in fungal assemblages were correlated with a decreased microbial capacity to degrade lignin and hemicellulose in leaf litter exposed to emersion. Additionally, some resilience was observed in leaf litter mass loss, bacterial biomass, some enzyme activities and structure of fungal assemblages. Our study shows that drought can strongly alter structural and functional aspects of microbial decomposers. Therefore, the exposure of leaf litter to increasing emersion periods in temperate streams is expected to affect decomposer communities and overall decomposition of plant material by decelerating carbon cycling in streams.

Terroir is a key driver of seed-associated microbial assemblages.

Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces.

Habitat, water quality, seasonality, or site? Identifying environmental correlates of the distribution of groundwater biota

The distribution of biota in aquatic ecosystems, including aquifers, is collectively influenced by habitat structure, water quality, seasonality, and local variations in environmental conditions. However, little is known about the nature and relative influences of such factors in groundwater ecosystems. Our aims were to identify the key environmental variables influencing the distribution of biota within the Gwydir River alluvial aquifer in northwestern New South Wales, Australia, and to consider the relative importance of environmental variables, in terms of habitat structure, water quality, seasonality, and site attributes, to both microbial and invertebrate (stygofauna) assemblages. Stygofauna distribution was primarily influenced by habitat variables (predominantly sediment structure) followed by site variables (abundance of trees), with water quality and seasonality having relatively little influence. These results indicate that it is the aquifer conditions relating to habitat structure, water flow, and the supply of organic matter that are most important for determining stygofauna distribution. Microbial assemblage structure was not strongly correlated with habitat variables, possibly because habitat restraints do not exist because of their smaller size. Instead, seasonality and water-quality variables had the greatest influence on microbial assemblages. Microbes might respond to seasonal (particularly rainfall induced) changes in water quality more quickly than do stygofauna, which may explain the relatively greater importance of seasonality and water quality to microbial assemblages. Given that stygofauna are most influenced by habitat and site variables, and microbial assemblages are most influenced by seasonality and water quality, disturbance to any of these factors may threaten the stability and integrity of the groundwater ecosystem.

Predicting ecosystem emergent properties at multiple scales.

Predicting ecosystem emergent properties at multiple scales.

Influence of hyporheic zone characteristics on the structure and activity of microbial assemblages

Summary The hyporheic zone is a pivotal environment for biogeochemical processes in riverine ecosystems. However, the responses of hyporheic microbial assemblage structure and activity to environmental variables remain poorly understood. The objective of this study was to determine the influence of hyporheic zone characteristics on microbial assemblages in three French rivers (Usses, Isère and Drôme). For each river, microbial structure (assemblage composition and abundance) and activity were measured at three sites with contrasting environmental characteristics (e.g. effective streambed porosity, oxygen and nutrient concentrations). Firstly, we expected that the structure and activity of the hyporheic microbial assemblage would be significantly affected by the environmental characteristics of the hyporheic zone. We also expected a strong relationship between the structure and activity of hyporheic microbial communities in the Usses River, due to greater spatial heterogeneity (i.e. greater porosity differences between the studied sites) compared with the two other rivers. Our results showed that porosity reduction, greatest in the Usses River, affected the exchanges of flows and energy through the hyporheic zone and, consequently, led to a distinct microbial assemblage composition in comparison with the two other rivers. Significant relationships between bacterial assemblage structure and activity were detected for the Usses and Drôme rivers, due to the greater spatial variability in sediment and physicochemical variables observed in these two rivers than in the Isère. Hyporheic zone characteristics (sediment permeability, water chemistry, particulate organic matter) appear to be the key factors controlling microbial structure and activity in riverine environments. As the hyporheic zone is essential for biogeochemical processes, including those attenuating pollution, a better quantification of the influences of environmental factors controlling microbial activity is needed to understand and predict ecosystem processes in the hyporheic zone.

Microbial community analysis of Deepwater Horizon oil-spill impacted sites along the Gulf coast using functional and phylogenetic markers

We investigated the impact of the Deepwater Horizon oil spill on microbial communities in wetland sediment and seawater samples collected from sites along the Gulf shore. Based on GC/MS analysis, the sediment from Bay Jimmy, LA had detectable signs of hydrocarbon contamination, identified as n-alkanes in the GC/MS spectrum similar to that of the Deepwater Horizon source oil (MC-252). To identify changes in microbial assemblage structure and functional diversity in response to hydrocarbon contamination, five genes (bacterial 16S rRNA, Pseudomonas-specific 16S rRNA, alkB, P450, and PAH-RHDα) were selected based on the specific enzymes encoded by bacteria to degrade alkanes or polycyclic aromatic hydrocarbons. A quantitative PCR analysis revealed the presence of alkane and PAH-degrading genes in both contaminated and non-contaminated samples with no significant difference in gene content between contaminated and non-contaminated samples. However, the ribotype analysis based on pyrosequencing identified 17 bacteria genera known for their capacity to degrade hydrocarbons, including Mycobacterium, Novosphingobium, Parvibaculum, Pseudomonas, and Sphingomonas, in the contaminated sediment sample. Furthermore, the contaminated sample had a very high relative abundance of 16S rRNA gene sequences affiliated with the genus Parvibaculum, members of which have been characterized for their degradative abilities. These data suggest that specific bacterial taxa within the genus Parvibaculum have the capacity for hydrocarbon degradation and could use the hydrocarbons as a carbon and energy source, resulting in a dominant population in a hydrocarbon-contaminated soil. In summary, when exposed to the spilled oil, the distinct wetland microbial communities responded with decreased diversity and increased abundance of selective degradative species.

Variation in ecosystem function in Appalachian streams along an acidity gradient

Acidification is a widespread phenomenon that damages aquatic systems, and it has been the focus of intensive management efforts. While most management has focused on community structure as an endpoint, ecosystem function is also sensitive to acidification and important in stream health. We examined how a key ecosystem function in streams, leaf breakdown, varied along a gradient of pH resulting from acid deposition, natural conditions, and liming. We also measured how invertebrate and microbial assemblage structure and microbial function were related to altered leaf breakdown rates. Leaf breakdown rates declined more than threefold along a gradient of stream acidity from pH 6.8 to 4.9. The diversity of leaf-shredding invertebrates, bacteria, and fungi showed little response to variation in pH. The abundance of one acid-sensitive caddisfly, Lepidostoma, declined with acidification, and Lepidostoma abundance explained 37% of the variation in leaf breakdown rates among sites. Microbial respiration was suppressed along the acidity gradient, although the pattern was weaker than that for breakdown rate. In short-term laboratory incubations, microbes at acidic and circumneutral sites demonstrated adaptation to ambient pH. The activity of microbial extracellular enzymes was strongly influenced by pH. In particular, the pattern of activity of phosphatase indicated increasing P limitation of microbes with increasing acidification. Our results show that leaf breakdown is a sensitive tool for examining the response of stream function to acidification and also for defining the mechanisms that drive functional response. Future management efforts should focus on key taxa that are particularly sensitive and effective at shredding leaves and also the role of shifting acidity in mediating the availability of phosphorus to microbial films that are important for stream function.

Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world

Araruama Lagoon is an environment characterized by high salt concentrations. The low raining and high evaporation rates in this region favored the development of many salty ponds around the lagoon. In order to reveal the microbial composition of this system, we performed a 16S rRNA gene survey. Among archaea, most clones were related to uncultured environmental Euryarchaeota. In lagoon water, we found some clones related to Methanomicrobia and Methanothermococcus groups, while in the saline pond water members related to the genus Haloarcula were detected. Bacterial community was dominated by clones related to Gamma-proteobacteria, Actinobacteria, and Synechococcus in lagoon water, while Salinibacter ruber relatives dominated in saline pond. We also detected the presence of Alpha-proteobacteria, Pseudomonas-like bacteria and Verrucomicrobia. Only representatives of the genus Ralstonia were cosmopolitan, being observed in both systems. The detection of a substantial number of clones related to uncultured archaea and bacteria suggest that the hypersaline waters of Araruama harbor a pool of novel prokaryotic phylotypes, distinct from those observed in other similar systems. We also observed clones related to halophilic genera of cyanobacteria that are specific for each habitat studied. Additionally, two bacterioplankton molecular markers with ecological relevance were analyzed, one is linked to nitrogen fixation (nifH) and the other is linked to carbon fixation by bacterial photosynthesis, the protochlorophyllide genes, revealing a specific genetic distribution in this ecosystem. This is the first study of the biogeography and community structure of microbial assemblages in Brazilian tropical hypersaline environments. This work is directed towards a better understanding of the free-living prokaryotic diversity adapted to life in hypersaline waters.

Antibiotic resistance of benthic bacteria in fish-farm and control sediments of the Western Mediterranean

The effects of fish farming on bacterial density, biomass, community structure and their possible link to antibiotic resistance have been investigated in coastal sediments of the Ligurian Sea (Western Mediterranean). The top 2 cm of the sediment under a fish farm and control areas were analysed during summer 2000. Bacterial density and biomass were three folds higher (up to 3×10 10 cells/g and 2602.7 μC/g) (ANOVA, p<0,01) in sediments beneath the fish cages compared to the control sediments. The number of Colony Forming Units (CFUs) for culturable bacteria and microbiological investigations indicated a shift in the relative importance of the Gram-negative bacteria in impacted sediments. Gram-positive bacteria increased their relevance in the control site where they represented up to 90% of total isolates. Antibiotic sensitivity tests showed a high percentage of resistant strains in both control and impacted sediments, which indicates a widespread antibiotic resistance within bacterial populations in areas surrounding fish farms. A high frequency of antibiotic resistance was observed for ampicillin (AMP) in impacted sediments (ANOVA, p<0.05). Gram-negative bacteria displayed the highest resistance to ampicillin, and streptomycin (STR) (ANOVA, p<0.05) and the shift in the structure of microbial assemblage was apparently related to the presence of Gram-negative resistant strains in fish-farm sediments. The incidence of multiple resistance patterns in bacterial isolates was also greater in impacted sediments and the presence of Bacillus strains producing antimicrobial compounds may be related to the high level of drug resistance. This study highlighted a major change occurring in the structure of the benthic bacterial community most probably due to fish farming and its close association with antibiotic resistance patterns.