Particle-associated Bacterial Communities Research Articles

Free-Living and Particle-Associated Microbial Communities of Lake Baikal Differ by Season and Nutrient Intake

In an aquatic ecosystem, the supply of nutrients is essential for the biogeochemical cycle, and it affects the taxonomic composition of the microbial communities. Here, by using high-throughput sequencing (HTS) of the 16S and 18S rRNA gene fragments, we compared free-living (FL) and particle-associated (PA) bacterial communities and microeukaryotic communities in the areas with different nutrient intakes in freshwater Lake Baikal during the ice-covered and summer periods. Samples were taken at the inflow of the Selenga River, which is the main tributary of the lake, and at several established coastal research stations. The metabolic potential of the bacterial communities was predicted using PICRUSt. Differences were found in both FL and PA communities of the river mouth compared to the photic zone of the lake. The composition of FL communities was significantly different between the sampling sites in the ice-covered period, which is most likely influenced by different hydrochemical conditions. In contrast, the PA communities were more similar during the ice-covered period, but they changed considerably from spring to summer and their diversity increased. The diversity of the microeukaryotic communities also increased in summer, which may have contributed to the increase in bacterial diversity. In co-occurrence networks analysis, the number of interconnected bacterial OTUs in FL exceeded those for PA. The FL communities were dominated by Actinobacteriota, while the major PA OTUs belonged to a mixed cluster, which were mainly assigned to the phyla Bacteroidota and Verrucomicrobiota. As a result, PA communities were enriched in pathways responsible for the metabolism of sulfur, fucose, cellulose and urea. Our results confirm the difference between the FL and PA bacterial communities in Lake Baikal. These results also highlight the complex pattern of interactions between bacteria and microeukaryotes in a natural freshwater ecosystem across spatial and temporal scales.

Particles act as 'specialty centers' with expanded enzymatic function throughout the water column in the western North Atlantic.

Heterotrophic bacteria initiate the degradation of high molecular weight organic matter by producing an array of extracellular enzymes to hydrolyze complex organic matter into sizes that can be taken up into the cell. These bacterial communities differ spatially and temporally in composition, and potentially also in their enzymatic complements. Previous research has shown that particle-associated bacteria can be considerably more active than bacteria in the surrounding bulk water, but most prior studies of particle-associated bacteria have been focused on the upper ocean - there are few measurements of enzymatic activities of particle-associated bacteria in the mesopelagic and bathypelagic ocean, although the bacterial communities in the deep are dependent upon degradation of particulate organic matter to fuel their metabolism. We used a broad suite of substrates to compare the glucosidase, peptidase, and polysaccharide hydrolase activities of particle-associated and unfiltered seawater microbial communities in epipelagic, mesopelagic, and bathypelagic waters across 11 stations in the western North Atlantic. We concurrently determined bacterial community composition of unfiltered seawater and of samples collected via gravity filtration (>3 μm). Overall, particle-associated bacterial communities showed a broader spectrum of enzyme activities compared with unfiltered seawater communities. These differences in enzymatic activities were greater at offshore than at coastal locations, and increased with increasing depth in the ocean. The greater differences in enzymatic function measured on particles with depth coincided with increasing differences in particle-associated community composition, suggesting that particles act as ‘specialty centers’ that are essential for degradation of organic matter even at bathypelagic depths.

Stochastic processes shape the aggregation of free‐living and particle‐attached bacterial communities in the Yangtze River Estuary, China

An estuary plays an important role in material and energy exchange between the land and sea, where complex physical, chemical, and biological processes occur. Here, we investigated the assembly processes of free-living (FL) and particle-associated (PA) bacterial communities in two seawater layers at five stations in the Yangtze River Estuary (YRE) by using 16S rRNA sequencing methods. The results indicated that Proteobacteria was the most abundant phylum in the YRE. The α-diversity of PA community was significantly higher than FL community, and analysis of similarity showed significantly different (Global R = 0.2809, p < 0.005). RDA revealed that phosphate (PO4 3- ) was significantly correlated with PA bacterial community abundance (p < 0.05). An ecological null model showed that both PA and FL bacterial communities were mainly influenced by stochastic processes (PA: 100%, FL: 70%), which PA attached to nutrient particles and are less affected by environmental filtration. Dispersal limitation (50%) was the main assembly process of the PA community, while homogeneous selection (30%) and drift (30%) were important processes in the FL community assembly. The available substrate for colonization limits the transformation from FL to PA bacteria. This study would improve our understanding of FL and PA bacterial community structure and factors affecting assembly process in estuarine environments.

Diversity and dynamics of particle-associated and free-living bacteria in eelgrass (Zostera marina) bed along the coast of Japan

As the seagrass leaves remain underwater, the primary source of leaf microbes is considered to be seawater heterotrophic bacterioplankton, which possess the ability to degrade biopolymers and are known to attach to surface and form biofilms. In this study, 16S rRNA gene amplicon sequencing was used to assess bacterial diversity and dynamics of the particle associated (PA) and free-living (FL) fraction of the seagrass-covering seawater (inside) and bulk seawater (outside) among different seagrass bed around Japan. Samples were collected from the three Zostera marinabeds (Ikuno-shima Is., Hiroshima; Nanao Bay, Ishikawa; Mutsu Bay, Aomori Prefecture) around Japan during summer (June-August 2015; July 2016). Prokaryotic DNA was extracted from samples using a FastDNA spin kit according to the manufacturer’s protocol. After extracting DNA, 16S ribosomal RNA (16S rRNA) genes were sequenced by Illumina Miseq platform. The Results showed that PA bacterial communities had a higher (p &lt;0.001) diversity than FL ones. Compared to the outside of the seagrass bed, the inside had lower diversity both in PA and FL fraction. Taxonomic analysis revealed a different community composition between lifestyle (PA vs FL) and sampling point (inside vs outside). Differential abundance analysis showed that PA were significantly enriched in a diversity of Cyanobacteria (Synechococcaceae), Saprospiraceae and Hyphomonadaceae. Conversely, FL were more abundant in Gammaproteobacteria (including Halomonadaceae, Alteromonadaceae), Microbacteriaceae, Campylobacteraceae, Pelagibacteraceae,Acidimicrobiia(OCS155). The present data provide a comprehensive description of the PA and FL microbial community in the seagrass bed and can be useful for better understanding the seagrass microbe interactions.

Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea.

Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.

Spatially resolved assembly, connectivity and structure of particle-associated and free-living bacterial communities in a high Arctic fjord.

ABSTRACTThe assembly processes that underlie the composition and connectivity of free-living (FL) and particle-associated (PA) bacterial communities from surface to deep waters remain little understood. Here, using phylogenetic null modeling, we quantify the relative influence of selective and stochastic mechanisms that assemble FL and PA bacterial communities throughout the water column in a high Arctic fjord. We demonstrate that assembly processes acting on FL and PA bacterial communities are similar in surface waters, but become increasingly distinct in deep waters. As depth increases, the relative influence of homogeneous selection increases for FL but decreases for PA communities. In addition, dispersal limitation and variable selection increase with depth for PA, but not for FL communities, indicating increased residence time of taxa on particles and less frequent decolonization. As a consequence, beta diversity of PA communities is greater in bottom than in surface waters. The limited connectivity between these communities with increasing depth leads to highly distinct FL and PA bacterial communities in bottom waters. Finally, depth-related trends for FL and PA beta diversity and connectivity in this study are consistent with previous observations in the open ocean, suggesting that assembly processes for FL and PA bacterial communities may also be distinct in other aquatic environments.

Changes in Free-Living and Particle-Associated Bacterial Communities Depending on the Growth Phases of Marine Green Algae, Tetraselmis suecica

Bacteria are remarkably associated with the growth of green algae Tetraselmis which are used as a feed source in aquaculture, but Tetraselmis-associated bacterial community is characterized insufficiently. Here, as a first step towards characterization of the associated bacteria, we investigated the community composition of free-living (FLB) and particle-associated (PAB) bacteria in each growth phase (lag, exponential, stationary, and death) of Tetraselmis suecica P039 culture using pyrosequencing. The percentage of shared operational taxonomic units (OTUs) between FLB and PAB communities was substantially high (≥92.4%), but their bacterial community compositions were significantly (p = 0.05) different from each other. The PAB community was more variable than the FLB community depending on the growth phase of T. suecica. In the PAB community, the proportions of Marinobacter and Flavobacteriaceae were considerably varied in accordance with the cell number of T. suecica, but there was no clear variation in the FLB community composition. This suggests that the PAB community may have a stronger association with the algal growth than the FLB community. Interestingly, irrespective of the growth phase, Roseobacter clade and genus Muricauda were predominant in both FLB and PAB communities, indicating that bacterial communities in T. suecica culture may positively affect the algae growth and that they are potentially capable of enhancing the T. suecica growth.

Impacts of Extreme Weather Events on Bacterial Community Composition of a Temperate Humic Lake

Extreme weather events are projected to increase in frequency and intensity as climate change continues. Heterotrophic bacteria play a critical role in lake ecosystems, yet little research has been done to determine how they are affected by such extremes. The purpose of this study was to use high-throughput sequencing to explore the bacterial community composition of a humic oligotrophic lake on the North Atlantic Irish coast and to assess the impacts on composition dynamics related to extreme weather events. Samples for sequencing were collected from Lough Feeagh on a fortnightly basis from April to November 2018. Filtration was used to separate free-living and particle-associated bacterial communities and amplicon sequencing was performed for the 16S rRNA V4 region. Two named storms, six high discharge events, and one drought period occurred during the sampling period. These events had variable, context-dependent effects on bacterial communities in Lough Feeagh. The particle-associated community was found to be more likely to respond to physical changes, such as mixing, while the free-living population responded to changes in nutrient and carbon concentrations. Generally, however, the high stability of the bacterial community observed in Lough Feeagh suggests that the bacterial community is relatively resilient to extreme weather events.

Comparative analysis of free-living and particle-associated bacterial communities of Lake Baikal during the ice-covered period

Free-living (FLC) and particle-associated (PAC) bacterial communities contribute differentially to the cycling of matter in the environment. In this work we have for the first time studied the taxonomic composition and diversity of FLC and PAC in the oligotrophic freshwater Lake Baikal during the under-ice plankton peak. The communities on the bottom ice surface and in the water column under the ice were studied. Analysis by light microscopy showed that the bottom surface of the ice was dominated by green algae Chlorella spp. A complex of microalgae developed in the water column: green algae Monoraphidium griffithii, Monoraphidium contortum, Chlorella spp., chrysophyte Dinobryon cylindricum, haptophyte Chrysochromulina parva, and diatom Synedra acus. Algal abundance on the ice sub-surface was several orders of magnitude higher than that in the water column. According to pyrosequencing data of the bacterial 16S rRNA V3-V4 region, diversity of FLC (as measured by Shannon, Simpson, Chao1 and ACE indices) was higher than that of PAC. Proteobacteria (Burkholderiaceae) dominated the FLC associated with ice; FLC of the water column under ice were dominated by Actinobacteria (Sporichthyaceae and Ilumatobacteraceae) and Verrucomicrobia (Methylacidiphilaceae). PAC associated with ice were dominated by Bacteroidetes (Flavobacteriaceae), while water column-associated PAC were dominated by Verrucomicrobia (FukuN18_freshwater_group, Methylacidiphilaceae) and cyanobacteria (Cyanobiaceae). The difference between free-living and particle-associated, as well as between water column and ice sub-surface bacterial communities, were explored on operational taxonomic unit (OTU) and phylotype levels.

Size-fractioned aggregates within phycosphere define functional bacterial communities related to Microcystis aeruginosa and Euglena sanguinea blooms

Phytoplankton growth and degradation are associated with bacterial communities in phycosphere. We compared the bacterial communities in two algal blooms (Microcystis aeruginosa and Euglena sanguinea). In particular, large particle-associated, small particle-associated, and free-living bacteria were collected in succession using membranes with three different pore sizes (10 µm, 1 µm, and 0.22 µm) in this study. The results showed that Proteobacteria and Bacteroidetes were the dominant phyla in both blooms. Significant differences in the structure, function, and assembly were observed between large particle-associated and free-living bacterial community in both blooms. Specifically, relative abundance of Roseomonas was higher in the large-size (> 10 µm) aggregates, while Candidate_division_TM7 and Candidate_division_SR1 were more abundant in the free-living bacterial community (0.22–1 µm). The large particle-associated bacterial community was mainly driven by heterogeneous selection and dispersal limitation, whereas the small particle-associated and free-living bacterial communities were mostly determined by dispersal limitation. Besides, some specific bacterial subgroups were found between M. aeruginosa and E. sanguinea blooms. Chlorobi, Chloroflexi, and Fusobacteria were abundant in the M. aeruginosa blooms, whereas Deinococcus–Thermus was abundant in the E. sanguinea blooms. Those specific bacteria provide competitive advantages for the dominated algae. Altogether, these findings indicate that the phycosphere of bloom-forming algae provides different ecological niches where different functional bacterial groups can adapt.

Bacterial communities associated with scyphomedusae at Helgoland Roads

Different modes of asexual and sexual reproduction are typical for the life history of scyphozoans, and numerous studies have focused on general life history distribution, reproductive strategies, strobilation-inducing factors, growth rates, and predatory effects of medusae. However, bacteria associated with different life stages of Scyphozoa have received less attention. In this study, bacterial communities associated with different body compartments and different life stages of two common scyphomedusae (Cyanea lamarckii and Chrysaora hysoscella) were analyzed via automated ribosomal intergenic spacer analysis (ARISA). We found that the bacterial community associated with these two species showed species-specific structuring. In addition, we observed significant differences between the bacterial communities associated with the umbrella and other body compartments (gonads and tentacles) of the two scyphomedusan species. Bacterial community structure varied from the early planula to the polyp and adult medusa stages. We also found that the free-living and particle-associated bacterial communities associated with different food sources had no impact on the bacterial community associated with fed polyps.

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints

The general consensus is that the abundance of tap water bacteria is greatly influenced by water purification and distribution. Those bacteria that are released from biofilm in the distribution system are especially considered as the major potential risk for drinking water bio-safety. For the first time, this full-scale study has captured and identified the proportional contribution of the source water, treated water, and distribution system in shaping the tap water bacterial community based on their microbial community fingerprints using the Bayesian “SourceTracker” method. The bacterial community profiles and diversity analyses illustrated that the water purification process shaped the community of planktonic and suspended particle-associated bacteria in treated water. The bacterial communities associated with suspended particles, loose deposits, and biofilm were similar to each other, while the community of tap water planktonic bacteria varied across different locations in distribution system. The microbial source tracking results showed that there was not a detectable contribution of source water to bacterial community in the tap water and distribution system. The planktonic bacteria in the treated water was the major contributor to planktonic bacteria in the tap water (17.7–54.1%). The particle-associated bacterial community in the treated water seeded the bacterial community associated with loose deposits (24.9–32.7%) and biofilm (37.8–43.8%) in the distribution system. In return, the loose deposits and biofilm showed a significant influence on tap water planktonic and particle-associated bacteria, which were location dependent and influenced by hydraulic changes. This was revealed by the increased contribution of loose deposits to tap water planktonic bacteria (from 2.5% to 38.0%) and an increased contribution of biofilm to tap water particle-associated bacteria (from 5.9% to 19.7%) caused by possible hydraulic disturbance from proximal to distal regions. Therefore, our findings indicate that the tap water bacteria could possibly be managed by selecting and operating the purification process properly and cleaning the distribution system effectively.

Differences in free-living and particle-associated bacterial communities and their spatial variation in Kongsfjorden, Arctic

High throughput V3-16S rRNA amplicon sequencing data was used for evaluating differences between free-living (FL, <1.2-0.2 μm) and particle-associated (PA, >1.2 μm) bacterial communities, and their spatial variation between inner fjord (IF) and outer fjord (OF) of Kongsfjorden. A total of 4,454,142 high quality sequences obtained clustered into 32,058 OTUs. A majority of these sequences were affiliated with Proteobacteria (59.8%), followed by Bacteroidetes (29.02%), Firmicutes (5.9%), Actinobacteria (2.84%), Cyanobacteria (1.04%), and others (1.4%). The highest bacterial diversity was recorded in the inner fjord free-living (IF_FL) fraction whilst the lowest was observed in the outer fjord free-living (OF_FL) fraction. There was a clear spatial variation among FL bacterial communities, while PA communities remained similar at both sampling locations. The free-living bacterial community differs from particle-associated community and had relatively higher abundance (>4-fold) of Alteromonas and Pseudoalteromonas, while PA community was relatively more enriched with Balneatrix, Ulvibacter, Formosa, Candidatus Planktomarina, Sulfitobacter, Loktanella, members of SAR116, and Acidimicrobiales. In addition, two major bacterial taxa, Polaribacter and SAR11, co-occurred in both FL and PA fractions with varied proportions in IF and OF. These results suggest co-occurrence of PA specialist as well as generalist bacterial groups in Kongsfjorden. Further, high bacterial diversity in the IF_FL fraction indicates possible role of glacial inputs in modulating diversity of free-living bacterial community in Kongsfjorden.

Diversity and community composition of particle‐associated and free‐living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: Evidence of dispersal limitation in the Bransfield Strait

AbstractThe Southern Ocean constitutes about 10% of the global oceans' volume and is characterized by high primary production. Particulate organic matter (POM) is exported from the photic zone to the deep ocean and sustains life of particle associated (PA) and free‐living (FL) bacterial communities in the dark realm. Little is known about the composition and diversity of PA and FL bacterial communities below the photic zone and how they differ among various regions of the Southern Ocean. Therefore, we investigated the composition of small (3–8 μm) and large (&gt; 8 μm) PA and FL (0.2–3 μm) bacterial communities between 500 m and 3600 m in the Bransfield Strait, Drake Passage, and the south Atlantic Ocean featuring also Southern Ocean water masses. PA bacterial communities had a higher OTU richness and evenness than FL ones. Taxonomic analysis revealed a different community composition between FL and PA bacteria. A large number of OTUs belonging to diverse phyla (Bacteroidetes, Planctomycetes, Betaproteobacteria, Deltaproteobacteria, and Verrucomicrobia) were significantly enriched on particles; in contrast very few bacterial lineages were FL specialists. Life‐style (FL vs. PA) and region (Bransfield basin vs. other regions) strongly influenced bacterial communities. Depth explained only marginal fraction of the total variation (∼ 12%), suggesting that selective processes driven by depth have a smaller effect in the Southern Ocean when compared to life‐style (25%) and region (31%). Overall these data indicate a strong influence of isolated water masses such as the basin of the Bransfield Strait on the composition of bacterial communities in the dark ocean.

Dynamics of size-fractionated bacterial communities during the coastal dispersal of treated municipal effluents.

Everyday huge amount of treated municipal wastewater is discharged into the coastal seawater. However, microbial biomarkers for the municipal effluent instead of the fecal species from raw sewage have not been proposed. Meanwhile, bacterial taxa for degrading large amounts of input organics have not been fully understood. In this study, raw effluent and serial water samples were collected from the coastal dispersal of two sewage treatment plants in Xiamen, China. Free-living (FL) and particle-associated (PA) bacterial communities were analyzed via high-throughput sequencing of 16S rRNA gene and quantitative PCR to measure bacterial abundance. The PA bacterial communities in our samples exhibited higher cell abundance, alpha diversity, and population dynamics than the FL bacterial communities, which supports greater environmental significance of the PA bacterial communities. Two non-fecal but typical genera in activated sludge, Zoogloea and Dechloromonas, exhibited decreased but readily detectable abundance along the effluent dispersal distance. Furthermore, the dominating microbial species near the outfalls were related to well-known marine indigenous taxa, such as SAR11 clade, OM60 clade, low-GC Actinobacteria, and unclassified Flavobacteriales, as well as the less understood taxa like Pseudohongiella and Microbacteriaceae. It is interesting that these taxa exhibited two types of correlation patterns with COD concentration. Our study suggested Zoogloea as a potential indicator of municipal effluents and also proposed potential utilizers of residual effluent COD in marine environments.

Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla.

Despite their homogeneous appearance, aquatic systems harbour heterogeneous habitats resulting from nutrient gradients, suspended particulate matter and stratification. Recent reports suggest phylogenetically conserved habitat preferences among bacterioplankton, particularly for particle-associated (PA) and free-living (FL) habitats. Here, we show that independent of lake nutrient level and layer, PA and FL abundance-weighted bacterial community composition (BCC) differed and that inter-lake BCC varied more for PA than for FL fractions. In low-nutrient lakes, BCC differences between PA and FL fractions were larger than those between lake layers. The reverse was true for high-nutrient lakes. Nutrient level affected BCC more in hypolimnia than in epilimnia, likely due to hypolimnetic hypoxia in high-nutrient lakes. In line with previous reports, we observed within-phylum operational taxonomic unit (OTU) habitat preference conservation, although not for all phyla, including the phylum with the highest average relative abundance across all habitats (Bacteroidetes). Consistent phylum-level habitat preferences may indicate that the functional traits that underpin ecological adaptation of freshwater bacteria to lake habitats can be phylogenetically conserved, although the levels of conservation are phylum dependent. Resolving taxa preferences for freshwater habitats sets the stage for identification of traits that underpin habitat specialization and associated functional traits that influence differences in biogeochemical cycling across freshwater lake habitats.

Bacterial diversity along a 2600 km river continuum

SummaryThe bacterioplankton diversity in large rivers has thus far been under‐sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA‐gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free‐living and particle‐associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the P olynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater‐affiliated bacteria. Based on views of the meta‐community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity.

Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns

Seasonal changes in environmental conditions have a strong impact on microbial community structure and dynamics in aquatic habitats. To better elucidate the response of bacterial communities to environmental changes, we have measured a large variety of limnetic variables and investigated bacterial community composition (BCC) and dynamics over seven consecutive years between 2003 and 2009 in mesotrophic Lake Tiefwaren (NE Germany). We separated between free-living (FL, >0.2, <5.0 μm) and particle-associated (PA, >5.0 μm) bacteria to account for different bacterial lifestyles and to obtain a higher resolution of the microbial diversity. Changes in BCC were studied by DGGE based on PCR-amplified 16S rRNA gene fragments. Sequencing of DGGE bands revealed that ca. 70 % of all FL bacteria belonged to the Actinobacteria, whereas PA bacteria were dominated by Cyanobacteria (43 %). FL communities were generally less diverse and rather stable over time compared to their PA counterpart. Annual changes in reoccurring seasonal patterns of dominant freshwater bacteria were supported by statistical analyses, which revealed several significant correlations between DGGE profiles and various environmental variables, e.g. temperature and nutrients. Overall, FL bacteria were generally less affected by environmental changes than members of the PA fraction. Close association of PA bacteria with phytoplankton and zooplankton suggests a tight coupling of PA bacteria to organisms of higher trophic levels. Our results indicate substantial differences in bacterial lifestyle of pelagic freshwater bacteria, which are reflected by contrasting seasonal dynamics and relationships to a number of environmental variables.

Regional patterns of bacterial community composition and biogeochemical properties in the southern North Sea

The German Bight of the North Sea is characterized by intertidal flats, with high loads of suspended particulate matter (SPM) and estuarine inputs of organic matter, as well as pelagic off- shore regions. Due to tidal and wind-induced currents, the hydrography of this area is highly dynamic. In order to examine how these properties affect the regional distribution and composition of the bacterioplankton we conducted 2 surveys, in June 2002 and June 2003; in these surveys we assessed the composition of the free-living (FL) and particle-associated (PA) bacterial communities together with hydrographic properties (salinity, temperature) and biogeochemical properties (SPM, particulate organic carbon, chlorophyll, phytoplankton composition). The bacterial community com- position was determined by denaturing gradient gel electrophoretic (DGGE) analysis of 16S rRNA gene fragments, PCR-amplified by Bacteria-, Alphaproteobacteria- and Bacteroidetes-specific primer sets, and sequencing of excised bands. The results, and a multidimensional scaling (MDS) analysis of the DGGE banding patterns, showed distinct differences in the bacterial community com- position of the FL and PA fractions and also between the inshore and offshore stations. A canonical correspondence analysis (CCA), including the DGGE banding patterns, temperature, salinity and biogeochemical parameters, further showed that the community patterns and the inshore and off- shore gradients can be explained to a great extent by the hydrographic and biogeochemical condi- tions. Several prominent bands, identified as phylotypes affiliated to the Roseobacter clade, persisted throughout all 10 stations visited, whereas other phylotypes occurred only at distinct stations, inshore and offshore.

Microbial Community Structure and Biodegradation Activity of Particle-Associated Bacteria in a Coal Tar Contaminated Creek

The Chattanooga Creek Superfund site (Chattanooga, TN) is one of the most polluted waterways in the southeastern U.S. with high polycyclic aromatic hydrocarbon (PAH) concentrations in the sediments. PAHs associate with suspended solids in the water column, and may be redeposited onto the floodplain. These suspended particles represent an interesting but understudied environment for PAH-degrading microbial communities. This study tested the hypotheses that particle-associated bacterial (PAB) communities have genotypic potential (PAH-dioxygenase genes) and activity (naphthalene and pyrene mineralization), and can contribute to natural attenuation of PAHs in Chattanooga Creek. Upstream of the Superfund site, mineralization ranged from 0.2 to 2.0% of added 14C-naphthalene and 0 to 0.1% 14C-pyrene (after 40 h), with first order biodegradation rate constants (k1) ranging from 1.09 to 9.18 x 10(-5) h(-1) and 0 to 1.13 x 10(-6) h(-1), respectively. Mineralization was significantly greater in PAB communities within the contaminated zone, with 11.8 to 31.2% 14C-naphthalene (k1 5.34 to 14.2 x 10(-4) h(-1)) and 1.3 to 6.6% 14C-pyrene mineralized (k1 2.89 to 15.0 x 10(-5) h(-1)). Abundances of nagAc (naphthalene dioxygenase) and nidA (pyrene dioxygenase) genes indicated that PAB communities harbored populations with genetic potential for both low- and high-molecularweight PAH degradation, and quantification of Mycobacterium 16S rDNA genes indicated that PAH-degrading mycobacteria are also prevalent in this environment. Phylogenetic comparisons (T-RFLPs) between PAB and sediments indicated these microbial communities were taxonomically distinct, but shared some functional similarities, namely PAH catabolic genotypes, mineralization capabilities, and community structuring along a contamination gradient