Patterns and governing forces in aquatic microbial communities

In this review we survey recent publications employing molecular techniques to investigate the distribution of microbial species in aquatic environments. We analyzed the occurrence of microbial phyla in freshwater and marine habitats and observed patterns of distribution that could be explained by the adaptation of microorganisms to physical and biological parameters that vary in aquatic habitats. The gram-positive bacteria, the Verrucomicrobiales and the a- and ?-subdivisions of the Proteobacteria are distributed throughout a range of aquatic habitats, while other phylogenetic groups appear to be adapted to more narrowly defined environmental niches such as anoxic water and sediments (d-Proteobacteria) or floating aggregates (Cytophaga-Flexibacter-Bacteroides phylum). ß-proteobacterial sequence types have been detected throughout freshwater habitats, but these organisms are largely absent from open ocean environments. Within several of these divisions, clusters of closely related small sub unit ribosomal RNA sequence types have been detected in geographically disparate environments, suggesting that some microbial species are globally distributed. In addition to physical variables such as salinity and pH, biological variables also influence microbial community composition. This was illustrated by changes that occurred in the eukaryotic and bacterial species composition in laboratory mesocosms after a viral outburst. We conclude that physical and biological forces govern the composition of aquatic microbial communities and result in divergent evolutionary histories of the indigenous microbial species. [KEYWORDS: bacteria, community composition, diversity, freshwater, marine, ribosomal RNA]

Ammonium addition inhibits 13C-methane incorporation into methanotroph membrane lipids in a freshwater sediment

To investigate the effect of ammonium addition on the species composition and activity of freshwater methane oxidizing bacteria, intact sediment cores were labeled with (CH4)-C-13 and incubated under ambient and elevated ammonium concentrations. After 7 days, methanotroph activity was assessed by quantifying the isotopic composition of the carbon in membrane lipids. The 16-carbon rather than the 18-carbon methanotroph-specific biomarkers showed a clear enrichment in C-13, suggesting the importance of group I methanotrophs in these sediments. Ammonium addition resulted in a depleted isotopic signal compared to ambient controls, suggesting that high ammonium concentrations inhibit methane incorporation into cellular components. These results compare favorably with studies that showed ammonium inhibition of methane oxidation, and extend these findings by demonstrating the effect of nitrogen fertilization on methanotroph lipid synthesis. [KEYWORDS: methane; freshwater; sediment; ammonium; lipid; stable carbon isotope Methane oxidation; fatty-acid; atmospheric methane; community structure; loosdrecht lakes; peaty sediments; eutrophic lake; bacteria; carbon; nitrification]

Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria

We compared bacterial 16S ribosomal RNA gene sequences recovered from Lake Loosdrecht, the Netherlands, to reported sequences from lakes in Alaska and New York State. In each of the three lake systems, which differ in pH and trophic state, some sequence types were found without related sequences (sequence identity <90%) in the data sets from the other two systems. Two sequences in the Actinomycetes and Verrucomicrobia radiations were more closely related to sequences from the New York: lakes data set than to any other sequence in the global databases. However, the most striking similarities were found in the subdivisions alpha and beta of the Proteobacteria. In these subdivisions three different clusters of highly related bacteria were identified (97-100% sequence identity) that were represented in all three lake regions. The clusters contained no members other than freshwater bacteria. One cluster falls within a monophyletic aquatic supergroup that apparently diverged early in evolution into an exclusive freshwater cluster and an exclusive marine cluster, the so-called SAR11 cluster. The detection of these three bacterial clades in lakes distinguished by geographic distance as well as physical and chemical diversity suggests that these organisms are dispersed globally and that they possess unique functional capabilities enabling successful competition in a wide range of freshwater environments. [KEYWORDS: global distribution; freshwater bacteria; ribosomal RNA; SAR11 cluster; Proteobacteria; dispersal; bacterioplankton; community analysis; lakes Gradient gel-electrophoresis; ribosomal-rna genes; phylogenetic diversity; euplotes-aediculatus; sar11 cluster; arctic lake; endosymbiont; populations; communities; alignment]

Identification of Meiothermus as the dominant genus in a storage system for spent nuclear fuel

Aims: To characterize the biofilms in an interim wet storage system (CLAB) for spent nuclear fuel. Methods and Results: Planktonic cells and biofilms were analysed with fluorescence microscopy, and scanning and transmission electron microscopy. The organisms in the biofilms were filamentous, consisting of sheaths with series of rod-shaped cells in them. Planktonic cell populations ranged between 1Æ4 · 103 and 5Æ2 · 103 ml)1, correlated with the system configuration, and was inversely correlated with total organic carbon (TOC) levels. Analysis of 16S rDNA indicated that a potentially novel Meiothermus sp. was dominant in the CLAB biofilms. A Meiothermus-specific probe was designed, and statistical analysis of fluorescence in situ hybridization results confirmed that Meiothermus sp. composed up to 98% of the biofilm. The low TOC levels (2–55 lg l)1) in the system combined with elevated water temperatures (ca 36C) mimic the natural environments of Meiothermus sp. as well as the recommended conditions for isolating Meiothermus sp., thus supporting the results of the 16S rDNA analysis. Conclusions: A possibly novel Meiothermus sp. is the predominant genus found in the CLAB biofilms. Significance and Impact of the Study: TOC levels are often kept low to protect industrial systems from biofouling. However, the present study shows that, rather than protecting industrial systems against biofouling per se, maintaining low TOC levels might still result in biofilms, dominated by new, unknown bacterial species