In order to identify patterns in bacterial community composition in freshwater habitats, we analyzed the available database of 16S rDNA sequences from freshwater plankton, including 24 new sequences from Parker River (Massachusetts, USA), 42 from Lake Soyang (South Korea) and 148 from Lake IJssel (The Netherlands). At this point, combined diversity studies using random cloning have deposited 689 bacterial and 75 plastid 16S rDNA sequences from the water column of rivers and lakes in North America, Europe and Asia. Systematic comparisons with the global database showed that the majority of the bacterial sequences were most closely related to other freshwater clones or isolates, while relatively few were closest to sequences recovered from soils or marine habitats. This habitat-specific clustering suggests that the clustered 16S rDNA sequences represent species or groups of species that are indigenous to freshwater. We have discerned 34 phylogenetic clusters of closely related sequences that are either restricted to freshwater or dominated by freshwater sequences. Of these clusters, 23 contained no cultivated organisms. These putative freshwater clusters were found among the alpha-, beta-and gamma-Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides group, the Cyanobacteria, the Actinobacteria, the Verrucomicrobia, the green non-sulfur bacteria and candidate division OP10. This study shows that rivers and lakes have a specific planktonic bacterial community distinct from bacteria in neighboring environments such as soil and sediments. It also points out that these planktonic bacteria are distributed in diverse freshwater ecosystems around the world.KEY WORDS: Microbial diversity · Ribosomal RNA gene · Freshwater · Habitat · Polymerase chain reaction · Phylogeny · Nucleotide sequence database Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 28: [141][142][143][144][145][146][147][148][149][150][151][152][153][154][155] 2002 has made it possible to obtain information on microbial community composition directly, without cultivation (Giovannoni et al. 1990). An environmental sample can be inventoried for taxa present by direct nucleic acid isolation, followed by amplification of particular marker genes and analysis of the sequence of base pairs. The most widely used marker gene is the small subunit rRNA gene (16S rDNA), and the recent application of molecular techniques in a variety of habitats has produced a large set of sequences from this gene. This growing database has taught us that the diversity of the microbial world is much larger than we were able to estimate before the use of molecular techniques (Pace 1997, Hugenholtz et al. 1998). However, a clear view of the species or groups of species that we can expect in particular environments is still lacking. This is due in part to the great diversity of bacteria. In addition, an overview is lacking due to the focused approach followed in many molecular diversity studies. While most studies compare ret...

There is a vivid debate on the relative importance of local and regional factors in shaping microbial communities, and on whether microbial organisms show a biogeographic signature in their distribution. Taking a metacommunity approach, spatial factors can become important either through dispersal limitation (compare large spatial scales) or mass effects (in case of strongly connected systems). We here analyze two datasets on bacterial communities [characterized by community fingerprinting through denaturing gradient gel electrophoresis (DGGE)] in meso-to eutrophic shallow lakes to investigate the importance of spatial factors at three contrasting scales. Variation partitioning on datasets of both the bacterial communities of 11 shallow lakes that are part of a strongly interconnected and densely packed pond system <1 km apart, three groups of shallow lakes Ϸ100 km apart, as well as these three groups of shallow lakes combined that span a large part of a North-South gradient in Europe (>2,500 km) shows a strong impact of local environmental factors on bacterial community composition, with a marginal impact of spatial distance. Our results indicate that dispersal is not strongly limiting even at large spatial scales, and that mass effects do not have a strong impact on bacterial communities even in physically connected systems. We suggest that the fast population growth rates of bacteria facilitate efficient species sorting along environmental gradients in bacterial communities over a very broad range of dispersal rates. dispersal limitation ͉ metacommunity biology ͉ microbial biogeography ͉ microbial community ͉ mass effects

The distribution of 15 typical freshwater bacterial groups in 15 diverse lakes in northern Europe was investigated using reverse line blot hybridization. Statistical evaluation of the data in relation to the characteristics of the lakes showed that pH, temperature, and the theoretical hydrological retention time of the lakes were most strongly related to variations in the distribution of bacterial taxa. This suggests that pH and temperature are steering factors in the selection of taxa and supports the notion that communities in lakes with short water turnover times are influenced by the input of bacterial cells from the drainage areas. Within the beta subdivision of the Proteobacteria (Betaproteobacteria), as well as within the divisions Actinobacteria and Verrucomicrobia, different subgroups were associated differently with environmental variables.While huge efforts to explore the diversity of the bacterial kingdom have been made, very little understanding of the factors that drive the actual composition of bacterial communities has been gained. A number of studies have sought associations between molecular community fingerprints, such as those obtained by denaturing gradient gel electrophoresis, and environmental factors. In studies of lakes, multivariate analyses showed that factors such as the biomass of other plankton groups (11,15,16,22,26), pH (24, 28), nutrient concentrations (24, 26, 29), temperature (11,22,24,26,28,29), and water flow (11, 24) covary with bacterioplankton fingerprints. Such associations suggest that these environmental factors are important in determining the distribution of taxa. However, fingerprinting methods are not well suited for revealing the identities of the various taxa. An alternative method for characterizing bacterial communities is fluorescence in situ hybridization (FISH), in which taxon-specific probes are used, which improves identification. In addition, FISH provides information on cell number and shape. However, the amount of work involved in FISH soon prohibits analysis of a set of taxa in a set of habitats, a requirement for finding taxon-environment associations. Therefore, little information about which environmental variables determine the abundance of individual bacterial groups is available.The aims of this study were to further explore possible determinative factors for bacterioplankton community composition in lakes and, in particular, to identify factors that influence the appearance of individual bacterial groups. We used reverse line blot hybridization with probes targeted at the 16S rRNA gene in order to analyze the distribution of 15 bacterial groups in relation to environmental gradients. The groups chosen were previously designated "putative typical freshwater bacterial clusters" since they were shown to occur in several freshwater bodies and the 16S rRNA gene sequences in the database for these groups contained more sequences from freshwater sources than from terrestrial or marine sources (30, 31).

The influence of altitude and salinity on bacterioplankton community composition (BCC) in 16 highmountain lakes located at altitudes of 2,817 to 5,134 m on the Eastern Qinghai-Xizang (Tibetan) Plateau, China, spanning a salinity gradient from 0.02% (freshwater) to 22.3% (hypersaline), was investigated. Three different methods, fluorescent in situ hybridization, denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing, and reverse line blot hybridization (RLB) with probes targeting 17 freshwater bacterial groups, were used for analysis of BCC. Furthermore, the salt tolerances of 47 strains affiliated with groups detected in or isolated from the Tibetan habitats were investigated. Altitude was not found to influence BCC significantly within the investigated range. Several groups of typical freshwater bacteria, e.g., the ACK-M1 cluster and the Polynucleobacter group, were detected in habitats located above 4,400 m. Salinity was found to be the dominating environmental factor controlling BCC in the investigated lakes, resulting in only small overlaps in the BCCs of freshwater and hypersaline lakes. The relative abundances of different classes of Proteobacteria showed a sharp succession along the salinity gradient. Both DGGE and RLB demonstrated that a few freshwater bacterial groups, e.g., GKS98 and LD2, appeared over wide salinity ranges. Six freshwater isolates affiliated with the GKS98 cluster grew in ecophysiological experiments at maximum salinities of 0.3% to 0.7% (oligosaline), while this group was detected in habitats with salinities up to 6.7% (hypersaline). This observation indicated ecologically significant differences in ecophysiological adaptations among members of this narrow phylogenetic group and suggested ecological significance of microdiversity.Saline lakes constitute 45 percent of total inland water (running and stagnant waters) (47). Despite the quantitative importance of saline lakes, only a few studies have investigated the diversity of bacterioplankton in such habitats (13,15,23). By contrast, the influence of salinity on bacterioplankton community composition (BCC) in dynamic saline systems, such as estuaries (6,11,12,25,26,37) and coastal solar salterns (3,7,8), has been well investigated. Therefore, the current knowledge on the influence of salinity on BCC is almost completely based on investigations of systems characterized by rapid changes in salinity. These systems are too dynamic to allow inhabitants to evolutionarily adapt to the changing environment. All studies on such systems indicate that salinity strongly controls BCC, i.e., changes in salinity are assumed to result in replacement of suboptimally adapted taxa by taxa better adapted to the current salinity conditions. By contrast, the slow evolution of large saline lakes from freshwater lakes may have allowed bacterial taxa originally adapted to freshwater conditions to adapt to saline conditions. In order to reveal the influence of salinity on the BCC of stagnant inland waters, 16 lakes located at the Qingha...