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Aquatic Microbial Ecology

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AME 28:141-155 (2002)  -  doi:10.3354/ame028141

Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers

Gabriel Zwart1,*, Byron C. Crump2, Miranda P. Kamst-van Agterveld1, Ferry Hagen1, Suk-Kyun Han3

1Centre for Limnology, Netherlands Institute of Ecology, Royal Netherlands Academy of Arts and Sciences, Rijksstraatweg 6, 3631 AC Nieuwersluis, The Netherlands
2The Ecosystem Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA
3University of Dankook, Laboratory of Microbial Ecology, Anseo San 29, South Korea

ABSTRACT: 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

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