MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, Mar. 2011, p. 14–49 Vol. 75, No. 1 1092-2172/11/$12.00 doi:10.1128/MMBR.00028-10 Copyright © 2011, American Society for Microbiology. All Rights Reserved. A Guide to the Natural History of Freshwater Lake Bacteria† Ryan J. Newton,1 Stuart E. Jones,2 Alexander Eiler,3 Katherine D. McMahon,4 and Stefan Bertilsson3* Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin1; Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana2; Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden3; and Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin4 INTRODUCTION .........................................................................................................................................................14 Historical Perspectives.............................................................................................................................................15 CREATING A MODERN VIEW OF FRESHWATER LAKE BACTERIA ...........................................................16 Phylogenetic Tree Reconstructions and Cluster Classification..........................................................................17 Common Lineages of Freshwater Lake Bacteria..................................................................................................17 Phylum Actinobacteria...............................................................................................................................................18 Actinobacteria 16S rRNA gene-based phylogeny ...............................................................................................19 Ecology of the freshwater lake Actinobacteria ...................................................................................................19 Actinobacteria summary ........................................................................................................................................23 Phylum Bacteroidetes.................................................................................................................................................23 Bacteroidetes 16S rRNA gene-based phylogeny..................................................................................................23 Ecology of the freshwater lake Bacteroidetes .....................................................................................................23 Bacteroidetes summary ..........................................................................................................................................26 Phylum Cyanobacteria...............................................................................................................................................26 Cyanobacteria 16S rRNA gene-based phylogeny................................................................................................26 Phylum Proteobacteria...............................................................................................................................................26 Class Alphaproteobacteria .........................................................................................................................................26 Alphaproteobacteria 16S rRNA gene-based phylogeny ......................................................................................26 Ecology of the freshwater lake Alphaproteobacteria ..........................................................................................26 Alphaproteobacteria summary...............................................................................................................................29 Class Betaproteobacteria............................................................................................................................................29 Betaproteobacteria 16S rRNA gene-based phylogeny.........................................................................................29 Ecology of the freshwater lake Betaproteobacteria.............................................................................................30 Betaproteobacteria summary .................................................................................................................................31 Class Gammaproteobacteria......................................................................................................................................31 Gammaproteobacteria 16S rRNA gene-based phylogeny...................................................................................33 Ecology of the freshwater lake Gammaproteobacteria.......................................................................................33 Phylum Verrucomicrobia ...........................................................................................................................................33 Verrucomicrobia 16S rRNA gene-based phylogeny............................................................................................33 Ecology of the freshwater lake Verrucomicrobia................................................................................................33 Minor Freshwater Lake Phyla ................................................................................................................................34 16S rRNA gene-based phylogenies of minor phyla ..........................................................................................34 Ecology of minor freshwater lake phyla ............................................................................................................34 Summary of minor phyla.....................................................................................................................................34 META-ANALYSIS: LIFE HISTORY PATTERNS OF FRESHWATER LAKE BACTERIA ..............................34 Natives, Vagabonds, or Tourists?...........................................................................................................................34 Biogeography of the Freshwater Lake Tribes.......................................................................................................35 OUTLOOK: HOW TO USE THIS GUIDE...............................................................................................................42 Nucleotide sequence accession numbers............................................................................................................44 ACKNOWLEDGMENTS .............................................................................................................................................44 REFERENCES ..............................................................................................................................................................44 INTRODUCTION put the “microbial ooze” at the center of a diagram depicting the trophic dynamics in a northern temperate lake, Cedar The biogeochemical importance of bacteria in freshwater Creek Bog (121). Since this early recognition of the critical role ecosystems was first recognized in the 1940s, when Lindeman of bacteria in regenerating and mobilizing nutrients in fresh- water food webs, it has become clear that aquatic bacteria * Corresponding author. Mailing address: Department of Ecology & drive transformations and the cycling of most biologically ac- Genetics, Limnology, Uppsala University, Uppsala SE-75236, Sweden. tive elements in these ecosystems. This key position held in Phone: 46-18-4712712. Fax: 46-18-4712000. E-mail: [email protected]. † Supplemental material for this article may be found at http://mmbr essentially all biogeochemical cycles does not merely stem .asm.org/. from the role of bacteria as the principal degraders and min- 14 VOL. 75, 2011 PHYLOGENY AND ECOLOGY OF FRESHWATER LAKE BACTERIA 15 eralizers of organic compounds to their inorganic constituents for freshwater lake bacterial taxa, our approach to this natural (30, 36) but also results from their biomass production and history guide was to gather all published freshwater lake 16S trophic coupling to eukaryote predators, which, by fueling the rRNA gene sequences, construct high-quality phylogenies, and food web, has a profound impact on elemental fluxes and water propose a new vocabulary that unifies taxon names and pro- quality in the ecosystem (154). Given the facts that lakes and vides a platform with which to discuss these important fresh- other inland waters play a more critical role in the global water lake taxa (akin to the approach taken by Zwart and carbon budget than previously recognized (31) and that lakes colleagues [238]). We use a classification system that is hier- have been described as early indicators (i.e., sentinels) of both archical like Linnaean taxonomy but based on phylogenetics. regional and global environmental change (133, 228), the role Our classification system is also designed to maintain the phy- of microbes in these processes is of renewed interest. logenetic context by which freshwater bacterial gene sequences Despite the recognition that bacteria occupy a prominent historically have been identified, clustered, and named. With role in lake ecosystem processes and greatly impact lake water this natural history guide, we are not endorsing “phylogenetic” quality, the bacterial taxa participating in these activities re- over “Linnaean” systematization (debate reviewed in refer- main largely undescribed. Molecular biology tools