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ISME J. 2014 Dec;8(12):2503-16. doi: 10.1038/ismej.2014.135. Epub 2014 Aug 5.

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage.

Author information

1
Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
2
1] Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA [2] Jena School for Microbial Communication (JSMC) and Microbial Ecology Group at Friedrich Schiller University Jena, Jena, Germany.
3
DOE Joint Genome Institute, Walnut Creek, CA, USA.
4
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
5
Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
6
1] DOE Joint Genome Institute, Walnut Creek, CA, USA [2] Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
7
1] Department of Limnology of Stratified Lakes, Leibniz-Institute for Freshwater Ecology and Inland Fisheries, Stechlin, Germany [2] Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany.
8
Jena School for Microbial Communication (JSMC) and Microbial Ecology Group at Friedrich Schiller University Jena, Jena, Germany.
9
Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
10
1] Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA [2] Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.

Abstract

Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.

PMID:
25093637
PMCID:
PMC4260696
DOI:
10.1038/ismej.2014.135
[Indexed for MEDLINE]
Free PMC Article

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