Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

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Title: Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
Authors: Garcia, Sarahi L. | McMahon, Katherine D. | Martinez-Garcia, Manuel | Srivastava, Abhishek | Sczyrba, Alexander | Stepanauskas, Ramunas | Grossart, Hans-Peter | Woyke, Tanja | Warnecke, Falk
Research Group/s: Ecología Microbiana Molecular
Center, Department or Service: Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología
Keywords: Freshwater Actinobacteria | Metabolic potential | Single-cell genomics
Knowledge Area: Microbiología
Issue Date: 19-Jul-2012
Publisher: Nature Publishing Group
Citation: The ISME Journal (2013) 7, 137–147; doi:10.1038/ismej.2012.86
Abstract: Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (~42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (~15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria.
Sponsor: This work was supported by NSF grants DEB-841933 and OCE-821374 to RS. HPG and Abhishek Srivastava were supported by a grant given by the German Science foundation (DFG GR 1540/17-1). SLG and FW thank JSMC for funding and support. We also thank Drs Rohit Ghai and Francisco Rodriguez-Valera at the Universidad Miguel Hernandez, Alicante, Spain, for access to custom perl scripts. We thank Todd Miller for collecting the lake water sample used to recover the SAG sequence. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. KDM acknowledges funding from the United States National Science Foundation Microbial Observatories program (MCB-0702395), the Long Term Ecological Research program (NTL-LTER DEB-0822700), a CAREER award (CBET-0738309) and the Swedish Wenner-Gren Foundation.
ISSN: 1751-7362 (Print) | 1751-7370 (Online)
DOI: 10.1038/ismej.2012.86
Language: eng
Type: info:eu-repo/semantics/article
Rights: This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivative Works 3.0 Unported License. To view a copy of this license, visit
Peer Review: si
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Appears in Collections:INV - EMM - Artículos de Revistas

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