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Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
University of Wisconsin—Madison, Madison, USA.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.ORCID iD: 0000-0002-8622-0308
University of Wisconsin—Madison, Madison, USA.
University of Wisconsin—Madison, Madison, USA.
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2017 (English)In: mSystems, E-ISSN 2379-5077, Vol. 2, no 4, article id e00091-17Article in journal (Refereed) Published
Abstract [en]

An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the “seed set framework,” which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482–14487, 2008, https://doi.org/10.1073/pnas.0806162105 ), enables computational analysis of metabolic reconstructions while providing new insights into a microbe’s metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs.

Place, publisher, year, edition, pages
2017. Vol. 2, no 4, article id e00091-17
Keyword [en]
freshwater microbial ecology, metabolism, metagenomics, metatranscriptomics, physiology, systems biology
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-339041DOI: 10.1128/mSystems.00091-17OAI: oai:DiVA.org:uu-339041DiVA, id: diva2:1174364
Available from: 2018-01-15 Created: 2018-01-15 Last updated: 2018-01-19Bibliographically approved

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Garcia, Sarahi L.Bertilsson, Stefan
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LimnologyScience for Life Laboratory, SciLifeLab
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