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Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community

  • Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton.Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.show moreshow less

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Metadaten
Author:Sarahi L. Garcia, Moritz Buck, Katherine D. McMahon, Hans-Peter GrossartORCiDGND, Alexander Eiler, Falk Warnecke
DOI:https://doi.org/10.1111/mec.13319
ISSN:0962-1083 (print)
ISSN:1365-294X (online)
Pubmed Id:http://www.ncbi.nlm.nih.gov/pubmed?term=26179741
Parent Title (English):Molecular ecology
Publisher:Wiley-Blackwell
Place of publication:Hoboken
Document Type:Article
Language:English
Year of first Publication:2015
Year of Completion:2015
Release Date:2017/03/27
Tag:community; cultures; interactions; metagenomics; populations
Volume:24
Issue:17
Pagenumber:11
First Page:4449
Last Page:4459
Funder:Swedish research council VR [2012-4592]; German Science Foundation [DFG 1540/17-1]; JSMC; United States National Science Foundation Microbial Observatories program [MCB-0702395]; Long Term Ecological Research program [NTL-LTER DEB-0822700]; INSPIRE award [DEB-1344254]; Joint Genome Institute; Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie
Peer Review:Referiert