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Metagenome-assembled genomes uncover a global brackish microbiome
KTH Royal Institute of Technology.
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. (Centre for Ecology and Evolution in Microbial model Systems - EEMiS)
KTH Royal Institute of Technology.
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.ORCID iD: 0000-0002-7120-4145
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2015 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 16, 279Article in journal (Refereed) Published
Abstract [en]

Background: Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. Results: We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing thegenomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts. Conclusions: We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.

Place, publisher, year, edition, pages
BioMed Central, 2015. Vol. 16, 279
Keyword [en]
Metagenome, Bacterioplankton, Ecology, Evolution, Marine, Brackish, Baltic Sea
National Category
Microbiology
Research subject
Natural Science, Aquatic Ecology
Identifiers
URN: urn:nbn:se:lnu:diva-48486DOI: 10.1186/s13059-015-0834-7ISI: 000366898100001PubMedID: 26667648OAI: oai:DiVA.org:lnu-48486DiVA: diva2:885953
Available from: 2015-12-21 Created: 2015-12-21 Last updated: 2016-10-25Bibliographically approved

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Larsson, JohnLindh, Markus V.Legrand, CatherinePinhassi, Jarone
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CiteExportLink to record
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