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Metagenome-assembled genomes uncover a global brackish microbiome
KTH, School of Biotechnology (BIO), Gene Technology.
KTH, School of Biotechnology (BIO), Gene Technology.
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2015 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 16, 279Article in journal (Refereed) PublishedText
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 the genomes 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
Genetics Microbiology
Identifiers
URN: urn:nbn:se:kth:diva-180496DOI: 10.1186/s13059-015-0834-7ISI: 000366898100001ScopusID: 2-s2.0-84949761326OAI: oai:DiVA.org:kth-180496DiVA: diva2:895134
Note

QC 20160118

Available from: 2016-01-18 Created: 2016-01-14 Last updated: 2016-05-04Bibliographically approved
In thesis
1. High-throughput DNA Sequencingin Microbial Ecology: Methods and Applications
Open this publication in new window or tab >>High-throughput DNA Sequencingin Microbial Ecology: Methods and Applications
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Microorganisms play central roles in planet Earth’s geochemical cycles, in food production, and in health and disease of humans and livestock. In spite of this, most microbial life forms remain unknown and unnamed, their ecological importance and potential technological applications beyond the realm of speculation. This is due both to the magnitude of microbial diversity and to technological limitations. Of the many advances that have enabled microbiology to reach new depth and breadth in the past decade, one of the most important is affordable high-throughput DNA sequencing. This technology plays a central role in each paper in this thesis.

Papers I and II are focused on developing methods to survey microbial diversity based on marker gene amplification and sequencing. In Paper I we proposed a computational strategy to design primers with the highest coverage among a given set of sequences and applied it to drastically improve one of the most commonly used primer pairs for ecological surveys of prokaryotes. In Paper II this strategy was applied to an eukaryotic marker gene. Despite their importance in the food chain, eukaryotic microbes are much more seldom surveyed than bacteria. Paper II aimed at making this domain of life more amenable to high-throughput surveys.

In Paper III, the primers designed in papers I and II were applied to water samples collected up to twice weekly from 2011 to 2013 at an offshore station in the Baltic proper, the Linnaeus Microbial Observatory. In addition to tracking microbial communities over these three years, we created predictive models for hundreds of microbial populations, based on their co-occurrence with other populations and environmental factors.

In paper IV we explored the entire metagenomic diversity in the Linnaeus Microbial Observatory. We used computational tools developed in our group to construct draft genomes of abundant bacteria and archaea and described their phylogeny, seasonal dynamics and potential physiology. We were also able to establish that, rather than being a mixture of genomes from fresh and saline water, the Baltic Sea plankton community is composed of brackish specialists which diverged from other aquatic microorganisms thousands of years before the formation of the Baltic itself.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2016. x, 46 p.
Series
TRITA-BIO-Report, ISSN 1654-2312
Keyword
Microbial ecology; Baltic Sea; Next-generation sequencing; Amplicon sequencing; Metagenomics
National Category
Microbiology Ecology Bioinformatics and Systems Biology
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-186162 (URN)978-91-7595-967-2 (ISBN)
Public defence
2016-05-27, Farmakologi salen, Karolinska instituet, Nobelsväg 2, Solna, 09:15 (English)
Opponent
Supervisors
Funder
Swedish Research Council, 2011-5689
Note

QC 20150505

Available from: 2016-05-04 Created: 2016-05-03 Last updated: 2016-05-04Bibliographically approved

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