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Metagenome-assembled genomes uncover a global brackish microbiome
KTH, Skolan för bioteknologi (BIO), Genteknologi.
KTH, Skolan för bioteknologi (BIO), Genteknologi.ORCID-id: 0000-0002-2467-008X
Visa övriga samt affilieringar
2015 (Engelska)Ingår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 16, artikel-id 279Artikel i tidskrift (Refereegranskat) Published
Resurstyp
Text
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.

Ort, förlag, år, upplaga, sidor
BioMed Central, 2015. Vol. 16, artikel-id 279
Nyckelord [en]
Metagenome, Bacterioplankton, Ecology, Evolution, Marine, Brackish, Baltic Sea
Nationell ämneskategori
Genetik Mikrobiologi
Identifikatorer
URN: urn:nbn:se:kth:diva-180496DOI: 10.1186/s13059-015-0834-7ISI: 000366898100001Scopus ID: 2-s2.0-84949761326OAI: oai:DiVA.org:kth-180496DiVA, id: diva2:895134
Anmärkning

QC 20160118

Tillgänglig från: 2016-01-18 Skapad: 2016-01-14 Senast uppdaterad: 2018-05-15Bibliografiskt granskad
Ingår i avhandling
1. High-throughput DNA Sequencingin Microbial Ecology: Methods and Applications
Öppna denna publikation i ny flik eller fönster >>High-throughput DNA Sequencingin Microbial Ecology: Methods and Applications
2016 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Stockholm: KTH Royal Institute of Technology, 2016. s. x, 46
Serie
TRITA-BIO-Report, ISSN 1654-2312
Nyckelord
Microbial ecology; Baltic Sea; Next-generation sequencing; Amplicon sequencing; Metagenomics
Nationell ämneskategori
Mikrobiologi Ekologi Bioinformatik och systembiologi
Forskningsämne
Bioteknologi
Identifikatorer
urn:nbn:se:kth:diva-186162 (URN)978-91-7595-967-2 (ISBN)
Disputation
2016-05-27, Farmakologi salen, Karolinska instituet, Nobelsväg 2, Solna, 09:15 (Engelska)
Opponent
Handledare
Forskningsfinansiär
Vetenskapsrådet, 2011-5689
Anmärkning

QC 20150505

Tillgänglig från: 2016-05-04 Skapad: 2016-05-03 Senast uppdaterad: 2016-05-04Bibliografiskt granskad
2. Bioinformatic Methods in Metagenomics
Öppna denna publikation i ny flik eller fönster >>Bioinformatic Methods in Metagenomics
2018 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

Microbial organisms are a vital part of our global ecosystem. Yet, our knowledge of them is still lacking. Direct sequencing of microbial communities, i.e. metagenomics, have enabled detailed studies of these microscopic organisms by inspection of their DNA sequences without the need to culture them. Furthermore, the development of modern high- throughput sequencing technologies have made this approach more powerful and cost-effective. Taken together, this has shifted the field of microbiology from previously being centered around microscopy and culturing studies, to largely consist of computational analyses of DNA sequences. One such computational analysis which is the main focus of this thesis, aims at reconstruction of the complete DNA sequence of an organism, i.e. its genome, directly from short metagenomic sequences.

This thesis consists of an introduction to the subject followed by five papers. Paper I describes a large metagenomic data resource spanning the Baltic Sea microbial communities. This dataset is complemented with a web-interface allowing researchers to easily extract and visualize detailed information. Paper II introduces a bioinformatic method which is able to reconstruct genomes from metagenomic data. This method, which is termed CONCOCT, is applied on Baltic Sea metagenomics data in Paper III and Paper V. This enabled the reconstruction of a large number of genomes. Analysis of these genomes in Paper III led to the proposal of, and evidence for, a global brackish microbiome. Paper IV presents a comparison between genomes reconstructed from metagenomes with single-cell sequenced genomes. This further validated the technique presented in Paper II as it was found to produce larger and more complete genomes than single-cell sequencing.

Abstract [sv]

Mikrobiella organismer är en vital del av vårt globala ekosystem. Trots detta är vår kunskap om dessa fortfarande begränsad. Sekvensering direkt applicerad på mikrobiella samhällen, så kallad metagenomik, har möjliggjort detaljerade studier av dessa mikroskopiska organismer genom deras DNA-sekvenser. Utvecklingen av modern sekvenseringsteknik har vidare gjort denna strategi både mer kraftfull och mer kostnadseffektiv. Sammantaget har detta förändrat mikrobiologi-fältet, från att ha varit centrerat kring mikroskopi, till att till stor del bero på dataintensiva analyser av DNA-sekvenser. En sådan analys, som är det huvudsakliga fokuset för den här avhandlingen, syftar till att återskapa den kompletta DNA-sekvensen för en organism, dvs. dess genom, direkt från korta metagenom-sekvenser.

Den här avhandlingen består av en introduktion till ämnet, följt av fem artiklar. Artikel I beskriver en omfattande databas för metagenomik över Östersjöns mikrobiella samhällen. Till denna databas hör också en webbsida som ger forskare möjlighet att lätt extrahera och visualisera detaljerad information. Artikel II introducerar en bioinformatisk metod som kan återskapa genom från metagenom. Denna metod, som kallas CONCOCT, används för data från Östersjön i artikel III och Artikel V. Detta möjliggjorde återskapandet av ett stort antal genom. Analys av dessa genom presenterad i Artikel III ledde till hypotesen om, och belägg för, ett globalt brackvattenmikrobiom. Artikel IV innehåller en jämförelse mellan genom återskapade från metagenom och individuellt sekvenserade genom. Detta validerade metoden som presenterades i Artikel II ytterligare då denna metod visade sig producera större och mer kompletta genom än sekvensering av individuella celler.

Ort, förlag, år, upplaga, sidor
Stockholm: KTH Royal Institute of Technology, 2018. s. 51
Serie
TRITA-CBH-FOU ; 2018:25
Nyckelord
Bioinformatics, Metagenomics, Microbiome, Binning, Baltic Sea, Bioinformatik, Metagenomik, Mikrobiom, Binning, Östersjön
Nationell ämneskategori
Bioinformatik och systembiologi Bioinformatik (beräkningsbiologi) Mikrobiologi
Identifikatorer
urn:nbn:se:kth:diva-227965 (URN)978-91-7729-799-4 (ISBN)
Disputation
2018-06-08, Air and Fire, Science for Life Laboratory, Tomtebodavägen 23, Solna, 10:00 (Engelska)
Opponent
Handledare
Forskningsfinansiär
BONUS - Science for a better future of the Baltic Sea region, Art 185
Anmärkning

QC 20180516

Tillgänglig från: 2018-05-16 Skapad: 2018-05-15 Senast uppdaterad: 2018-05-16Bibliografiskt granskad

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