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Seasonal dynamics and interactions among Baltic Sea prokaryoticand eukaryotic plankton assemblages
KTH, School of Biotechnology (BIO), Gene Technology. Science for Life Laboratory. (Environmental genomics)ORCID iD: 0000-0001-5432-1764
Centre for Ecology and Evolution in Microbial model Systems - Linnaeus University.
KTH, School of Biotechnology (BIO), Gene Technology. (Environmental Genomics)
Centre for Ecology and Evolution in Microbial model Systems - Linnaeus University.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

One of the main goals of microbial ecology is to identify the mechanismsthat regulate patterns in community structure at temporal scalescompatible with populations’ turnover times across complete seasonalcycles. Here, we examined high-frequency temporal dynamics of marineplankton from a sampling effort covering 2011-2013, roughly twice weekly,comprising 144 samples. Bacterial and eukaryotic communities wereprofiled by 16S and 18S high-throughput sequencing, respectively.Interestingly, we found that no combination of the measured environmentalparameters could predict a significant proportion of the variation inpopulation dynamics of bacterioplankton, and even less so for eukaryoticplankton. Large differences in physicochemical conditions and communitycomposition typical of temperate climates mean that different regimes canquickly succeed each other over the year, with the relative importance ofdifferent drivers changing equally rapidly. Nevertheless, our approachrevealed interesting recurrent co-occurrence patterns across distinctenvironmental changes. Hence, we could make abundance predictions formore than half of the most frequent OTUs based on interactions with otherOTUs. These results suggests that a complex set of biotic interactions arecontributing to temporal patterns among planktonic assemblages despiterapid changes in environmental conditions.

Keyword [en]
Microbiology; Plankton; Baltic Sea; Environmental modelling; Food web; Network
National Category
Microbiology Ecology
Research subject
URN: urn:nbn:se:kth:diva-186160OAI: diva2:925857
Swedish Research Council, 2011-5689Swedish Research Council Formas, ECOCHANGE

QC 20160504

Available from: 2016-05-03 Created: 2016-05-03 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.
TRITA-BIO-Report, ISSN 1654-2312
Microbial ecology; Baltic Sea; Next-generation sequencing; Amplicon sequencing; Metagenomics
National Category
Microbiology Ecology Bioinformatics and Systems Biology
Research subject
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)
Swedish Research Council, 2011-5689

QC 20150505

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

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Hugerth, LuisaSjöqvist, ConnyAndersson, Anders
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