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Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.ORCID iD: 0000-0002-2025-2198
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-3627-6899
2016 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, 679Article in journal (Refereed) Published
Resource type
Text
Abstract [en]

Microbial plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities sampled in summer along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. In contrast, no clear trends in alpha-diversity for bacterial or eukaryotic communities could be detected along the transect. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but groups novel to the Baltic Sea were also identified, such as relatives to the coccolithophore Erniliana huxleyi detected in the northern Baltic Sea. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.

Place, publisher, year, edition, pages
Frontiers Media , 2016. Vol. 7, 679
Keyword [en]
Baltic Sea, protists, bacterioplankton, brackish, metabarcoding, marine microbiology, microbial ecology
National Category
Microbiology
Identifiers
URN: urn:nbn:se:kth:diva-188057DOI: 10.3389/fmicb.2016.00679ISI: 000375685400001Scopus ID: 2-s2.0-84973541011OAI: oai:DiVA.org:kth-188057DiVA: diva2:937437
Note

QC 20160615

Available from: 2016-06-15 Created: 2016-06-03 Last updated: 2017-04-03Bibliographically approved
In thesis
1. Microbial DNA Sequencing in Environmental Studies
Open this publication in new window or tab >>Microbial DNA Sequencing in Environmental Studies
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The field of microbial ecology has just entered a new era of rapid technological development and generation of big data. The high-throughput sequencing techniques presently available provide an opportunity to extensively inventorize the blueprints of life. Now, millions of microbes of natural microbial communities can be studied simultaneously without prior cultivation. New species and new functions (genes) can be discovered just by mining sequencing data. However, there is still a tremendous number of microorganisms not yet examined, nor are the ecosystem functions these carry out. The modern genomic technologies can contribute to solve environmental problems and help us understand ecosystems, but to most efficiently do so, methods need to be continuously optimised.

 

During my Ph. D. studies, I developed a method to survey eukaryotic microbial diversity with a higher accuracy, and applied various sequencing-based approaches in an attempt to answer questions of importance in environmental research and ecology. In PAPER-I, we developed a set of 18S rRNA gene PCR primers with high taxonomic coverage, meeting the requirements of currently popular sequencing technologies and matching the richness of 18S rRNA reference sequences accumulated so far. In PAPER-II, we conducted the first sequencing-based spatial survey on the combined eukaryotic and bacterial planktonic community in the Baltic Sea to uncover the relationship of microbial diversity and environmental conditions. Here, the 18S primers designed in PAPER-I and a pair of broad-coverage 16S primers were employed to target the rRNA genes of protists and bacterioplankton for amplicon sequencing. In PAPER-III, we integrated metagenomic, metabarcoding, and metatranscriptomic data in an effort to scrutinise the protein synthesis potential (i.e., activity) of microbes in the sediment at a depth of 460 m in the Baltic Sea and, thus, disclosing microbial diversity and their possible ecological functions within such an extreme environment. Lastly, in PAPER-IV, we compared the performance of E. coli culturing, high-throughput sequencing, and portable real-time sequencing in tracking wastewater contamination in an urban stormwater system. From the aspects of cost, mobility and accuracy, we evaluated the usage of sequencing-based approaches in civil engineering, and for the first time, validated the real-time sequencing device in use within water quality monitoring.

 

In summary, these studies demonstrate how DNA sequencing of microbial communities can be applied in environmental monitoring and ecological research.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2017. 63 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2017:8
Keyword
DNA sequencing; Metabarcoding; Microbial ecology; Baltic Sea; Microbial community; Illumina; Oxford Nanopore; Source tracking; Stormwater
National Category
Microbiology Civil Engineering Ecology Bioinformatics and Systems Biology
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-204897 (URN)978-91-7729-322-4 (ISBN)
Public defence
2017-04-21, Air-and-Fire Lecture Hall, Tomtebodavägen 23a (Science for Life Laboratory, Stockholm), Solna, 10:00 (English)
Opponent
Supervisors
Note

Yue Hu was supported by a scholarship from the China Scholarship Council (CSC #201206950024)

Yue Hu has been publishing papers under the name "Yue O. O. Hu".

QC 20170403

Available from: 2017-04-03 Created: 2017-04-03 Last updated: 2017-04-04Bibliographically approved

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