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Accumulation of DNA in an anoxic sediment – rDNA and rRNA presence of members of the microbial community from Landsort Deep, the Baltic Sea
Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science..
KTH, School of Biotechnology (BIO). (Anders Andersson)ORCID iD: 0000-0002-2025-2198
University of Milano-Bicocca, Milano, Italy..
Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science..ORCID iD: 0000-0002-5802-5126
Show others and affiliations
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms in the Landsort Deep sediment. To further elucidate which taxa may contribute to ecosystem function at this site, we here present three different datasets – rDNA amplicons, rDNA reads from a shotgun metagenome and expressed rRNA from a shotgun metatranscriptome. By comparing the three datasets and the ratios between rRNA and rDNA we seek to estimate the protein synthesis potential of the community members in order to provide an indication of what taxa may have cellular activity and metabolic potential. The variation in protein synthesis potential was large, both within and between taxa, in the sediment community. Many typically anaerobic taxa, e.g. from Deltaproteobacteria and Euryarchaeota, showed a high protein synthesis potential, while typical aerobes like Flavobacteria showed a low protein synthesis potential. More surprisingly, some common Baltic Sea surface water bacteria also displayed a high protein synthesis potential, suggesting they have an active role in the anoxic sediment ecosystem at 460 m depth. Both filamentous and unicellular Cyanobacteria exhibited very high protein synthesis potential, which implies a more complex role of these bacteria in carbon cycling in the Baltic Sea than previously suggested. Moreover, Mycobacteria, that were abundant in Landsort Deep sediment metagenome compared with other marine sediment metagenomes, showed protein synthesis potentials consistent with a functional role in the sediment community. Our results provide a new window of insight into the complexities of the microbial community of Landsort Deep with implications for the understanding of other anoxic accumulation sediments.

Keyword [en]
Sediment, Protein synthesis potential, Dormancy, Microbial activity, rDNA, rRNA, metabarcoding
National Category
Environmental Sciences Microbiology Ecology
Research subject
Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-204662OAI: oai:DiVA.org:kth-204662DiVA: diva2:1085964
Note

QC 20170403

Available from: 2017-03-30 Created: 2017-03-30 Last updated: 2017-05-03Bibliographically 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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PAPER_III_LandsortDeep(4566 kB)6 downloads
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https://peerj.com/preprints/2051/

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