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Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems
KTH, School of Biotechnology (BIO). (Anders Andersson)ORCID iD: 0000-0002-2025-2198
Karolinska Institutet, Department of Medical Epidemiology and Biostatistics (MEB). (Weiming Ye)ORCID iD: 0000-0001-5297-5107
KTH, School of Biotechnology (BIO). (Anders Andersson)ORCID iD: 0000-0002-2467-008X
KTH, School of Biotechnology (BIO).
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Urban sewer systems consist of wastewater and stormwater sewers, of which typically only

the wastewater is processed before being discharged. Occasionally, misconnections or

damages in the network occur, resulting in wastewater entering the stormwater system and

being discharged without prior processing. Cultivation of faecal indicator bacteria, such as

Escherichia coli (E. coli), is the current standard for tracing wastewater contamination. This

method is cheap but cannot be employed in the field and is characterised by its limited

specificity. Here, we compared the E. coli culturing approach with two different DNA

sequencing-based methodologies (i.e., 16S rRNA amplicon sequencing on the Illumina

MiSeq platform and shotgun metagenomic sequencing on an Oxford Nanopore MinIOn

device), analysing 73 stormwater samples collected throughout the Stockholm city areas.

High correlations were obtained between E. coli culturing counts and frequencies of human

gut microbiome sequencing reads (via amplicon sequencing), indicating that E. coli is indeed

a good indicator of faecal contamination. In contrast to E.coli culturing, amplicon sequencing

could, however, further distinguish between two different sources of contamination in an

area, where misconnections in the stormwater system were later on detected. Shotgun

metagenomic sequencing on a subset of the samples using the portable Oxford Nanopore

MinION real-time sequencing device correlated well with the amplicon sequencing data. In

summary, this study shows that DNA sequencing allows distinguishing different

contamination sources in stormwater systems and demonstrates the potential of using a

portable sequencing device in the field for tracking faecal contamination.

Keyword [en]
stormwater, metabarcoding, oxford nanopore, illumina, microbial community, source tracking
National Category
Environmental Engineering Civil Engineering
Research subject
Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-204668OAI: oai:DiVA.org:kth-204668DiVA: diva2:1085975
Note

QC 20170403

Available from: 2017-03-30 Created: 2017-03-30 Last updated: 2017-04-06Bibliographically 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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