KOPS - Das Institutionelle Repositorium der Universität Konstanz

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

Zitieren

Dateien zu dieser Ressource

Dateien Größe Format Anzeige

Zu diesem Dokument gibt es keine Dateien.

PELIKAN, Claus, Craig W. HERBOLD, Bela HAUSMANN, Albert L. MÜLLER, Michael PESTER, Alexander LOY, 2016. Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics. In: Environmental Microbiology. 18(9), pp. 2994-3009. ISSN 1462-2912. eISSN 1462-2920

@article{Pelikan2016-09Diver-32727, title={Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics}, year={2016}, doi={10.1111/1462-2920.13139}, number={9}, volume={18}, issn={1462-2912}, journal={Environmental Microbiology}, author={Pelikan, Claus and Herbold, Craig W. and Hausmann, Bela and Müller, Albert L. and Pester, Michael and Loy, Alexander} }

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/32727"> <dc:creator>Pester, Michael</dc:creator> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/32727"/> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-01-26T14:43:03Z</dcterms:available> <dc:creator>Loy, Alexander</dc:creator> <dc:creator>Herbold, Craig W.</dc:creator> <dc:contributor>Hausmann, Bela</dc:contributor> <dc:contributor>Pester, Michael</dc:contributor> <dc:language>eng</dc:language> <dc:contributor>Herbold, Craig W.</dc:contributor> <dcterms:abstract xml:lang="eng">Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB PCR products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches, and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. While tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.</dcterms:abstract> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-01-26T14:43:03Z</dc:date> <dc:creator>Pelikan, Claus</dc:creator> <dc:contributor>Pelikan, Claus</dc:contributor> <dc:contributor>Müller, Albert L.</dc:contributor> <dc:creator>Hausmann, Bela</dc:creator> <dcterms:title>Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics</dcterms:title> <dcterms:issued>2016-09</dcterms:issued> <dc:creator>Müller, Albert L.</dc:creator> <dc:contributor>Loy, Alexander</dc:contributor> </rdf:Description> </rdf:RDF>

Das Dokument erscheint in:

KOPS Suche


Stöbern

Mein Benutzerkonto