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Article: A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments

TitleA comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments
Authors
Keywords16S RNA gene
Anammox bacteria
Hzo gene
Marine sediments
Primer sets
Issue Date2010
PublisherSpringer. The Journal's web site is located at http://link.springer.de/link/service/journals/00253/index.htm
Citation
Applied Microbiology And Biotechnology, 2010, v. 86 n. 2, p. 781-790 How to Cite?
AbstractPublished polymerase chain reaction primer sets for detecting the genes encoding 16S rRNA gene and hydrazine oxidoreductase (hzo) in anammox bacteria were compared by using the same coastal marine sediment samples. While four previously reported primer sets developed to detect the 16S rRNA gene showed varying specificities between 12% and 77%, an optimized primer combination resulted in up to 98% specificity, and the recovered anammox 16S rRNA gene sequences were >95% sequence identical to published sequences from anammox bacteria in the Candidatus "Scalindua" group. Furthermore, four primer sets used in detecting the hzo gene of anammox bacteria were highly specific (up to 92%) and efficient, and the newly designed primer set in this study amplified longer hzo gene segments suitable for phylogenetic analysis. The optimized primer set for the 16S rRNA gene and the newly designed primer set for the hzo gene were successfully applied to identify anammox bacteria from marine sediments of aquaculture zone, coastal wetland, and deep ocean where the three ecosystems form a gradient of anthropogenic impact. Results indicated a broad distribution of anammox bacteria with high niche-specific community structure within each marine ecosystem. © 2010 Springer-Verlag.
Persistent Identifierhttp://hdl.handle.net/10722/124077
ISSN
2015 Impact Factor: 3.376
2015 SCImago Journal Rankings: 1.262
ISI Accession Number ID
Funding AgencyGrant Number
The University of Hong KongHKU765507M
National Natural Science Foundation of China3080032
Guangdong Province Natural Science Foundation84510301001692
UofL-EVPR office
US National Science FoundationEF-0412129
Funding Information:

This research was supported by a Ph. D. studentship from The University of Hong Kong and in part by HKU765507M to J-DG and by the National Natural Science Foundation of China (3080032) and Guangdong Province Natural Science Foundation (84510301001692) to Y-GH. MGK was funded by incentive funds provided by the UofL-EVPR office and the US National Science Foundation (EF-0412129). We thank Jessie Lai for the laboratory assistance.

References

 

DC FieldValueLanguage
dc.contributor.authorLi, Men_HK
dc.contributor.authorHong, Yen_HK
dc.contributor.authorKlotz, MGen_HK
dc.contributor.authorGu, JDen_HK
dc.date.accessioned2010-10-20T07:11:02Z-
dc.date.available2010-10-20T07:11:02Z-
dc.date.issued2010en_HK
dc.identifier.citationApplied Microbiology And Biotechnology, 2010, v. 86 n. 2, p. 781-790en_HK
dc.identifier.issn0175-7598en_HK
dc.identifier.urihttp://hdl.handle.net/10722/124077-
dc.description.abstractPublished polymerase chain reaction primer sets for detecting the genes encoding 16S rRNA gene and hydrazine oxidoreductase (hzo) in anammox bacteria were compared by using the same coastal marine sediment samples. While four previously reported primer sets developed to detect the 16S rRNA gene showed varying specificities between 12% and 77%, an optimized primer combination resulted in up to 98% specificity, and the recovered anammox 16S rRNA gene sequences were >95% sequence identical to published sequences from anammox bacteria in the Candidatus "Scalindua" group. Furthermore, four primer sets used in detecting the hzo gene of anammox bacteria were highly specific (up to 92%) and efficient, and the newly designed primer set in this study amplified longer hzo gene segments suitable for phylogenetic analysis. The optimized primer set for the 16S rRNA gene and the newly designed primer set for the hzo gene were successfully applied to identify anammox bacteria from marine sediments of aquaculture zone, coastal wetland, and deep ocean where the three ecosystems form a gradient of anthropogenic impact. Results indicated a broad distribution of anammox bacteria with high niche-specific community structure within each marine ecosystem. © 2010 Springer-Verlag.en_HK
dc.languageeng-
dc.publisherSpringer. The Journal's web site is located at http://link.springer.de/link/service/journals/00253/index.htmen_HK
dc.relation.ispartofApplied Microbiology and Biotechnologyen_HK
dc.subject16S RNA geneen_HK
dc.subjectAnammox bacteriaen_HK
dc.subjectHzo geneen_HK
dc.subjectMarine sedimentsen_HK
dc.subjectPrimer setsen_HK
dc.subject.meshBacteria - classification - enzymology - genetics - isolation and purification-
dc.subject.meshDNA Primers - genetics-
dc.subject.meshGeologic Sediments - microbiology-
dc.subject.meshMetagenomics - methods-
dc.subject.meshPolymerase Chain Reaction - methods-
dc.titleA comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sedimentsen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0175-7598&volume=86&issue=2&spage=781&epage=790&date=2010&atitle=A+comparison+of+primer+sets+for+detecting+16S+rRNA+and+hydrazine+oxidoreductase+genes+of+anaerobic+ammonium-oxidizing+bacteria+in+marine+sediments-
dc.identifier.emailGu, JD: jdgu@hkucc.hku.hken_HK
dc.identifier.authorityGu, JD=rp00701en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1007/s00253-009-2361-5en_HK
dc.identifier.pmid20107988-
dc.identifier.scopuseid_2-s2.0-77249133557en_HK
dc.identifier.hkuros172623-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77249133557&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume86en_HK
dc.identifier.issue2en_HK
dc.identifier.spage781en_HK
dc.identifier.epage790en_HK
dc.identifier.isiWOS:000274707600038-
dc.publisher.placeGermanyen_HK
dc.identifier.scopusauthoridLi, M=25628417400en_HK
dc.identifier.scopusauthoridHong, Y=7403393244en_HK
dc.identifier.scopusauthoridKlotz, MG=7005769022en_HK
dc.identifier.scopusauthoridGu, JD=7403129601en_HK

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