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Article: Cytochrome cd1 -containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing (anammox) bacteria

TitleCytochrome cd1 -containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing (anammox) bacteria
Authors
Issue Date2011
PublisherAmerican Chemical Society. The Journal's web site is located at http://pubs.acs.org/est
Citation
Environmental Science And Technology, 2011, v. 45 n. 8, p. 3547-3553 How to Cite?
AbstractA newly designed primer set (AnnirS), together with a previously published primer set (ScnirS), was used to detect anammox bacterial nirS genes from sediments collected from three marine environments. Phylogenetic analysis demonstrated that all retrieved sequences were clearly different from typical denitrifiers' nirS, but do group together with the known anammox bacterial nirS. Sequences targeted by ScnirS are closely related to Scalindua nirS genes recovered from the Peruvian oxygen minimum zone (OMZ), whereas sequences targeted by AnnirS are more closely affiliated with the nirS of Candidatus 'Kuenenia stuttgartiensis' and even form a new phylogenetic nirS clade, which might be related to other genera of the anammox bacteria. Analysis demonstrated that retrieved sequences had higher sequence identities (>60%) with known anammox bacterial nirS genes than with denitrifiers' nirS, on both nucleotide and amino acid levels. Compared to the 16S rRNA and hydrazine oxidoreductase (hzo) genes, the anammox bacterial nirS not only showed consistent phylogenetic relationships but also demonstrated more reliable quantification of anammox bacteria because of the single copy of the nirS gene in the anammox bacterial genome and the specificity of PCR primers for different genera of anammox bacteria, thus providing a suitable functional biomarker for investigation of anammox bacteria. © 2011 American Chemical Society.
Persistent Identifierhttp://hdl.handle.net/10722/139074
ISSN
2015 Impact Factor: 5.393
2015 SCImago Journal Rankings: 2.664
ISI Accession Number ID
Funding AgencyGrant Number
Agriculture, Fisheries and Conservation Department of the Hong Kong SAR Government
Funding Information:

This research was supported by a Ph.D. studentship (M.L.) and in part by the Agriculture, Fisheries and Conservation Department of the Hong Kong SAR Government. We thank Jessie Lai for laboratory assistance and Dr. Yi-guo Hong for the SCS sediment samples on South China Sea Open Cruise of R/V Shiyan 3.

References

 

DC FieldValueLanguage
dc.contributor.authorLi, Men_HK
dc.contributor.authorFord, Ten_HK
dc.contributor.authorLi, Xen_HK
dc.contributor.authorGu, JDen_HK
dc.date.accessioned2011-09-23T05:44:47Z-
dc.date.available2011-09-23T05:44:47Z-
dc.date.issued2011en_HK
dc.identifier.citationEnvironmental Science And Technology, 2011, v. 45 n. 8, p. 3547-3553en_HK
dc.identifier.issn0013-936Xen_HK
dc.identifier.urihttp://hdl.handle.net/10722/139074-
dc.description.abstractA newly designed primer set (AnnirS), together with a previously published primer set (ScnirS), was used to detect anammox bacterial nirS genes from sediments collected from three marine environments. Phylogenetic analysis demonstrated that all retrieved sequences were clearly different from typical denitrifiers' nirS, but do group together with the known anammox bacterial nirS. Sequences targeted by ScnirS are closely related to Scalindua nirS genes recovered from the Peruvian oxygen minimum zone (OMZ), whereas sequences targeted by AnnirS are more closely affiliated with the nirS of Candidatus 'Kuenenia stuttgartiensis' and even form a new phylogenetic nirS clade, which might be related to other genera of the anammox bacteria. Analysis demonstrated that retrieved sequences had higher sequence identities (>60%) with known anammox bacterial nirS genes than with denitrifiers' nirS, on both nucleotide and amino acid levels. Compared to the 16S rRNA and hydrazine oxidoreductase (hzo) genes, the anammox bacterial nirS not only showed consistent phylogenetic relationships but also demonstrated more reliable quantification of anammox bacteria because of the single copy of the nirS gene in the anammox bacterial genome and the specificity of PCR primers for different genera of anammox bacteria, thus providing a suitable functional biomarker for investigation of anammox bacteria. © 2011 American Chemical Society.en_HK
dc.languageengen_US
dc.publisherAmerican Chemical Society. The Journal's web site is located at http://pubs.acs.org/esten_HK
dc.relation.ispartofEnvironmental Science and Technologyen_HK
dc.subject.meshBacteria, Anaerobic - classification - genetics - metabolism-
dc.subject.meshBacterial Proteins - analysis - genetics - metabolism-
dc.subject.meshCytochromes - metabolism-
dc.subject.meshNitrite Reductases - metabolism-
dc.subject.meshQuaternary Ammonium Compounds - metabolism-
dc.titleCytochrome cd1 -containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing (anammox) bacteriaen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0013-936X&volume=45&issue=8&spage=3547&epage=3553&date=2011&atitle=Cytochrome+cd1-containing+nitrite+reductase+encoding+gene+nirS+as+a+new+functional+biomarker+for+detection+of+anaerobic+ammonium+oxidizing+(anammox)+bacteria-
dc.identifier.emailLi, X: xlia@hkucc.hku.hken_HK
dc.identifier.emailGu, JD: jdgu@hkucc.hku.hken_HK
dc.identifier.authorityLi, X=rp00222en_HK
dc.identifier.authorityGu, JD=rp00701en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1021/es103826wen_HK
dc.identifier.pmid21417444-
dc.identifier.scopuseid_2-s2.0-79954464368en_HK
dc.identifier.hkuros194845en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79954464368&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume45en_HK
dc.identifier.issue8en_HK
dc.identifier.spage3547en_HK
dc.identifier.epage3553en_HK
dc.identifier.eissn1520-5851-
dc.identifier.isiWOS:000289341300051-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridLi, M=35210975800en_HK
dc.identifier.scopusauthoridFord, T=26634948200en_HK
dc.identifier.scopusauthoridLi, X=26642887900en_HK
dc.identifier.scopusauthoridGu, JD=7403129601en_HK

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