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Article: Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge

TitleMetagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge
Authors
Issue Date2012
PublisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
Citation
PLoS One, 2012, v. 7 n. 5, article no. e38183 How to Cite?
AbstractThe present study applied both metagenomic and metatranscriptomic approaches to characterize microbial structure and gene expression of an activated sludge community from a municipal wastewater treatment plant in Hong Kong. DNA and cDNA were sequenced by Illumina Hi-seq2000 at a depth of 2.4 Gbp. Taxonomic analysis by MG-RAST showed bacteria were dominant in both DNA and cDNA datasets. The taxonomic profile obtained by BLAST against SILVA SSUref database and annotation by MEGAN showed that activated sludge was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Verrucomicrobia phyla in both DNA and cDNA datasets. Global gene expression annotation based on KEGG metabolism pathway displayed slight disagreement between the DNA and cDNA datasets. Further gene expression annotation focusing on nitrogen removal revealed that denitrification-related genes sequences dominated in both DNA and cDNA datasets, while nitrifying genes were also expressed in relative high levels. Specially, ammonia monooxygenase and hydroxylamine oxidase demonstrated the high cDNA/DNA ratios in the present study, indicating strong nitrification activity. Enzyme subunits gene sequences annotation discovered that subunits of ammonia monooxygenase (amoA, amoB, amoC) and hydroxylamine oxygenase had higher expression levels compared with subunits of the other enzymes genes. Taxonomic profiles of selected enzymes (ammonia monooxygenase and hydroxylamine oxygenase) showed that ammonia-oxidizing bacteria present mainly belonged to Nitrosomonas and Nitrosospira species and no ammonia-oxidizing Archaea sequences were detected in both DNA and cDNA datasets.
Persistent Identifierhttp://hdl.handle.net/10722/163853
ISSN
2015 Impact Factor: 3.057
2015 SCImago Journal Rankings: 1.395
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorYu, Ken_US
dc.contributor.authorZhang, Ten_US
dc.date.accessioned2012-09-20T07:52:32Z-
dc.date.available2012-09-20T07:52:32Z-
dc.date.issued2012en_US
dc.identifier.citationPLoS One, 2012, v. 7 n. 5, article no. e38183en_US
dc.identifier.issn1932-6203en_US
dc.identifier.urihttp://hdl.handle.net/10722/163853-
dc.description.abstractThe present study applied both metagenomic and metatranscriptomic approaches to characterize microbial structure and gene expression of an activated sludge community from a municipal wastewater treatment plant in Hong Kong. DNA and cDNA were sequenced by Illumina Hi-seq2000 at a depth of 2.4 Gbp. Taxonomic analysis by MG-RAST showed bacteria were dominant in both DNA and cDNA datasets. The taxonomic profile obtained by BLAST against SILVA SSUref database and annotation by MEGAN showed that activated sludge was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Verrucomicrobia phyla in both DNA and cDNA datasets. Global gene expression annotation based on KEGG metabolism pathway displayed slight disagreement between the DNA and cDNA datasets. Further gene expression annotation focusing on nitrogen removal revealed that denitrification-related genes sequences dominated in both DNA and cDNA datasets, while nitrifying genes were also expressed in relative high levels. Specially, ammonia monooxygenase and hydroxylamine oxidase demonstrated the high cDNA/DNA ratios in the present study, indicating strong nitrification activity. Enzyme subunits gene sequences annotation discovered that subunits of ammonia monooxygenase (amoA, amoB, amoC) and hydroxylamine oxygenase had higher expression levels compared with subunits of the other enzymes genes. Taxonomic profiles of selected enzymes (ammonia monooxygenase and hydroxylamine oxygenase) showed that ammonia-oxidizing bacteria present mainly belonged to Nitrosomonas and Nitrosospira species and no ammonia-oxidizing Archaea sequences were detected in both DNA and cDNA datasets.-
dc.languageengen_US
dc.publisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action-
dc.relation.ispartofPLoS Oneen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshEnzymes - genetics-
dc.subject.meshGene Expression Profiling-
dc.subject.meshMetagenomics-
dc.subject.meshNitrogen - isolation and purification - metabolism-
dc.subject.meshSewage - microbiology-
dc.titleMetagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludgeen_US
dc.typeArticleen_US
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1932-6203 (Electronic) 1932-6203 (Linkin&volume=7&issue=5&spage=e38183&epage=&date=2012&atitle=Metagenomic+and+metatranscriptomic+analysis+of+microbial+community+structure+and+gene+expression+of+activated+sludgeen_US
dc.identifier.emailZhang, T: zhangt@hkucc.hku.hken_US
dc.identifier.authorityZhang, T=rp00211en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1371/journal.pone.0038183-
dc.identifier.pmid22666477-
dc.identifier.pmcidPMC3364235-
dc.identifier.scopuseid_2-s2.0-84861633828-
dc.identifier.hkuros208075en_US
dc.identifier.volume7en_US
dc.identifier.issue5, article no. e38183en_US
dc.identifier.isiWOS:000305353400095-
dc.publisher.placeUnited States-
dc.identifier.citeulike10786110-

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