title: Improved PCR primers to amplify 16S rRNA genes from NC10 bacteria.
abstract: Anaerobic oxidation of methane (AOM) coupled to nitrite reduction (AOM-NIR) is ecologically significant for mitigating the methane-induced greenhouse effect. The microbes responsible for this reaction, NC10 bacteria, have been widely detected in diverse ecosystems. However, some defects were discovered in the commonly used NC10-specific primers, 202F and qP1F. In the present work, the primers were redesigned and improved to overcome the defects found in the previous primers. A new nested PCR method was developed using the improved primers to amplify 16S ribosomal RNA (rRNA) genes from NC10 bacteria. In the new nested PCR method, the qP1mF/1492R and 1051F/qP2R primer sets were used in the first and second rounds, respectively. The PCR products were sequenced, and more operational taxonomic units (OTUs) of the NC10 phylum were obtained using the new primers compared to the previous primers. The sensitivity of the new nested PCR was tested by the serial dilution method, and the limit of detection was approximately 10(3) copies g(-1) dry sed. for the environmental samples compared to approximately 10(5) copies g(-1) dry sed. by the previous method. Finally, the improved primer, qP1mF, was used in quantitative PCR (qPCR) to determine the abundance of NC10 bacteria, and the results agreed well with the activity of AOM-NIR measured by isotope tracer experiments. The improved primers are able to amplify NC10 16S rRNA genes more efficiently than the previous primers and useful to explore the microbial community of the NC10 phylum in different systems.
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Zhanfei
authors.initials: Z
authors.lastname: He
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Jiaqi
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Jiajie
authors.initials: J
authors.lastname: Hu
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Chaoyang
authors.initials: C
authors.lastname: Cai
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Jiaxian
authors.initials: J
authors.lastname: Shen
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Xinhua
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Zheng
authors.affiliation: Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China. blhu@zju.edu.cn.
authors.forename: Baolan
authors.initials: B
authors.lastname: Hu
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D003001:Cloning, Molecular; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D005798:Genes, Bacterial; D019015:Geologic Sediments / Q000382:microbiology; D008697:Methane / Q000378:metabolism; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000302:isolation & purification*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D009573:Nitrites; D012336:RNA, Ribosomal, 16S; D008697:Methane
keywords: AOM coupled to nitrite reduction (AOM-NIR); Anaerobic oxidation of methane (AOM); Annealing temperature; NC10 phylum; Nitrite-dependent anaerobic methane oxidation (n-damo); Primer optimization