title: Comparison among amoA primers suited for quantification and diversity analyses of ammonia-oxidizing bacteria in soil.
abstract: Ammonia monooxygenase subunit A gene (amoA) is frequently used as a functional gene marker for diversity analysis of ammonia-oxidizing bacteria (AOB). To select a suitable amoA primer for real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE), three reverse primers (degenerate primer amoA-2R; non-degenerate primers amoA-2R-GG and amoA-2IR) were examined. No significant differences were observed among the three primers in terms of quantitative values of amoA from environmental samples using real-time PCR. We found that PCR-DGGE analysis with the amoA-2IR primer gave the best results in this studied soil. These results indicate that amoA-2IR is a suitable primer for community analysis of AOB in the environment.
authors.affiliation: National Institute for Agro-Environmental Sciences, Tsukuba, Ibaraki, Japan. yshimo@affrc.go.jp
authors.forename: Yumi
authors.initials: Y
authors.lastname: Shimomura
authors.forename: Sho
authors.initials: S
authors.lastname: Morimoto
authors.forename: Yuko
authors.initials: Y
authors.lastname: Takada Hoshino
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Uchida
authors.forename: Hiroko
authors.initials: H
authors.lastname: Akiyama
authors.forename: Masahito
authors.initials: M
authors.lastname: Hayatsu
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001419:Bacteria / Q000145:classification / Q000201:enzymology / Q000235:genetics / Q000302:isolation & purification*; D001426:Bacterial Proteins / Q000235:genetics*; D044822:Biodiversity; D017931:DNA Primers / Q000235:genetics*; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase
references.citation: Can J Microbiol. 2005 Aug;51(8):709-14
references.pmid: 16234869
references.citation: Microbes Environ. 2010;25(4):281-7
references.pmid: 21576883
references.citation: Appl Environ Microbiol. 1985 May;49(5):1134-41
references.pmid: 16346787
references.citation: Environ Microbiol. 2006 Feb;8(2):214-22
references.pmid: 16423010
references.citation: J Biol Chem. 1981 Nov 10;256(21):10834-6
references.pmid: 7287737
references.citation: Appl Environ Microbiol. 2007 Jan;73(2):485-91
references.pmid: 17098920
references.citation: Microbes Environ. 2008;23(4):285-92
references.pmid: 21558720
references.citation: J Microbiol Methods. 1999 Dec;39(1):23-31
references.pmid: 10579504
references.citation: Biochim Biophys Acta. 1979 Nov 9;571(1):12-20
references.pmid: 497235
references.citation: Appl Environ Microbiol. 1997 Dec;63(12):4704-12
references.pmid: 9406389
references.citation: Environ Microbiol. 2003 Aug;5(8):691-705
references.pmid: 12871236
references.citation: Microbes Environ. 2009;24(1):21-7
references.pmid: 21566349
references.citation: J Microbiol Methods. 2006 Jul;66(1):147-55
references.pmid: 16343671
references.citation: Appl Environ Microbiol. 2006 Aug;72(8):5181-9
references.pmid: 16885263
references.citation: Appl Environ Microbiol. 2001 Aug;67(8):3426-33
references.pmid: 11472914
references.citation: Proc Natl Acad Sci U S A. 1989 Jan;86(1):232-6
references.pmid: 2643100
references.citation: J Microbiol Methods. 2002 Jul;50(2):189-203
references.pmid: 11997169
references.citation: J Mol Biol. 1966 Aug;19(2):548-55
references.pmid: 5969078
references.citation: Appl Environ Microbiol. 2002 Nov;68(11):5685-92
references.pmid: 12406765
references.citation: Biochem J. 1972 Mar;126(5):1181-91
references.pmid: 5073730
references.citation: Appl Environ Microbiol. 1996 Nov;62(11):4147-54
references.pmid: 8900005
references.citation: Microbes Environ. 2010;25(1):28-35
references.pmid: 21576849
references.citation: Biochem J. 1953 May;54(2):293-5
references.pmid: 13058873
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Biochemistry. 1978 Jul 25;17(15):2984-9
references.pmid: 698180