Browse > Article

Identification of the Nitrifying Archaeal Phylotype Carrying Specific amoA Gene by Applying Digital PCR  

Park, Byoung-Jun (Department of Microbiology, Chungbuk National University)
Park, Soo-Je (Department of Microbiology, Chungbuk National University)
Rhee, Sung-Keun (Department of Microbiology, Chungbuk National University)
Publication Information
Korean Journal of Microbiology / v.43, no.3, 2007 , pp. 232-235 More about this Journal
Abstract
Mesophilic Crenarchaeota have been known to be predominant among ammonia-oxidizing microorganisms in terrestrial and marine environments. In this study, we determined the archaeal phylotypes carrying specific amoA by combining digital PCR and multiplex-nested PCR. Analysis of samples in which amoA and 16S rRNA gene were amplified showed that amoA gene diversity was relatively higher than that of 16S rRNA gene. Nitrifying archaeal group I.1a was dominant over I.1b group of crenarchaota and euryarchaeota. This approach could be applied for interrelating a functional gene to a specific phylotype in natural environments.
Keywords
amoA; digital PCR; diversity; nitrifying archaea; tidal flat; 16S rRNA gene;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
Times Cited By SCOPUS : 0
연도 인용수 순위
1 Ahn, Y.B., S.K. Rhee, D.E. Fennell, L.J. Kerkhof, U. Hentschel, and M.M. Hggblom. 2003. Reductive dehalogenation of brominated phenolic compounds by microorganisms associated with the marine sponge Aplysina aerophoba. Appl. Environ. Microbiol. 69, 4159-4166   DOI
2 Leinger, S., T. Urich, M. Schloter, L. Schwark, J. Qi, G.W. Nicol, J.I. Prosser, S.C. Schuster, and C. Schleper. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806-809   DOI   ScienceOn
3 Thomson, J.D., D.G. Higgins, and T.J. Gibson. 1994. CLUSTAL W; Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680   DOI
4 Park, S.J., C.H. Kang, and S.K. Rhee. 2006. Characterization of the microbial diversity in a Korean solar saltern by 16S rRNA gene analysis. J. Microbiol. Biotechnol. 16, 1640-1645   과학기술학회마을
5 Whitehouse, C.A. and H.E. Hottel. 2007. Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Mol. Cell. Probes. 21, 92-96   DOI   ScienceOn
6 De Long, B.F. 1992. Archaea in coastal marine environments. Proc. Natal Acad Sci. USA. 89, 5685-5689
7 Di Pinto, A., F. VitoTony, M.C. Guastadisegni, C. Martino, F.P. Schena, and G. Tantillo. 2007. A comparison of DNA extraction methods for food analysis. Food Control. 18, 76-80   DOI   ScienceOn
8 Amann, R. 2000. Who is out there? Microbial aspects of biodiver- sity. Sys. Appl. Microbiol. 23, 1-8   DOI   ScienceOn
9 Kemnitz, D., S. Kolb, and R. Conrad. 2007. High abundance of Crenarchaeota in a temperate acidic forest soil. FEMS Microbiol. Ecol. 60, 442   DOI   ScienceOn
10 Briimmer, I.H.M., A. Felske, and I. Wagner-Dobler. 2003. Diversity and seasonal variability of$\beta$ -Proteobacterla in biofilms of polluted rivers: analysis by temperature gradient gel electrophoresis and cloning. Appl. Environ. Microbiol. 69, 4463-4473   DOI
11 Sebat, J.L., F.S. Colwell, and R.L. Crawford. 2003. Metagenomic profiling: Microarray analysis of an environmental genomic library. Appl. Environ. Microbiol. 69, 4927-4934   DOI
12 Tsai, Y.L. and B.H. Olson. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57, 1070-1074   PUBMED
13 Greene, K. 2002. New method for culturing bacteria. Science 296, 1000   PUBMED
14 Inagaki, F., M. Suzuki, K. Takai, H. Oida, T. Sakamoto, K. Aoki, K.H. Nealson, and K. Horikoshi. 2003. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microbiol. 69, 7224-7235   DOI
15 Stackebrandt, E., W. Liesack, and B.M. Goebel. 1993. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J. 7, 232-236   DOI   PUBMED
16 Ottesen, E.A., J. Hong, S.R. Quake, and J.R. Leadbetter. 2006. PCR enables multigene analysis of individual environmental bacteria. Science 314, 1464-1467   DOI   ScienceOn
17 Stepanauskas, R. and M.E. Sieracki. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc. Nat. Acad. Sci. USA. 104,9052-9057
18 Park, S.J., B.J. Park, M.S. Kim, and S.K. Rhee. 2007. Abundance and diversity of ammonia-oxidizing Archaea in marine sediments characterized by comparative analysis of archaeal 16S rRNA and amoA genes. Submitted
19 Beman, J.M. and C.A. Francis. 2006. Diversity of ammonia-oxidizing archaea and bacteria in the sediment of a hypemutrified subtropical estuary Bahia del Tobari, Mexico. Appl. Environ. Microbiol. 72, 7767-7777   DOI   ScienceOn
20 Kaeberlein, T., K. Lewis, and S.S. Epstein. 2002. Isolating 'Uncultivable' microorganism in pure culture in a simulated natural environment. Science 296, 1127-1129   DOI   ScienceOn
21 Kim, B.S., H.M. Oh, H. Kang, and J. Chun. 2005. Archaeal diversity in tidal and sediment as revealed by 16S rDNA analysis. J. Microbiol. 43, 144-151   과학기술학회마을