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          Institute: MPI für Evolutionsbiologie     Collection: Ecophysiology     Display Documents

ID: 430622.0, MPI für Evolutionsbiologie / Ecophysiology
Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon
Authors:Junier, Pilar; Kim, Ok-Sun; Junier, Thomas; Ahn, Tae-Seok; Imhoff, Johannes F.; Witzel, Karl-Paul
Date of Publication (YYYY-MM-DD):2009-05
Title of Journal:Applied Microbiology and Biotechnology
Journal Abbrev.:Appl Microbiol Biotechnol
Issue / Number:1
Start Page:175
End Page:188
Review Status:not specified
Audience:Not Specified
Abstract / Description:The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the three amo genes, suggesting that it might be a better molecular marker than the most frequently used amoA to resolve closely related AOB species. To test the suitability of using the amoCAB genes for community studies, a strategy involving nested PCR was employed. Primers to amplify the whole amoCAB operon and each individual gene were tested. The specificity of the products generated was analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The fragments obtained showed different grades of sequence identity to amoCAB sequences in the GenBank database. The nested PCR approach provides a possibility to increase the sensitivity of detection of amo genes in samples with low abundance of AOB. It also allows the amplification of the almost complete amoA gene, with about 300 bp more sequence information than the previous approaches. The coupled study of all three amo genes and the intergenic spacer regions that are under different selection pressure might allow a more detailed analysis of the evolutionary processes, which are responsible for the differentiation of AOB communities in different habitats.
Free Keywords:Ammonia-oxidizing betaproteobacteria; PCR primers; amoC; amoA; amoB
External Publication Status:published
Document Type:Article
Affiliations:MPI für Evolutionsbiologie/Abt. Ökophysiologie
External Affiliations:Ecole Polytech Fed Lausanne, ENAC, ISTE, EML, CH-1015 Lausanne, Switzerland; Seoul Natl Univ, Sch Biol Sci, Seoul 151742, South Korea; Seoul Natl Univ, Inst Microbiol, Seoul 151742, South Korea; Univ Geneva, CH-1211 Geneva, Switzerland; Kangwon Natl Univ, Dept Environm Sci, Chunchon 200701, South Korea; Univ Kiel, Leibniz Inst Marine Sci, D-24105 Kiel, Germany
Identifiers:ISSN:0175-7598 (print) [ID-No:1]
ISSN:1432-0614 (online) [ID-No:2]
DOI:10.1007/s00253-009-1923-x [ID-No:3]
LOCALID:2696/S 38997 [Listen-Nummer/S-Nummer]
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