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Review
. 2010 Jan;85(3):425-40.
doi: 10.1007/s00253-009-2228-9.

Phylogenetic and Functional Marker Genes to Study Ammonia-Oxidizing Microorganisms (AOM) in the Environment

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Free PMC article
Review

Phylogenetic and Functional Marker Genes to Study Ammonia-Oxidizing Microorganisms (AOM) in the Environment

Pilar Junier et al. Appl Microbiol Biotechnol. .
Free PMC article

Abstract

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.

Figures

Fig. 1
Fig. 1
Phylogenetic tree based on 16S rRNA gene sequences for different ammonia-oxidizing microorganisms. The sequences were aligned with Muscle (Edgar 2004) using a maximum of 24 iterations. A maximum-likelihood tree was built from the resulting alignment with PhyML (Guindon and Gascuel 2003) using the JTT model, 16 substitution rate classes, and maximum-likelihood estimates of parameters. Bootstrap values (%) from 1,000 bootstraps are indicated
Fig. 2
Fig. 2
Cumulative number of amoCAB/hao sequences submitted to the GenBank database. aamoA and hao/hzo genes. bamoB and amoC
Fig. 3
Fig. 3
Phylogenetic tree based on sequences homologs to orf4 and orf5 found in the genome of ammonia-oxidizing bacteria and methane-oxidizing bacteria. For methods, see Fig. 1

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