title: Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment.
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.
authors.affiliation: Laboratory of Microbial Ecology, University of Neuchatel, Neuchatel, Switzerland. Pilar.Junier@epfl.ch
authors.forename: Pilar
authors.initials: P
authors.lastname: Junier
authors.forename: Verónica
authors.initials: V
authors.lastname: Molina
authors.forename: Cristina
authors.initials: C
authors.lastname: Dorador
authors.forename: Ora
authors.initials: O
authors.lastname: Hadas
authors.forename: Ok-Sun
authors.initials: OS
authors.lastname: Kim
authors.forename: Thomas
authors.initials: T
authors.lastname: Junier
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Witzel
authors.forename: Johannes F
authors.initials: JF
authors.lastname: Imhoff
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000235:genetics* / Q000378:metabolism; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D004783:Environmental Microbiology; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics; D009573:Nitrites / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny
chemical_list: D009573:Nitrites; D000641:Ammonia; D009584:Nitrogen