title: NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira.
abstract: Nitrospira are the most widespread and diverse known nitrite-oxidizing bacteria and key nitrifiers in natural and engineered ecosystems. Nevertheless, their ecophysiology and environmental distribution are understudied because of the recalcitrance of Nitrospira to cultivation and the lack of a molecular functional marker, which would allow the detection of Nitrospira in the environment. Here we introduce nxrB, the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for Nitrospira. Phylogenetic trees based on nxrB of Nitrospira were largely congruent to 16S ribosomal RNA-based phylogenies. By using new nxrB-selective polymerase chain reaction primers, we obtained almost full-length nxrB sequences from Nitrospira cultures, two activated sludge samples, and several geographically and climatically distinct soils. Amplicon pyrosequencing of nxrB fragments from 16 soils revealed a previously unrecognized diversity of terrestrial Nitrospira with 1801 detected species-level operational taxonomic units (OTUs) (using an inferred species threshold of 95% nxrB identity). Richness estimates ranged from 10 to 946 coexisting Nitrospira species per soil. Comparison with an archaeal amoA dataset obtained from the same soils [Environ. Microbiol. 14: 525-539 (2012)] uncovered that ammonia-oxidizing archaea and Nitrospira communities were highly correlated across the soil samples, possibly indicating shared habitat preferences or specific biological interactions among members of these nitrifier groups.
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Ecology Centre, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Pester
authors.forename: Frank
authors.initials: F
authors.lastname: Maixner
authors.forename: David
authors.initials: D
authors.lastname: Berry
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.forename: Hanna
authors.initials: H
authors.lastname: Koch
authors.forename: Sebastian
authors.initials: S
authors.lastname: Lücker
authors.forename: Boris
authors.initials: B
authors.lastname: Nowka
authors.forename: Andreas
authors.initials: A
authors.lastname: Richter
authors.forename: Eva
authors.initials: E
authors.lastname: Spieck
authors.forename: Elena
authors.initials: E
authors.lastname: Lebedeva
authors.forename: Alexander
authors.initials: A
authors.lastname: Loy
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
authors.forename: Holger
authors.initials: H
authors.lastname: Daims
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D005798:Genes, Bacterial; D005819:Genetic Markers; D008969:Molecular Sequence Data; D009572:Nitrite Reductases / Q000235:genetics*; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny; D021122:Protein Subunits / Q000235:genetics; D012988:Soil Microbiology
chemical_list: D005819:Genetic Markers; D009573:Nitrites; D021122:Protein Subunits; D009572:Nitrite Reductases