Format

Send to

Choose Destination
Environ Microbiol. 2014 Oct;16(10):3055-71. doi: 10.1111/1462-2920.12300. Epub 2013 Nov 8.

NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira.

Author information

1
Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Ecology Centre, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.

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.

PMID:
24118804
DOI:
10.1111/1462-2920.12300
[Indexed for MEDLINE]

Publication type, MeSH terms, Substances, Secondary source IDs, Grant support

Publication type

MeSH terms

Substances

Secondary source IDs

Grant support

Supplemental Content

Full text links

Icon for Wiley
Loading ...
Support Center