Journal
ENVIRONMENTAL MICROBIOLOGY
Volume 16, Issue 10, Pages 3055-3071Publisher
WILEY
DOI: 10.1111/1462-2920.12300
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Funding
- Austrian Science Fund, FWF [P23117-B17, P25231-B21, P20185-B17, P25111-B22, P24101-B22]
- Vienna Science and Technology Fund, WWTF [LS216, LS09-40]
- German Federal Ministry of Science and Education (BIOLOG/BIOTA) [01LC0621D]
- European Research Council [Advanced Grant Nitrification Reloaded (NITRICARE)] [294343]
- Austrian Science Fund (FWF) [P25231, P23117, P25111, P24101] Funding Source: Austrian Science Fund (FWF)
- Austrian Science Fund (FWF) [P 24101, P 25111, P 23117, P 20185] Funding Source: researchfish
- European Research Council (ERC) [294343] Funding Source: European Research Council (ERC)
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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.
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