NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite‐oxidizing N itrospira

Abstract

Summary N itrospira 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 N itrospira to cultivation and the lack of a molecular functional marker, which would allow the detection of N itrospira in the environment. Here we introduce nxrB , the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for N itrospira . Phylogenetic trees based on nxrB of N itrospira were largely congruent to 16 S ribosomal RNA ‐based phylogenies. By using new nxrB ‐selective polymerase chain reaction primers, we obtained almost full‐length nxrB sequences from N itrospira 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 N itrospira 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 N itrospira species per soil. Comparison with an archaeal amoA dataset obtained from the same soils [ E nviron. M icrobiol. 14: 525–539 (2012)] uncovered that ammonia‐oxidizing archaea and N itrospira 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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