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.
Highlights
Nitrification, the microbially catalysed oxidation of ammonia to nitrate, is a key process of the biogeochemical nitrogen cycle in virtually all aerobic ecosystems
The major goal of this study was to establish a functional marker gene assay that targets nitrite-oxidizing bacteria (NOB) of the genus Nitrospira
As sequence homology of NxrB paralogs within a given strain was highest (Table S1), nxrB was selected for primer design and evaluation
Summary
Nitrification, the microbially catalysed oxidation of ammonia to nitrate, is a key process of the biogeochemical nitrogen cycle in virtually all aerobic ecosystems. Aside from its crucial role in nature, nitrification is essential in biological wastewater treatment for the removal of excess nitrogen (Daims and Wagner, 2010) but causes problems in agriculture by mobilizing nitrogen in fertilized soils (Prosser, 2011). In-depth biological knowledge of nitrification will be required to achieve a sustainable agriculture and reliable sewage treatment and to better assess the impact anthropogenic nitrogen deposition has on the nitrogen cycle (Gruber and Galloway, 2008). Because nitrifiers are generally recalcitrant to cultivation, molecular methods have been the tools of choice to detect and quantify these organisms in most studies on nitrification in natural or engineered systems. Used approaches to directly detect nitrifiers are 16S ribosomal RNA (rRNA) sequencing and fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes
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