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

• Published in: Environmental microbiology 2014-10, Vol.16 (10), p.3055-3071
• Main Authors: Pester, Michael, Maixner, Frank, Berry, David, Rattei, Thomas, Koch, Hanna, Lücker, Sebastian, Nowka, Boris, Richter, Andreas, Spieck, Eva, Lebedeva, Elena, Loy, Alexander, Wagner, Michael, Daims, Holger
• Format: Article
• Language: English
• Subjects: activated sludge; Archaea; bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; data collection; ecophysiology; ecosystems; genes; Genes, Bacterial; Genetic Markers; habitat preferences; Molecular Sequence Data; Nitrite Reductases - genetics; Nitrites - metabolism; Nitrospira; Oxidation-Reduction; Phylogenetics; Phylogeny; polymerase chain reaction; Protein Subunits - genetics; sequence analysis; soil; Soil Microbiology; soil sampling
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/1462-2920.12300

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.