NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite‐oxidizing Nitrospira. (8th November 2013)

• Record Type: Journal Article
• 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
• Is Part Of: Environmental microbiology. Volume 16:Number 10(2014:Oct.)
• Page Start: 3055
• Page End: 3071
• Publication Date: 2013-11-08
• Subjects: Microbial ecology -- Periodicals; Environmental Microbiology -- Periodicals; 579.17
• DOI: 10.1111/1462-2920.12300
• Languages: English
• ISSNs: 1462-2912

Abstract

<abstract abstract-type="main"> <title>Summary</title> <p> <italic>N</italic> <italic>itrospira</italic> 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 <italic>N</italic><italic>itrospira</italic> to cultivation and the lack of a molecular functional marker, which would allow the detection of <italic>N</italic><italic>itrospira</italic> in the environment. Here we introduce <italic>nxrB</italic>, the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for <italic>N</italic><italic>itrospira</italic>. Phylogenetic trees based on <italic>nxrB</italic> of <italic>N</italic><italic>itrospira</italic> were largely congruent to 16S ribosomal RNA‐based phylogenies. By using new <italic>nxrB</italic>‐selective polymerase chain reaction primers, we obtained almost full‐length <italic>nxrB</italic> sequences from <italic>N</italic><italic>itrospira</italic> cultures, two activated sludge samples, and several geographically and climatically distinct soils. Amplicon pyrosequencing of <italic>nxrB</italic> fragments from 16 soils revealed a previously unrecognized diversity of terrestrial <italic>N</italic><italic>itrospira</italic> with 1801 detected species‐level operational taxonomic units (OTUs) (using an inferred species threshold of 95% <italic>nxrB</italic> identity). Richness estimates ranged from 10 to 946 coexisting <italic>N</italic><italic>itrospira</italic> species per soil. Comparison with an archaeal <italic>amoA</italic> dataset obtained from the same soils [Environ. Microbiol. 14: 525–539 (2012)] uncovered that ammonia‐oxidizing archaea and <italic>N</italic><italic>itrospira</italic> communities were highly correlated across the soil samples, possibly indicating shared habitat preferences or specific biological interactions among members of these nitrifier groups.</p> </abstract>