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

Abstract

SummaryNitrospira 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 nxrBselective 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.

AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammoxNitrospirain the environment

“…Only clade A members were found in the WWTPs, the brackish lake sediment, and the river biofilm enrichment, whereas we retrieved only clade B amoA gene sequences from the forest soil ( Table 2). The widespread occurrence of comammox Nitrospira in the analyzed samples is consistent with the previously reported presence of mostly uncultured and uncharacterized Nitrospira members in the respective habitat types (e.g., Daims et al, 2001;Martiny et al, 2005;Ke et al, 2013;Pester et al, 2014). Future studies should determine which fraction of these environmental Nitrospira are strict NOB or comammox, respectively.…”

“…It should be noted that these OTUs might not delineate species, as an appropriate specieslevel sequence identity cutoff for comammox amoA remains unknown. This would need to be determined by correlating amoA sequence identities with 16S rRNA identities or with genome-wide average nucleotide identities (Purkhold et al, 2000;Richter and Rosselló-Móra, 2009;Pester et al, 2014) once more genomic data from comammox Nitrospira become available. A phylogenetic analysis of the amoA gene OTU representatives revealed a substantial diversity of comammox Nitrospira in almost all samples (Figure 1, Table 2, Table S1).…”

“…They are widespread in virtually all oxic natural and engineered ecosystems, and an impressively high diversity of coexisting uncultured Nitrospira strains has been detected in wastewater treatment plants and soils (Pester et al, 2014;GruberDorninger et al, 2015). All known comammox organisms belong to Nitrospira sublineage II (Daims et al, 2015;van Kessel et al, 2015;Palomo et al, 2016;Pinto et al, 2016).…”

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira

“…Accordingly, nitrifiers often tightly coaggregate in flocs and biofilms (14), and the abundances of AOA and Nitrospira in soils have been found to correlate (17). This classical scheme dictates that NOB strongly depend on AOM to initiate nitrification.…”

“…Nitrospira are well adapted to low nitrite concentrations (10,11) and form at least six phylogenetic lineages (15,16) that are globally distributed in soils (17,18), the oceans (19), freshwater habitats (20), hot springs (16), and many other oxic habitats (15). In addition, Nitrospira members are the key NOB in most WWTPs (14,15).…”