Metabolic and phylogenetic diversity in the phylum revealed by comparative genome analyses.

The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum . Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class . Moreover, although were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 genomes with focus on these understudied classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum and offers new avenues for the isolation and cultivation of these elusive bacteria.