ABSTRACTThe recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of theNitrospiragenus and are present in a variety of environments, including Biological Nutrient Removal (BNR) systems. However, the physiological traits within and between comammox- and nitrite oxidizing bacteria (NOB)-likeNitrospiraspecies have not been analyzed in these ecosystems. In this study, we identifiedNitrospirastrains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under micro-aerobic conditions. We recovered metagenomes-derived draft genomes from twoNitrospirastrains: (1)Nitrospirasp. UW-LDO-01, a comammox-like organism classified asCandidatusNitrospira nitrosa, and (2)Nitrospirasp. UW-LDO-02, a nitrite oxidizing strain belonging to theNitrospira defluviispecies. A comparative genomic analysis of these strains with otherNitrospira-likegenomes identified genomic differences inCa.Nitrospira nitrosa mainly attributed to each strains’ niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation and micro-aerobic metabolism, which might explain survival ofNitrospiraunder multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features ofCa.Nitrospira nitrosa, and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of theNitrospiragenus.