The genus Nitrospira represents the dominant group of nitrite-oxidizing bacteria in most wastewater treatment plants (WWTPs). The genus is phylogenetically divided into two major lineages (I and II), for which vast phylogenetic and functional diversity has been revealed by recent molecular ecophysiological analyses. However, the genetic basis underlying these phenotypic differences remains largely unknown, due to lack of genome sequences representing their diversity. To broaden comprehensive understanding of Nitrospira, we report comparative genomic analysis of two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively), previously isolated from a WWTP. Unexpectedly, genome of strain NJ1 lacked genes relevant to flagella and CRISPR-Cas systems, whereas most nitrifying bacteria including strain ND1 have these genome elements. Alternatively, strain NJ1 possesses a gene cluster of quorum sensing systems, not reported in previous Nitrospira genomic analyses. Moreover, a comparative analysis based on genes involved in nitrogen metabolism among all Nitrospira genomes, revealed that a urease locus of strain ND1 belonging to lineage I was obtained by horizontal gene transfer from Nitrospira lineage II, and that cytochrome c nitrite reductases were canonical nitrite reductases for nitrogen assimilation in Nitrospira. These findings indicate Nitrospira have diverse function and evolution beyond our expectation.
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