Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity

Abstract

The genus Nitrospira represents a dominant group of nitrite-oxidizing bacteria in natural and engineered ecosystems. This genus is phylogenetically divided into six lineages, 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 because of the lack of genome sequences representing their diversity. To gain a more comprehensive understanding of Nitrospira, we performed genomic comparisons between two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively) previously isolated from activated sludge. In addition, the genomes of these strains were systematically compared with previously reported six Nitrospira genomes to reveal their similarity and presence/absence of several functional genes/operons. Comparisons of Nitrospira genomes indicated that their genomic diversity reflects phenotypic differences and versatile nitrogen metabolisms. Although most genes involved in key metabolic pathways were conserved between strains ND1 and NJ1, assimilatory nitrite reduction pathways of the two Nitrospira strains were different. In addition, the genomes of both strains contain a phylogenetically different urease locus and we confirmed their ureolytic activity. During gene annotation of strain NJ1, we found a gene cluster encoding a quorum-sensing system. From the enriched supernatant of strain NJ1, we successfully identified seven types of acyl-homoserine lactones with a range of C10–C14. In addition, the genome of strain NJ1 lacks genes relevant to flagella and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated genes) systems, whereas most nitrifying bacteria including strain ND1 possess these genomic elements. These findings enhance our understanding of genomic plasticity and functional diversity among members of the genus Nitrospira.

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

“…7, 8). Prior to this observation, only canonical NOB Nitrospira were known to possess this gene [70,73,74,77,78]. The cynS genes were on long contigs (i.e., 182 kb and 121 kb, RBC069 and RBC093, respectively), and the primary sequences of most genes adjacent to the cynS genes, when queried against RefSeq using BLASTP, were most similar to genes belonging to known comammox Nitrospira.…”

“…Because the comammox Nitrospira MAGs did not contain any fdh genes for formate dehydrogenase (Fig. 7), the RBC populations represented by these MAGs likely cannot use formate as an alternative electron donor, which can be used by NOB Nitrospira and most clade B comammox bacteria [70][71][72][73]. Most clade A comammox bacteria described so far lack the genes for formate dehydrogenase [70], with the exception of Nitrospira bin RCA [74].…”

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

“…In addition to external ammonium sources, ammonium can also originate from the intracellular hydrolysis of urea, and both Rifle genomes encoded ureases and the corresponding ABC transport systems. The presence and activity of urease in both canonical and comammox Nitrospira indicate that hydrolysis of urea is a common metabolic feature within this genus (Koch et al, 2015;van Kessel et al, 2015;Ushiki et al, 2018). Intriguingly, while canonical Nitrospira employ a cyanase to utilize cyanate as an additional metabolic source of ammonium (Palatinszky et al, 2015;Ushiki et al, 2018) this function is absent in complete nitrifiers (Palomo et al, 2018).…”

“…Fascinatingly, some uncultured Nitrospira from activated sludge only assimilate formatederived carbon in the presence of nitrite (Gruber-Dorninger et al, 2015), and N. moscoviensis was shown to perform simultaneous formate and nitrite oxidation (Koch et al, 2015). So far, canonical and comammox clade B Nitrospira were described to possess a NADdependent formate dehydrogenase and a formate transporter (Lücker et al, 2010;Koch et al, 2015;Palomo et al, 2018;Ushiki et al, 2018), which were absent in RCB. Contrastingly, RCA possessed all genes necessary for formate uptake and oxidation (Fig.…”

Unexpected versatility in the metabolism and ecophysiology of globally relevant nitrite-oxidizingNitrotogabacteria

“…Urea is an important source of ammonia for many NOB (e.g., Nitrospina and some Nitrospira) (Daims et al, 2016;Ushiki et al, 2018). A urea-binding-like protein was found in the LAW genome located near most of the nitrogen transport systems (i.e., narK nitrite/nitrate transporter, nitrogen metabolism transcription factor ntrC, formate/nitrite transporter, nirK assimilatory nitrite reductase, and ammonia transporter amtB).…”