Comparative genomics sheds light on niche differentiation and the evolutionary history of comammoxNitrospira

Abstract

AbstractThe description of comammoxNitrospiraspp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria (β-AOB) in the environment, call into question the metabolic potential of comammoxNitrospiraand the evolutionary history of their ammonium oxidation pathway. We report four new comammoxNitrospiragenomes, constituting two novel species, and the first comparative genomic analysis on comammoxNitrospira.ComammoxNitrospirahas lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizingNitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to otherNitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to β-AOB, comammoxNitrospiragenomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammoxNitrospiraseems attuned to oligotrophy and hypoxia compared to β-AOB.β-AOBs are the clear origin of the ammonium oxidation pathway in comammoxNitrospira: reconciliation analysis indicates two separate earlyamoAgene transfer events from β-AOB to an ancestor of comammoxNitrospira, followed by clade specific losses. ForhaoA, one early transfer from β-AOB to comammoxNitrospirais predicted – followed by intra-clade transfers. We postulate that the absence of comammox genes in mostNitrospiragenomes is the result of subsequent loss.SignificanceThe recent discovery of comammox bacteria - members of theNitrospiragenus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammoxNitrospiraand related nitrifiers. Ammonium oxidation genes in comammoxNitrospirahad a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.