Niche differentiation and evolution of comammox Nitrospira through a comparative genomics analysis

Nitrification, the biological oxidation of ammonium to nitrate, is a fundamental process in the nitrogen cycle and plays an important role in natural and engineered systems. Throughout the last century, nitrification was assumed to be a two-step process executed by two different functional groups, ammonia oxidizing prokaryotes (AOP) and nitrite oxidizing bacteria (NOB). Recently, several articles have shown the capability of a single microorganism, belonging to the genus Nitrospira, to carry out the complete oxidation of ammonia to nitrate (comammox). Nitrospira spp. are widespread in both natural and engineered ecosystems associated with nitrogen cycling and different species are frequently observed to coexist in the same environment. Besides recent discoveries pointing towards versatile metabolism in some Nitrospira species, little is known about the functional potential of the two comammox Nitrospira clades, and the factors involved in niche-partitioning between comammox and canonical Nitrospira. A comparative genomics analysis was conducted with five genomes recovered from a groundwater-fed rapid sand filter (including both comammox clades and a nitrite-oxidizing Nitrospira population genome) and high quality published Nitrospira genomes, to reveal distinct genomic features within Nitrospira. In addition, we investigated the evolution of the ammonia oxidation pathway in comammox Nitrospira. This analysis revealed distinct genetic capabilities of the different comammox clades and canonical Nitrospira which can help to explain the coexistence and niche partitioning of Nitrospira spp. These divergences range from the nitrogen source utilization capacity to the ability for electron donor versatility, and other characteristics such as stress response. With respect to the evolutionary history of comammox Nitrospira, our analysis indicates transfer events with betaproteobacterial ammonia oxidizers. In addition, transfer events between comammox clade A and clade B w