Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira present in a reactor treating high-ammonia brackish landfill leachate

Nitrification is mediated by numerous different microorganisms, but knowledge of their ecophysiologies is insufficient. Leachate in the late stages of landfill operation provides a brackish environment with a high ammonia concentration, and methanol is added as an electron donor for denitrification. Such a unique environment may contain novel nitrifiers. Here, we present metagenomic analysis of the microbiome from a closed landfill leachate treatment facility to investigate the identity and functions of nitrifiers. Using a genome-centric approach with metagenomic analysis, we retrieved draft genomes for a novel complete ammonia-oxidizing (comammox) bacterium Nitrospira LAS72; and canonical Nitrospira LAS18, clustered within a novel sub-lineage VII of Nitrospira; Candidatus Nitrosocosmicus LAS21 and Nitrosarchaeum LAS73, belonging to the ammonia-oxidizing archaea (AOA). This is the first evidence of comammox Nitrospira in a high-ammonia-containing brackish environment. Canonical ammonia-oxidizing bacteria were not detected. Given the brackish environment and supplementation of methanol used in the facility, we also investigated the methanol metabolism of these nitrifiers and their potential to produce compatible solutes as osmoprotectants. Uniquely among Nitrospira, comammox Nitrospira LAS72 possesses genes associated with formaldehyde reductase and glycine betaine biosynthesis. Thus, Nitrospira LAS72 may proliferate because of the availability of formaldehyde upstream of carbon metabolism and adapt to fluctuating osmotic pressure by producing a variety of compatible solutes. The discovery of this novel comammox Nitrospira, and canonical Nitrospira forming a new sub-lineage VII in an ammonia-concentrated brackish environment broadens our knowledge of the diversity and functions of nitrifying microorganisms.