Acid tolerance and metabolic potential of comammox and nitrite-oxidizing Nitrospira enriched from soil

Abstract

Nitrification is the two-step microbial oxidation of ammonia to nitrate via nitrite, and it can contribute to environmental problems in soils. Some nitrifiers have been cultivated from acidic soils at pH <5.5, allowing their metabolic potential and phylogeny to be investigated through genomic analyses. However, the genomic features of the genus Nitrospira remain poorly understood in the context of acid tolerance, despite its wide distribution in acidic environments. This study aimed to characterize the physiology and genomics of acid-Tolerant Nitrospira enriched from an acidic soil. Using a metagenomic approach, two closed genomes of Nitrospira were reconstructed: A complete ammonia-oxidizing (comammox) bacterium and a nitrite-oxidizing bacterium (NOB). Both enriched Nitrospira survived at pH <5.5 in physiological tests, and the enriched comammox Nitrospira was phylogenetically close to clones derived from acidic soils. The active-site residues of hydroxylamine oxidase, a key nitrification enzyme, were conserved between the comammox Nitrospira characterized in this study and the previously reported betaproteobacterial ammonia oxidizers. This conservation suggests that existing nitrification inhibitors targeting this enzyme may also inhibit ammonia oxidation by comammox Nitrospira in acidic soils. Although the comammox and NOB Nitrospira in this study shared nearly all key metabolic pathways with Nitrospira species identified from neutral pH environments, both possessed passive urea transporters homologous to those found in acid-Tolerant bacteria. These results revealed the acid tolerance of the enriched Nitrospira at pH <5.5, as well as their genomic features shared with acid-Tolerant bacteria, rather than with previously reported Nitrospira species.