Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline‐alkaline lakes

Abstract

Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.

Ammonium-derived nitrous oxide is a global source in streams

“…The assembly and binning processes generated 198 high-quality (completeness >75%, contamination <15%) metagenome-assembled genomes (MAGs), 111 of which encoded genes involved in N 2 O production and reduction (Supplementary Data S 5 , S 6 ). Through species and functional gene annotation, we obtained eight MAGs containing amoABC , hao , or nxrAB genes, which have been identified as nitrifying bacteria, and seven MAGs that contained the nirK/S gene, identified as denitrifying bacteria 30 , 31 . The annotation results of the species and functional genes were further verified via phylogenetic analysis (Fig.…”

Nitrification in acidic and alkaline environments

“…Nitrification also occurs in saline-alkaline lakes and soda lakes ecosystems, as confirmed by ex situ incubations of lake sediments [ 82 , 73 ]. Multiple studies have shown that ammonia oxidisers mediate ammonia oxidation and primary production at high pH in these environments [ 74 , 67, 68, 71–73, 83 ].…”

“…In 2008, AOB affiliated with Nitrosomonas and AOA from Nitrososphaerales were suggested to be significant contributors of nitrification in the saline and alkaline Mono Lake, California [ 68 ]. Moreover, a recent study implicates both comammox and canonical Nitrospira , as well as several AOA phylotypes, in carrying out rapid nitrification in saline-alkaline lakes at pH up to 11 [ 73 ]. Analysis of an enrichment culture of the canonical nitrite oxidiser Ca .…”