Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted soils under contrasting management regimes - permanent bare fallow, grassland and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated that nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome. The AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soils amended or not with DCD (an inhibitor of AOB but not AOA) was highest in arable soils and lower in all soil microcosm assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.