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

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