Denitrification genotypes of endospore-forming Bacillota

Abstract

Denitrification is a key metabolic process in the global nitrogen cycle and is performed by taxonomically diverse microorganisms. Despite the widespread importance of this metabolism, challenges remain in identifying denitrifying populations and predicting their metabolic end-products based on their genotype. Here, genome-resolved metagenomics was used to explore the denitrification genotype of Bacillota enriched in nitrate-amended high temperature incubations with confirmed N2O and N2 production. A set of 12 hidden Markov models (HMMs) was created to target the diversity of denitrification genes in members of the phylum Bacillota. Genomic potential for complete denitrification was found in five metagenome-assembled genomes (MAGs) from nitrate-amended enrichments, including two novel members of the Brevibacillaceae family. Genomes of complete denitrifiers encode N2O reductase (nos) gene clusters with clade II-type nosZ and often include multiple variants of the nitric oxide reductase (nor) gene. The HMM set applied to all genomes of Bacillota from the Genome Taxonomy Database (GTDB) identified 17 genera inferred to contain complete denitrifiers based on their gene content. Among complete denitrifiers it was common for three distinct nitric oxide reductases to be present (qNOR, bNOR and sNOR) which may reflect the metabolic adaptability of Bacillota in environments with variable redox conditions.