Comparative diversity and abundance of ammonia monooxygenase genes in mulched and vegetated soils

► Ammonia oxidizers compared in vegetated, gravel-mulched and bark-mulched soils. ► Archaeal but not bacterial amoA abundance was altered by soil cover. ► Gravel-mulched soils supported distinct archaeal amoA genetic composition. ► Mulched soils showed greater genetic heterogeneity than vegetated soils. ► Hydrophobic regions of amoA had more nucleotide variability than hydrophilic regions.