Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N₂O emissions and nitrite accumulation in soil

Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.8). SoilA had severely delayed N₂O reduction despite early transcription of nosZ (mainly clade I), encoding N₂O reductase, by diverse denitrifiers. This shows that post-transcriptionally hampered maturation of the NosZ apo-protein at low pH is a generic phenomenon. Identification of transcript reads of several accessory genes in the nos cluster indicated that enzymes for NosZ maturation were present across a range of organisms, eliminating their absence as an explanation for the failure to produce a functional enzyme. nir transcript abundances (for NO₂ reductase) in SoilA suggest that low NO₂ concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to biological activity. The accumulation of NO₂ in neutral soil was ascribed to high nar expression (nitrate reductase). The -omics results revealed dominance of nirk over nirs in both soils while qPCR showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirk pool. qnor encoding NO reductase was strongly expressed in SoilA, implying an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO₂ accumulating soil, was estimated to be ten times higher from SoilA than from SoilN. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.