Abstract
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.
Highlights
During the past century human activities have accelerated the input of reactive N to the biosphere [1, 2]
We investigated to what extent the two nosZ clades were found in the MGs and MTs of two soils of differing pH; if nosZ gene transcripts originated from a few populations or represented diverse denitrifying bacteria; and if genes other than nosZ in the nos was used to assess the presence of residual genomic DNA in the purified RNA fractions, and only RNA fractions free of gDNA was used for further analysis
Kinetics of denitrification intermediates depict a pHdependent response to anoxia The denitrification kinetics of the two soils during 45 h of anoxic incubation are shown in Fig. 1, in which the sampling occasions for MT analyses are indicated
Summary
During the past century human activities have accelerated the input of reactive N to the biosphere [1, 2] This has escalated the emissions of N2O, a major greenhouse gas and contributor to ozone depletion [3,4,5], as well as nitric oxide (NO) and nitrous acid (HONO) which both influence chemical reactions in the troposphere, leading to formation of undesired ozone [6]. Some mitigation options have been identified through improved understanding of the organisms producing and reducing N2O and the environmental factors that control these emissions [12], and more are expected to emerge as we intensify our research on denitrification and denitrifying organisms in soil. Studies of denitrification kinetics during anoxic incubation of various denitrifying organisms always show temporal
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