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

Abstract

Denitrifier community phenotypes often result in transient accumulation of denitrification (NO3−→NO2−→NO→N2O→N2) intermediates. Consequently, anoxic spells drive NO-, N2O- and possibly HONO-emissions to the atmosphere, affecting both climate and tropospheric chemistry. Soil pH is a key controller of intermediate levels, and while there is a clear negative correlation between pH and emission of N2O, NO2− concentrations instead increase with pH. These divergent trends are probably a combination of direct effects of pH on the expression/activity of denitrification enzymes, and an indirect effect via altered community composition. This was studied by analyzing metagenomics/transcriptomics and phenomics of two soil denitrifier communities, one of pH 3.8 (Soil3.8) and the other 6.8 (Soil6.8). Soil3.8 had severely delayed N2O reduction despite early transcription of nosZ, encoding N2O reductase, by diverse denitrifiers, and of several nosZ accessory genes. This lends support to a post-transcriptional, pH-dependent mechanism acting on the NosZ apo-protein or on enzymes involved in its maturation. Metagenome/metatranscriptome reads of nosZ were almost exclusively clade I in Soil3.8 while clade II dominated in Soil6.8. Reads of genes and transcripts for NO2−-reductase were dominated by nirK over nirS in both soils, while qPCR-based determinations showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK community. The -omics results suggested that low NO2− concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to enzymatic activity. The NO reductase gene qnor was strongly expressed in Soil3.8, suggesting 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 Soil3.8 than from Soil6.8. 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.

Temperature Sensitivity and Composition of Nitrate-Reducing Microbiomes from a Full-Scale Woodchip Bioreactor Treating Agricultural Drainage Water

“…Ratios of nir / nosZ indicated similar genetic potential for production and consumption of N 2 O in the enrichment cultures and even an overcapacity of N 2 O consumption in the native woodchip microbiome, which could be related to the presence of non-denitrifying N 2 O reducers, found to play an important ecological role in many terrestrial ecosystems [ 70 ]. However, although gene numbers reflect a genetic potential, it is not a direct measure of realized metabolic activity [ 71 ]. Thus, under environmental conditions, the N 2 O/N 2 product ratio in bacteria with genetic capacity for full denitrification is controlled by factors such as pH and availability C and N, which may fluctuate over time in WBRs [ 20 ].…”

Sustained bacterial N2O reduction at acidic pH

“…RandomForest analysis revealed weak relationships between the presence of 'Ca. (34,35). In contrast, characterized N 2 O reducers from soil habitats consume N 2 O within a narrow pH window ranging from 6 to 8 with generally weak activity approaching pH 6.0 and no activity at lower pH (18,(36)(37)(38).…”

“…Soil acidification is a major concern relevant to N cycling and N 2 O emissions. Microbial processes (e.g., nitrification and denitrification) involved in N 2 O production have been reported to cause greater N 2 O emissions at pH < 6 than at circumneutral pH(34,35). In contrast, characterized N 2 O reducers from soil habitats consume N 2 O within a narrow pH window ranging from 6 to 8 with generally weak activity approaching pH 6.0 and no activity at lower pH(18,(36)(37)(38).…”

“…A few studies reported limited N 2 O reduction activity in acidic microcosms, but enrichment cultures for detailed experimentation were not obtained(12,35,39). Possible explanations for the observed N 2 O consumption in acidic microcosms include residual activity of existing N 2 Oreducing biomass, or the presence of microsites on soil particles where solid phase properties influence local pH, generating pH conditions not captured by bulk aqueous phase pH measurements(40,41).…”

Shifts in composition and function of bacterial communities reveal the effect of small barriers on nitrous oxide and methane accumulation in fragmented rivers

“…There is growing evidence that urban river networks may be hot spots for greenhouse gas (N 2 O, CH 4 ) emissions (Zhang W. et al, 2021). Inland waters are significant emitters of N 2 O (Gongqin et al, 2021), and the total estimated N 2 O from rivers is approximately 1.05 Tg N-N 2 O Yr −1 (global total emissions are 17.7 Tg N-N 2 O Yr −1 ; Frostegard et al, 2022). CH 4 is generally considered to be a more important greenhouse gas than N 2 O (Stein, 2020;Neubauer, 2021).…”