Showing papers by "Åsa Frostegård published in 2020"
TL;DR: In-depth analyses suggest that this was due to a competition between electron transport pathways, strongly favouring N2 O over NO3 - reduction, and one way to augment such populations in agricultural soils is to develop inoculants for legume crops with dual capabilities of efficient N2 -fixation and efficient N 2 O reduction.
Abstract: Bradyrhizobia are abundant soil bacteria, which can form nitrogen-fixing symbioses with leguminous plants, including important crops such as soybean, cowpea and peanut. Many bradyrhizobia can denitrify, but studies have hitherto focused on a few model organisms. We screened 39 diverse Bradyrhizobium strains, isolated from legume nodules. Half of them were unable to reduce N2 O, making them sources of this greenhouse gas. Most others could denitrify NO3- to N2 . Time-resolved gas kinetics and transcription analyses during transition to anaerobic respiration revealed a common regulation of nirK, norCB and nosZ (encoding NO2- , NO and N2 O reductases), and differing regulation of napAB (encoding periplasmic NO3- reductase). A prominent feature in all N2 -producing strains was a virtually complete hampering of NO3- reduction in the presence of N2 O. In-depth analyses suggest that this was due to a competition between electron transport pathways, strongly favouring N2 O over NO3- reduction. In a natural context, bacteria with this feature would preferentially reduce available N2 O, produced by themselves or other soil bacteria, making them powerful sinks for this greenhouse gas. One way to augment such populations in agricultural soils is to develop inoculants for legume crops with dual capabilities of efficient N2 -fixation and efficient N2 O reduction.
32 citations
TL;DR: It is concluded that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N2 O as a response to an abiotic NO production from the medium.
Abstract: Fungal denitrification is claimed to produce non‐negligible amounts of N2O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with urn:x-wiley:14622912:media:emi14980:emi14980-math-0001. Enzymatic reduction of urn:x-wiley:14622912:media:emi14980:emi14980-math-0002 (NIR) and NO (NOR) was assessed by correcting measured NO‐ and N2O‐kinetics for abiotic NO‐ and N2O‐production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N2O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N2O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N2O as a response to an abiotic NO production from the medium.
22 citations
Abstract: Liming acidic soils is often found to reduce their N2O emission due to lowered N2O/(N2O+N2) product ratio of denitrification. Some field experiments have shown the opposite effect, however, and the reason for this could be that liming stimulates nitrification-driven N2O production by enhancing nitrification rates, and by favoring ammonia oxidizing bacteria (AOB) over ammonia oxidizing archaea (AOA). AOB produce more N2O than AOA, and high nitrification rates induce transient/local hypoxia, thereby stimulating heterotrophic denitrification. To study these phenomena, we investigated nitrification and denitrification kinetics and the abundance of AOB and AOA in soils sampled from a field experiment 2 - 3 years after liming. The field trial compared traditional liming (carbonates) with powdered siliceous rocks. As expected, the N2O/(N2O+N2) product ratio of heterotrophic denitrification declined with increasing pH, and the potential nitrification rate and its N2O yield (YN2O: N2O-N/NO3-- N), as measured in fully oxic soil slurries, increased with pH, and both correlated strongly with the AOB/AOA gene abundance ratio. Soil microcosm experiments were monitored for nitrification, its O2-consumption and N2O emissions, as induced by ammonium fertilization. Here we observed a conspicuous dependency on waterfilled pore space (WFPS): at 60 and 70% WFPS, YN2O was 0.03-0.06% and 0.06-0.15%, respectively, increasing with increasing pH, as in the aerobic soil slurries. At 85% WFPS, however, YN2O was more than two orders of magnitude higher, and decreased with increasing pH. A plausible interpretation is that O2 consumption by fertilizer-induced nitrification cause hypoxia in wet soils, hence induce heterotrophic nitrification, whose YN2O decline with increasing pH. We conclude that while low emissions from nitrification in well-drained soils may be enhanced by liming, the spikes of high N2O emission induced by ammonium fertilization at high soil moisture may be reduced by liming, because the heterotrophic N2O reduction is enhanced by high pH.
19 citations
TL;DR: The -omics results suggested that low NO2− concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to enzymatic activity, and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.
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.
18 citations
TL;DR: In this paper, the authors present some novel options for mitigation of N2O emissions, beside liming, and develop inoculants for legumes that are strong reducers.
18 citations
TL;DR: It is proposed that this applies to all organisms which, like many bradyrhizobia, carry Nos and Nap but lack membrane-bond NO3− reductase (Nar), and Paracoccus denitrificans, which has Nap and Nar, reduced N2O and No3− simultaneously.
Abstract: The legume-rhizobium symbiosis accounts for the major part of the biological N2 fixation in agricultural systems. Despite their lower need for synthetic nitrogen fertilizers, legume-cropped fields are responsible for substantial N2O emissions. Several economically important legumes fix N2 through symbiosis with bacteria belonging to the genus Bradyrhizobium. Many bradyrhizobia are also denitrifiers, and inoculation of legumes with N2O-reducing strains has been suggested to mitigate N2O emissions. Here, we analyzed the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut nodules. All performed at least partial denitrification, but only 37% were complete denitrifiers. This group shared a common phenotype with a strong preference for N2O- over NO3−-reduction. We tested if this could be due to low quantities of NO3− reductase (periplasmic Nap) but found that Nap was more abundant than N2O reductase (Nos). This corroborates a recently proposed mechanism that the electron pathway from quinols to Nos via the cytochrome bc1 complex outcompetes that to Nap via the membrane-bound NapC. We propose that this applies to all organisms which, like many bradyrhizobia, carry Nos and Nap but lack membrane-bond NO3− reductase (Nar). Supporting this, Paracoccus denitrificans, which has Nap and Nar, reduced N2O and NO3− simultaneously.
16 citations
TL;DR: In this article, the authors demonstrate that digestates obtained after biogas production may provide a low-cost and widely applicable solution to mitigate N2O-emissions from soils.
Abstract: Mitigation of N2O-emissions from soils is needed to reduce climate forcing by food production. Inoculating soils with N2O-reducing bacteria would be effective, but costly and impractical as a standalone operation. Here we demonstrate that digestates obtained after biogas production may provide a low-cost and widely applicable solution. Firstly, we show that indigenous N2O-reducing bacteria in digestates grow to high levels during anaerobic enrichment under N2O. Gas kinetics and meta-omic analysis show that the N2O-respiring organisms, recovered as metagenome-assembled genomes (MAGs), grow by harvesting fermentation intermediates of the methanogenic consortium. Three digestate-derived denitrifying, N2O-reducing bacteria were obtained through isolation, one of which matched the recovered MAG of a dominant Dechloromonas-affiliated N2O reducer. While the identified N2O-reducers encoded genes required for a full denitrification pathway and could thus both produce and sequester N2O, their regulatory traits predicted that they act as N2O-sinks. Secondly, moving towards practical application, we show that these isolates grow by aerobic respiration in digestates, and that fertilization with these enriched digestates reduces N2O emissions. This shows that the ongoing implementation of biogas production in agriculture opens a new avenue for cheap and effective reduction of N2O emissions from food production.
2 citations