Nitrite kinetics during anoxia: the role of abiotic reactions versus microbial reduction

Anoxic spells in soil induce denitrification, i.e. the sequential reduction NO3-→NO2-→NO→N2O→N2, catalysed by the four enzymes NAR, NIR, NOR and NOS, respectively. Transient accumulation of all intermediates is inevitable, but the concentrations depend on the regulation of gene expression and the physical/chemical properties of the soil. Nitrite is chemically unstable at low pH, decomposing via a conglomerate of abiotic reactions with metals and organic compounds which can result in production of NO, N2O, N2 and nitrosated organic compounds (R-NO). There is evidence that acidic soils accumulate less nitrite than neutral soils, but it is unclear if this is due to high abiotic decomposition rate (VADEC) or fast enzymatic reduction of nitrite (VNIR) at low pH. To investigate this, we monitored the kinetics of NO2-, NO, N2O and N2 during anoxic incubations of three organic soils with pHCaCl2 ranging from 3.4 to 7.2, taken from a long-term liming experiment. In parallel, we determined the rate of abiotic nitrite decay (VADEC) and its product stoichiometry (NO, N2O and R-NO) in gamma-irradiated soils. VADEC was clearly first-order with respect to HNO2 (kHNO2 = 1.4 h-1), N-gas production (NO, N2O and N2) accounted for only ~50% of VADEC, the rest was ascribed to nitrosation (R-NO). During denitrification (live soil incubation), the nitrite concentrations reached 2-3 mM in the soils with pH 4.9 and 7.2, while the soil with pH 3.4 kept nitrite concentrations at 20-50 µM , except for a short spike reaching 160 μM. Estimated rates of nitrite scavenging by the two competing sinks (NIR and ADEC) showed that NIR was the strongst nitrite sink in soil with pH 3.4 (VNIR>VADEC), while VNIR ≈ VADEC in the soil with pH 5.9. In the soil with pH 7.2, VADEC was insignificant. Thus, the regulation of denitrification (high VNIR relative to VNAR) played a crucial role in determining nitrite kinetics, hence the fate of nitrite in acid soils. High nitrite reductase activity effectively minimized abiotic nitrite decomposition and nitrosation of soil organic matter. The results shed light on regulation of denitrification in acid soils, and its implications for the fate of nitrogen during denitrification events.Nitrite kinetics during anoxia: the role of abiotic reactions versus microbial reductionacceptedVersio

Presence of Actinobacterial and Fungal Communities in Clean and Petroleum Hydrocarbon Contaminated Subsurface Soil

Relatively little is known about the microbial communities adapted to soil environments contaminated with aged complex hydrocarbon mixtures, especially in the subsurface soil layers. In this work we studied the microbial communities in two different soil profiles down to the depth of 7 m which originated from a 30-year-old site contaminated with petroleum hydrocarbons (PHCs) and from a clean site next to the contaminated site. The concentration of oxygen in the contaminated soil profile was strongly reduced in soil layers below 1 m depth but not in the clean soil profile. Total microbial biomass and community composition was analyzed by phospholipid fatty acid (PLFA) measurements. The diversity of fungi and actinobacteria was investigated more in detail by construction of rDNA-based clone libraries. The results revealed that there was a significant and diverse microbial community in subsoils at depth below 2 m, also in conditions where oxygen was limiting. The diversity of actinobacteria was different in the two soil profiles; the contaminated soil profile was dominated by Mycobacterium -related sequences whereas sequences from the clean soil samples were related to other, generally uncultured organisms, some of which may represent two new subclasses of actinobacteria. One dominating fungal sequence which matched with the ascomycotes Acremonium sp. and Paecilomyces sp. was identified both in clean and in contaminated soil profiles. Thus, although the relative amounts of fungi and actinobacteria in these microbial communities were highest in the upper soil layers, many representatives from these groups were found in hydrocarbon contaminated subsoils even under oxygen limited conditions

Denitrification by bradyrhizobia under feast and famine and the role of the bc1 complex in securing electrons for N2O reduction.

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Using amplicon sequencing of rpoB for identification of inoculant rhizobia from peanut nodules

To improve the nitrogen fixation, legume crops are often inoculated with selected effective rhizobia. However, there is large variation in how well the inoculant strains compete with the indigenous microflora in soil. To assess the success of the inoculant, it is necessary to distinguish it from other, closely related strains. Methods used until now have generally been based either on fingerprinting methods or on the use of reporter genes. Nevertheless, these methods have their shortcomings, either because they do not provide sufficiently specific information on the identity of the inoculant strain, or because they use genetically modified organisms that need prior authorization to be applied in the field or other uncontained environments. Another possibility is to target a gene that is naturally present in the bacterial genomes. Here we have developed a method that is based on amplicon sequencing of the bacterial housekeeping gene rpoB, encoding the beta-subunit of the RNA polymerase, which has been proposed as an alternative to the 16S rRNA gene to study the diversity of rhizobial populations in soils. We evaluated the method under laboratory and field conditions. Peanut seeds were inoculated with various Bradyrhizobium strains. After nodule development, DNA was extracted from selected nodules and the nodulating rhizobia were analysed by amplicon sequencing of the rpoB gene. The analyses of the sequence data showed that the method reliably identified bradyrhizobial strains in nodules, at least at the species level, and could be used to assess the competitiveness of the inoculant compared to other bradyrhizobia.Peer reviewe

Rapid Succession of Actively Transcribing Denitrifier Populations in Agricultural Soil During an Anoxic Spell

Denitrification allows sustained respiratory metabolism during periods of anoxia, an advantage in soils with frequent anoxic spells. However, the gains may be more than evened out by the energy cost of producing the denitrification machinery, particularly if the anoxic spell is short. This dilemma could explain the evolution of different regulatory phenotypes observed in model strains, such as sequential expression of the four denitrification genes needed for a complete reduction of nitrate to N2, or a “bet hedging” strategy where all four genes are expressed only in a fraction of the cells. In complex environments such strategies would translate into progressive onset of transcription by the members of the denitrifying community. We exposed soil microcosms to anoxia, sampled for amplicon sequencing of napA/narG, nirK/nirS, and nosZ genes and transcripts after 1, 2 and 4 h, and monitored the kinetics of NO, N2O, and N2. The cDNA libraries revealed a succession of transcribed genes from active denitrifier populations, which probably reflects various regulatory phenotypes in combination with cross-talks via intermediates (NO2−, NO) produced by the “early onset” denitrifying populations. This suggests that the regulatory strategies observed in individual isolates are also displayed in complex communities, and pinpoint the importance for successive sampling when identifying active key player organisms

Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions

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A bet-hedging strategy for denitrifying bacteria curtails their release of N2O

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Regulation of denitrification at the cellular level: a clue to the understanding of N2O emissions from soils

Denitrifying prokaryotes use NOx as terminal electron acceptors in response to oxygen depletion. The process emits a mixture of NO, N2O and N2, depending on the relative activity of the enzymes catalysing the stepwise reduction of NO3− to N2O and finally to N2. Cultured denitrifying prokaryotes show characteristic transient accumulation of NO2−, NO and N2O during transition from oxic to anoxic respiration, when tested under standardized conditions, but this character appears unrelated to phylogeny. Thus, although the denitrifying community of soils may differ in their propensity to emit N2O, it may be difficult to predict such characteristics by analysis of the community composition. A common feature of strains tested in our laboratory is that the relative amounts of N2O produced (N2O/(N2+N2O) product ratio) is correlated with acidity, apparently owing to interference with the assembly of the enzyme N2O reductase. The same phenomenon was demonstrated for soils and microbial communities extracted from soils. Liming could be a way to reduce N2O emissions, but needs verification by field experiments. More sophisticated ways to reduce emissions may emerge in the future as we learn more about the regulation of denitrification at the cellular level

Impaired Reduction of N2O to N2 in Acid Soils Is Due to a Posttranscriptional Interference with the Expression of nosZ

Accumulating empirical evidence over the last 60 years has shown that the reduction of N2O toN2 is impaired by low soil pH, suggesting that liming of acid soils may reduce N2O emissions. This option has not gained much momentum in global change research, however, possibly due to limited understanding of why low pH interferes with N2O reductase. We hypothesized that the reason is that denitrifying organisms in soils are unable to assemble functional N2O reductase (N2OR) at low pH, as shown to be the case for the model strain Paracoccus denitrificans. We tested this by experiments with bacteria extracted from soils by density gradient centrifugation. The soils were sampled from a long-term liming experiment (soil pH 4.0, 6.1, and 8.0). The cells were incubated (stirred batches, He atmosphere) at pH levels ranging from 5.7 to 7.6, while gas kinetics (NO, N2O, and N2) and abundances of relevant denitrification genes (nirS, nirK, and nosZ) and their transcripts were monitored. Cells from the most acidic soil (pH 4.0) were unable to reduce N2O at any pH. These results warrant a closer inspection of denitrification communities of very acidic soils. Cells from the neutral soils were unable to produce functional N2OR at pH values of<6.1, despite significant transcription of the nosZ gene. The N2OR expressed successfully at pH 7.0, however, was functional over the entire pH range tested (5.7 to 7.6). These observations lend strong support to our hypothesis: low soil pH diminishes/prevents reduction of N2O, primarily by precluding a successful assembly of functional N2O reductase.publishedVersio

A common mechanism for efficient N2O reduction in diverse isolates of nodule-forming bradyrhizobia

Bradyrhizobia are abundant soil bacteria, which can formnitrogen-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 N2O, making them sources of this greenhouse gas. Most others could denitrify NO3 − to N2. Timeresolved gas kinetics and transcription analyses during transition to anaerobic respiration revealed a common regulation of nirK, norCB and nosZ (encoding NO2 −, NO and N2O 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 N2O. In-depth analyses suggest that this was due to a competition between electron transport pathways, strongly favouring N2OoverNO3 − reduction. In a natural context, bacteria with this feature would preferentially reduce available N2O, 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 N2O reduction.A common mechanism for efficient N2O reduction in diverse isolates of nodule-forming bradyrhizobiapublishedVersio