Denitrification

Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation

Natural-abundance measurements of nitrate and nitrite (NO_x) isotope ratios (δ¹⁵N and δ¹⁸O) can be a valuable tool to study the biogeochemical fate of NO_x species in the environment. A prerequisite for using NO_x isotopes in this regard is an understanding of the mechanistic details of isotope fractionation (¹⁵ε, ¹⁸ε) associated with the biotic and abiotic NO_x transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NO_x reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO₃^–) and nitrite (NO₂^–) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that ¹⁵ε and ¹⁸ε values obtained for heterotrophic (¹⁵ε-NO₃^–: 17.6 ± 2.8‰, ¹⁸ε-NO₃^–:18.1 ± 2.5‰; ¹⁵ε-NO₂^–: 14.4 ± 3.2‰) vs. mixotrophic (¹⁵ε-NO₃^–: 20.2 ± 1.4‰, ¹⁸ε-NO₃^–: 19.5 ± 1.5‰; ¹⁵ε-NO₂^–: 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NO_x reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics (¹⁵ε-NO₂^–: –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NO_x reduction. The similar isotope effects detected during mixotrophic and heterotrophic NO_x reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NO_x reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.

Influence of long-term intensive use of irrigated meadow-chernozem soil on the biological activity and productivity of the arable layer

The research was carried out on the territory of the Russian Federation in the forest-steppe region of the south Western Siberia (Omsk state), in the long-term (43 years) stationary experiment. Sprinkling was used for irrigation in the experiment. The number of different physiological groups of microorganisms, the cellulolytic activity of the soil, and nitrification capacity were determined under the sowing of an eight-field grain-grass crop rotation (perennial grasses (Bunias orientalis L. + Bromopsis inermis L. + Galega orientalis Lam. 6-8 years old), spring barley Hordeum vulgare Leyss.-variety Sasha). Immobilization processes predominated in the soil under the sowed crops, it contributes to the preservation of soil organic matter (mineralization coefficient SAA/MPA < 1). The highest transformation ratio of soil organic matter, i.e. increased conversion of plant residues into organic matter, was noted with applying nitrogen-phosphorus fertilizers (N60P60) under the barley. The combination of irrigation factors and the use of mineral fertilizers (N30-60P60) were contributed to the growth of the microorganisms' population, the amplification of decomposition of cellulose, and improvement of nitrification capacity in the soil. The perennial irrigation of the meadow-chernozem soil and the application of intensive technology of cultivation of crops in crop rotation stimulated the growth of the microorganisms' population and didn't detriment the ecological state of the soil.

Identification and characterization of a novel hydroxylamine oxidase, DnfA, that catalyzes the oxidation of hydroxylamine to N2

Nitrogen (N₂) gas in the atmosphere is partially replenished by microbial denitrification of ammonia. Recent study has shown that Alcaligenes ammonioxydans oxidizes ammonia to dinitrogen via a process featuring the intermediate hydroxylamine, termed “Dirammox” (direct ammonia oxidation). However, the unique biochemistry of this process remains unknown. Here, we report an enzyme involved in Dirammox that catalyzes the conversion of hydroxylamine to N₂. We tested previously annotated proteins involved in redox reactions, DnfA, DnfB, and DnfC, to determine their ability to catalyze the oxidation of ammonia or hydroxylamine. Our results showed that none of these proteins bound to ammonia or catalyzed its oxidation; however, we did find DnfA bound to hydroxylamine. Further experiments demonstrated that, in the presence of NADH and FAD, DnfA catalyzed the conversion of ¹⁵N-labeled hydroxylamine to ¹⁵N₂. This conversion did not happen under oxygen (O₂)-free conditions. Thus, we concluded that DnfA encodes a hydroxylamine oxidase. We demonstrate that DnfA is not homologous to any known hydroxylamine oxidoreductases and contains a diiron center, which was shown to be involved in catalysis via electron paramagnetic resonance experiments. Furthermore, enzyme kinetics of DnfA were assayed, revealing a K_m of 92.9 ± 3.0 μM for hydroxylamine and a k_cat of 0.028 ± 0.001 s⁻¹. Finally, we show that DnfA was localized in the cytoplasm and periplasm as well as in tubular membrane invaginations in HO-1 cells. To the best of our knowledge, we conclude that DnfA is the first enzyme discovered that catalyzes oxidation of hydroxylamine to N₂.

Effects of macrophytes and environmental factors on sediment denitrification in a subtropical reservoir

Sediment denitrification plays an important role in nitrogen removal in aquatic systems. However, the importance in nitrogen removal in reservoirs, with a focus on seasonal differences of conditions such as macrophyte beds and environmental factors, is less well understood. This study examined sediment denitrification rate (D_n), and their potential controlling factors were determined in both macrophyte beds and deeper waters in the subtropical reservoir. The mean D_n in the reservoir annually was 18.0 ± 6.3 (mean ± S.E.) mmol N m^-2 d^-1, with significant seasonal variation (p < 0.01), i.e. 43.2 ± 12.8, 6.7 ± 6.3, and 4.0 ± 2.2 mmol N m^-2 d^-1 in winter, spring and summer respectively. There were no statistical differences in D_n between shallow waters with macrophyte beds and deeper waters without macrophyte beds, although macrophyte beds had higher denitrification rates in summer. The D_n rates were significantly correlated with temperature, conductivity, dissolved oxygen, pH, nitrate-nitrogen concentration (NO₃^--N) (p < 0.01) and turbidity (p < 0.05). Linear regression models demonstrated environmental variables explained between 36% and 76% of the variation in D_n. The correlation with NO₃^--N concentrations suggests that it may be a limited factor for D_n. Annual nitrogen removal of the reservoir by a combination of sediment and water denitrification was totally estimated to be 370 t N with an annual removal efficiency of approximately 11%. Nitrogen removal was much higher in winter than other seasons, with about 305 t N removed, accounting for 12% of the total nitrogen inputs. Therefore, denitrification appears to play a minor role throughout much of the year, but in winter months when nitrate accumulates, it may play a more major role.

The influences of soil sulfate content on the transformations of nitrate and sulfate during the reductive soil disinfestation (RSD) process

The transformations and products of sulfate (SO₄^2-) and nitrate (NO₃^-), especially the influences of SO₄^2- content on the transformations during RSD process, are unclear. In this study, a series of soil SO₄^2- contents (from 333 to 3000 mg S kg^-1) were prepared before RSD treatment. The results indicated that nearly all the cumulative NO₃^- (>98.6%) was removed and not affected by the soil SO₄^2- content. The ¹⁵N recovery results showed that 0.57-1.24% and 2.94-4.59% of NO₃^- translated into ammonium (NH₄⁺) and organic N, respectively, and high SO₄^2- contents stimulated the processes of NO₃^- dissimilatory reduction and NO₃^- immobilization. The soluble SO₄^2- contents decreased by 397-922 mg S kg^-1, but the contents of total sulfur, sulfide, and sulfate precipitation varied slightly after RSD, indicating that the decreased SO₄^2- was mainly immobilized into organic sulfur in all soils. In addition, a fraction of decreased SO₄^2- was adsorbed to the soil with a relatively high SO₄^2- content. The leaching of SO₄^2- was high (42.9-602 mg S kg^-1) during the RSD process, and the leaching amounts increased with increasing soil SO₄^2- content. In terms of the gases emitted from the transformations of NO₃^- and SO₄^2-, the cumulative emissions of nitrous oxide (N₂O) and six sulfurous gases (hydrogen sulfide, carbonyl sulfide, carbon disulfide, methyl mercaptan, dimethyl sulfide, and dimethyl disulfide) were in the ranges of 17.1-21.2 mg N kg^-1 and 7.78-23.5 μg S kg^-1, respectively, during the whole RSD process. The emissions of sulfurous gases were inhibited by high soil SO₄^2- content, but the N₂O emissions were unaffected. In conclusion, the soil SO₄^2- content influenced the transformations of NO₃^- and SO₄^2- during RSD process, and the SO₄^2- leaching and N₂O emissions might threaten the environment which should be concerned.

Multi-objective optimization-based reactive nitrogen transport modeling for the water-environment-agriculture nexus in a basin-scale coastal aquifer

The quantification of trade-offs between social-economic and environmental effects is of great importance, especially in the semi-arid coastal areas with highly developed agriculture. The study presents an integrated multi-objective simulation-optimization (S-O) framework to evaluate the basin-scale water-environment-agriculture (WEA) nexus. First, the variable-density groundwater model (SEAWAT) is coupled to the reactive transport model (RT3D) for the first attempt to simulate the environmental effects subject to seawater intrusion (SWI) and nitrate pollution (NP). Then, the surrogate assisted multi-objective optimization algorithm is utilized to investigate the trade-offs between the net agricultural benefits and extents of SWI and NP while considering the water supply, food security, and land availability simultaneously. The S-O modeling methodology is applied to the Dagu River Basin (DRB), a typical SWI region with intensive agricultural irrigation in China. It is shown that the three-objective space based on Pareto-optimal front can be achieved by optimizing planting area in the irrigation districts, indicating the optimal evolution of the WEA nexus system. The Pareto-optimal solutions generated by multi-objective S-O model are more realistic and pragmatic, avoiding the decision bias that may often lead to cognitive myopia caused by the low-dimensional objectives. Although the net agricultural benefits in Pareto-optimal solutions are declined to some extent, the environmental objectives (the extents of SWI and NP) are improved compared to those in the pre-optimized scheme. Therefore, the proposed multi-objective S-O framework can be applied to the WEA nexus in the river basin with intensive agriculture development, which is significant to implement the integrated management of water, food, and environment, especially for the semi-arid coastal aquifers.

Extracellular Electron Transfer by Pseudomonas aeruginosa in Biocorrosion: A Review

Microorganisms with extracellular electron transfer (EET) capability have gained significant attention for their different biotechnological applications, like biosensors, bioremediation, and microbial fuel cells. Current research affirmed that microbial EET potentially promotes corrosion of iron structures, termed microbiologically influenced corrosion (MIC). The sulfate-reducing (SRB) and nitrate-reducing (NRB) bacteria are the most investigated among the different MIC-promoting bacteria. Unlike extensively studied SRB corrosion, NRB corrosion has received less attention from researchers. Hence, this review focuses on EET by Pseudomonas aeruginosa, a pervasive bacterium competent for developing biofilms in marine habitats and oil pipelines. A comprehensive discussion on the fundamentals of EET mechanisms in MIC is provided first. After that, the review offers state-of-the-art insights into the latest research on the EET-assisted MIC by Pseudomonas aeruginosa. The role of electron transfer mediators has also been discussed to understand the mechanisms involved in a better way. This review will be beneficial to open up new opportunities for developing strategies for combating biocorrosion.

Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production. IMPORTANCEMiscanthus × giganteus is a promising candidate for bioeconomy cropping systems; however, it remains unclear how the soil microbiome supplies nitrogen to this low-input crop. DNA-based techniques are used to provide community characterization, but may miss important metabolically active taxa. By analyzing both DNA- and actively transcribed RNA-based microbial communities, we found that nitrogen cycling taxa in the soil microbiome may be underestimated using only DNA-based approaches. Accurately understanding the role of microbes and how they cycle nutrients is important for the development of sustainable bioenergy crops, and RNA-based approaches are recommended as a complement to DNA approaches to better understand the microbial, plant, and management interactions.

Variability of Potential Soil Nitrogen Cycling Rates in Stormwater Bioretention Facilities

Low-impact development (LID) is a common management practice used to infiltrate and filter stormwater through vegetated soil systems. The pollutant reduction potential of these systems is often characterized by a single pollutant removal rate; however, the biophysical properties of soils that regulate the removal of pollutants can be highly variable depending on environmental conditions. The goal of this study was to characterize the variability of soil properties and nitrogen (N) cycling rates in bioretention facilities (BRFs). Soil properties and potential N cycling processes were measured in nine curbside bioretention facilities (BRFs) in Portland, OR during summer and winter seasons, and a subset of six sites was sampled seasonally for two consecutive years to further assess temporal variability in soil N cycling. Potential N cycling rates varied markedly across sites, seasons, and years, and higher variability in N cycling rates was observed among sites with high infiltration rates. The observed seasonal and annual changes in soil parameters suggest that nutrient removal processes in BRFs may be highly variable across sites in an urban landscape. This variability has important implications for predicting the impacts of LID on water quality through time, particularly when estimated removal rates are used as a metric to assess compliance with water quality standards that are implemented to protect downstream ecosystems.

Extracellular production of azurin from Pseudomonas aeruginosa in the presence of Triton X-100 or Tween 80

Azurin which is a bacterial secondary metabolite has attracted much attention as potential anticancer agent in recent years. This copper-containing periplasmic redox protein supresses the tumor growth selectively. High-level secretion of proteins into the culture medium offers a significant advantage over periplasmic or cytoplasmic expression. The aim of this study was to investigate the effect of nonionic surfactants on the expression of the Pseudomonas aeruginosa azurin. Different concentrations of Triton X-100 and Tween 80 were used as supplements in growth media and extracellular azurin production was stimulated by both surfactants. According to western blot analysis results, in the presence of Triton X-100, maximum azurin expression level was achieved with 96 h of incubation at 1% concentration, and 48 h at 2% concentration. On the other hand, maximum azurin expression level was achieved in the presence of 1% Tween 80 at 72 h incubation. This study suggested for the first time a high level of azurin secretion from P. aeruginosa in the presence of Triton X-100 or Tween 80, which would be advantageous for the purification procedure.

Evaluation of the Effectiveness of the SED-BIO System in Reducing the Inflow of Selected Physical, Chemical and Biological Pollutants to a Lake

The aim of this study was to assess the efficiency of the innovative SED-BIO system in limiting the inflow of pollutants to Jelonek Lake. The analyses were conducted in the Gniezno Lake District in Greater Poland (the western part of Poland). Physical and chemical analyses were conducted in the years 2016–2019. The results demonstrate that the system is highly effective in the reduction of such nutrients as nitrogen (NO3−—63%; NH4+—14.9%) and phosphorus (PO43−—19.3%). Although the presence of cyanobacteria was confirmed practically throughout the whole monitoring period of the system (2016), the specimens found in most samples were not toxigenic genotypes with a potential to produce microcystins. Microcystins (3 µg·L−1) were detected only once, immediately after the SED-BIO system had been installed in the river and pond, which demonstrates that this natural toxin was eliminated from the additional pool of contaminants that might be transported to Jelonek Lake.

Simultaneous reduction of perchlorate and nitrate using fast-settling anoxic sludge

Fast-settling, anoxic sludge (FAS) was cultivated and utilized in this study to simultaneously reduce elevated levels of perchlorate and nitrate in an anaerobic sequencing batch reactor (AnSBR). Average perchlorate and nitrate removal efficiencies of 96.5 ± 8.44 % and 99.8 ± 0.32 %, respectively, were achieved from an average perchlorate and nitrate loading rate of 159 ± 101 g ClO₄^-/m³·d and 10.8 ± 7.25 g NO₃^--N/m³·d, respectively, throughout long-term operation (>500-d). Batch activity tests revealed a preferential utilization of nitrate over perchlorate, where significant perchlorate reduction inhibition occurred when nitrate was present as a competing electron acceptor under carbon-limiting conditions. Specific perchlorate and nitrate reduction rates were shown to increase as the hydraulic retention time (HRT) of the AnSBR was step-wise decreased and subsequently the perchlorate and nitrate loading rates were step-wise increased. Functional, mRNA-based expression of the nitrite reductase (nirS and nirK), nitrous oxide reductase (nosZ), perchlorate reductase subunit A (pcrA), and the chlorite dismutase (cld) genes illustrated the simultaneous activity of heterotrophic denitrification and perchlorate reduction occurring throughout a complete standard reactor operational cycle, and allowed for expression trends to be documented as the HRT of the AnSBR was reduced from 5-d to 1.25-d. Nitrous oxide (N₂O) production was detected as a result of incomplete denitrification, where the largest N₂O production occurred at the highest nitrate loading rates investigated in this study. Thauera species were heavily enriched at a longer HRT of 5-d, but were out-competed by Dechloromonas species as the HRT of the AnSBR was step-wise reduced to 1.25-d.

The Presence of Denitrifiers In Bacterial Communities of Urban Stormwater Best Management Practices (BMPs)

Stormwater best management practices (BMPs) are engineered structures that attempt to mitigate the impacts of stormwater, which can include nitrogen inputs from the surrounding drainage area. The goal of this study was to assess bacterial community composition in different types of stormwater BMP soils to establish whether a particular BMP type harbors more denitrification potential. Soil sampling took place over the summer of 2015 following precipitation events. Soils were sampled from four bioretention facilities, four dry ponds, four surface sand filters, and one dry swale. 16S rRNA gene analysis of extracted DNA and RNA amplicons indicated high bacterial diversity in the soils of all BMP types sampled. An abundance of denitrifiers was also indicated in the extracted DNA using presence/absence of nirS, nirK, and nosZ denitrification genes. BMP soil bacterial communities were impacted by the surrounding soil physiochemistry. Based on the identification of a metabolically-active community of denitrifiers, this study has indicated that denitrification could potentially occur under appropriate conditions in all types of BMP sampled, including surface sand filters that are often viewed as providing low potential for denitrification. The carbon content of incoming stormwater could be providing bacterial communities with denitrification conditions. The findings of this study are especially relevant for land managers in watersheds with legacy nitrogen from former agricultural land use.

Soil N2O and CH4 emissions from fodder maize production with and without riparian buffer strips of differing vegetation

PURPOSE

Nitrous oxide (N₂O) and methane (CH₄) are some of the most important greenhouse gases in the atmosphere of the 21st century. Vegetated riparian buffers are primarily implemented for their water quality functions in agroecosystems. Their location in agricultural landscapes allows them to intercept and process pollutants from adjacent agricultural land. They recycle organic matter, which increases soil carbon (C), intercept nitrogen (N)-rich runoff from adjacent croplands, and are seasonally anoxic. Thus processes producing environmentally harmful gases including N₂O and CH₄ are promoted. Against this context, the study quantified atmospheric losses between a cropland and vegetated riparian buffers that serve it.

METHODS

Environmental variables and simultaneous N₂O and CH₄ emissions were measured for a 6-month period in a replicated plot-scale facility comprising maize (Zea mays L.). A static chamber was used to measure gas emissions. The cropping was served by three vegetated riparian buffers, namely: (i) grass riparian buffer; (ii) willow riparian buffer and; (iii) woodland riparian buffer, which were compared with a no-buffer control.

RESULTS

The no-buffer control generated the largest cumulative N₂O emissions of 18.9 kg ha^- 1 (95% confidence interval: 0.5-63.6) whilst the maize crop upslope generated the largest cumulative CH₄ emissions (5.1 ± 0.88 kg ha^- 1). Soil N₂O and CH₄-based global warming potential (GWP) were lower in the willow (1223.5 ± 362.0 and 134.7 ± 74.0 kg CO₂-eq. ha^- 1 year^- 1, respectively) and woodland (1771.3 ± 800.5 and 3.4 ± 35.9 kg CO₂-eq. ha^- 1 year^- 1, respectively) riparian buffers.

CONCLUSIONS

Our results suggest that in maize production and where no riparian buffer vegetation is introduced for water quality purposes (no buffer control), atmospheric CH₄ and N₂O concerns may result.

A hillslope-scale aquifer-model to determine past agricultural legacy and future nitrate concentrations in rivers

The long-term fate of agricultural nitrate depends on rapid subsurface transfer, denitrification and storage in aquifers. Quantifying these processes remains an issue due to time varying subsurface contribution, unknown aquifer storage and heterogeneous denitrification potential. Here, we develop a parsimonious modelling approach that uses long-term discharge and river nitrate concentration time-series combined with groundwater age data determined from chlorofluorocarbons in springs and boreholes. To leverage their informational content, we use a Boussinesq-type equivalent hillslope model to capture the dynamics of aquifer flows and evolving surface and subsurface contribution to rivers. Nitrate transport was modelled with a depth-resolved high-order finite-difference method and denitrification by a first-order law. We applied the method to three heavily nitrate loaded catchments of a crystalline temperate region of France (Brittany). We found that mean water transit time ranged 10-32 years and Damköhler ratio (transit time/denitrification time) ranged 0.12-0.55, leading to limited denitrification in the aquifer (10-20%). The long-term trajectory of nitrate concentration in rivers appears determined by flows stratification in the aquifer. The results suggest that autotrophic denitrification is controlled by the accessibility of reduced minerals which occurs at the base of the aquifer where flows decrease. One interpretation is that denitrification might be an interfacial process in zones that are weathered enough to transmit flows and not too weathered to have remaining accessible reduced minerals. Consequently, denitrification would not be controlled by the total aquifer volume and related mean transit time but by the proximity of the active weathered interface with the water table. This should be confirmed by complementary studies to which the developed methodology might be further deployed.

Improved accuracy and reduced uncertainty in greenhouse gas inventories by refining the IPCC emission factor for direct N2 O emissions from nitrogen inputs to managed soils

Most national GHG inventories estimating direct N2 O emissions from managed soils rely on a default Tier 1 emission factor (EF1 ) amounting to 1% of nitrogen inputs. Recent research has, however, demonstrated the potential for refining the EF1 considering variables that are readily available at national scales. Building on existing reviews, we produced a large dataset (n = 848) enriched in dry and low latitude tropical climate observations as compared to former global efforts and disaggregated the EF1 according to most meaningful controlling factors. Using spatially explicit N fertilizer and manure inputs, we also investigated the implications of using the EF1 developed as part of this research and adopted by the 2019 IPCC refinement report. Our results demonstrated that climate is a major driver of emission, with an EF1 three times higher in wet climates (0.014, 95% CI 0.011-0.017) than in dry climates (0.005, 95% CI 0.000-0.011). Likewise, the form of the fertilizer markedly modulated the EF1 in wet climates, where the EF1 for synthetic and mixed forms (0.016, 95% CI 0.013-0.019) was also almost three times larger than the EF1 for organic forms (0.006; 95% CI 0.001-0.011). Other factors such as land cover and soil texture, C content, and pH were also important regulators of the EF1 . The uncertainty associated with the disaggregated EF1 was considerably reduced as compared to the range in the 2006 IPCC guidelines. Compared to estimates from the 2006 IPCC EF1 , emissions based on the 2019 IPCC EF1 range from 15% to 46% lower in countries dominated by dry climates to 7%-37% higher in countries with wet climates and high synthetic N fertilizer consumption. The adoption of the 2019 IPCC EF1 will allow parties to improve the accuracy of emissions' inventories and to better target areas for implementing mitigation strategies.

Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential

The concentration of nitrous oxide (N₂O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N₂O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjacent restored wetlands in the Sacramento-San Joaquin Delta in California, USA. We found that the abundances of nirS and nirK genes were highest at the intensively managed organic-rich cornfield and significantly outnumber any other gene abundances, suggesting very high N₂O production potential. The quantity of nitrogen transforming genes, particularly those responsible for denitrification, nitrification and DNRA, were highest in the agricultural sites, whereas nitrogen fixation and ANAMMOX was strongly associated with the wetland sites. Although the abundance of nosZ genes was also high at the agricultural sites, the ratio of nosZ genes to nir genes was significantly higher in wetland sites indicating that these sites could act as a sink of N₂O. These findings suggest that wetland restoration could be a promising natural climate solution not only for carbon sequestration but also for reduced N₂O emissions.

In-depth analysis of N2O fluxes in tropical forest soils of the Congo Basin combining isotope and functional gene analysis

Primary tropical forests generally exhibit large gaseous nitrogen (N) losses, occurring as nitric oxide (NO), nitrous oxide (N₂O) or elemental nitrogen (N₂). The release of N₂O is of particular concern due to its high global warming potential and destruction of stratospheric ozone. Tropical forest soils are predicted to be among the largest natural sources of N₂O; however, despite being the world's second-largest rainforest, measurements of gaseous N-losses from forest soils of the Congo Basin are scarce. In addition, long-term studies investigating N₂O fluxes from different forest ecosystem types (lowland and montane forests) are scarce. In this study we show that fluxes measured in the Congo Basin were lower than fluxes measured in the Neotropics, and in the tropical forests of Australia and South East Asia. In addition, we show that despite different climatic conditions, average annual N₂O fluxes in the Congo Basin's lowland forests (0.97 ± 0.53 kg N ha^-1 year^-1) were comparable to those in its montane forest (0.88 ± 0.97 kg N ha^-1 year^-1). Measurements of soil pore air N₂O isotope data at multiple depths suggests that a microbial reduction of N₂O to N₂ within the soil may account for the observed low surface N₂O fluxes and low soil pore N₂O concentrations. The potential for microbial reduction is corroborated by a significant abundance and expression of the gene nosZ in soil samples from both study sites. Although isotopic and functional gene analyses indicate an enzymatic potential for complete denitrification, combined gaseous N-losses (N₂O, N₂) are unlikely to account for the missing N-sink in these forests. Other N-losses such as NO, N₂ via Feammox or hydrological particulate organic nitrogen export could play an important role in soils of the Congo Basin and should be the focus of future research.

A predictive model for N2O production in anammox-granular sludge reactors: Combined effects of nitrite/ammonium ratio and organic matter concentration

Once the use of anammox reactors has been increasing on a global scale, it is important to understand the mechanisms of N₂O emissions and how to minimise the emissions by optimising the operating conditions. In this study, the influence of chemical oxygen demand (COD) (from 0 mgO₂ L^-1 to 100 mgO₂ L^-1) and nitrite/ammonium ratio from 0.79 to 2.21 (maintaining ammonium at 100 mgN L^-1 and varying nitrite from 79 mgN L^-1 to 221 mgN L^-1) in the N₂O emissions from anammox-granular sludge reactor was investigated in two steps. Step 1 consisted of batch tests, using central composite design, and Step 2, long-term operation of a 6.5 L continuous up-flow reactor. The results showed that the N₂O emissions were minimized by controlling, in the influent, the NO₂^--N/NH₄⁺-N ratio from 1.1 to 1.3 and maintaining the COD concentration below 100 mgO₂ L^-1. TN removal efficiencies were higher than 70% in all conditions tested".

Identifying hotspots and representative monitoring locations of field scale N2O emissions from agricultural soils: A time stability analysis

Greenhouse gas sampling from agricultural fields is laborious and time-consuming. Soil and topographical heterogeneity cause spatiotemporal variations, making nitrous oxide (N₂O) estimation and management a challenge. Identification of representative monitoring locations, hotspots, and coldspots could facilitate the mitigation of agricultural N₂O emissions. The objective of this study was to identify and characterize representative monitoring locations, hotspots, and coldspots of N₂O emissions in agricultural fields (Baggs farm; BF and Research North farm; RN) in Cambridge, Ontario, Canada, under humid continental climate. Soil in both fields was classified as Orthic Melanic Brunisol, with some areas categorized as Gleyed Brunisolic Gray Brown Luvisol and Orthic Humic Gleysol. In total, 28 sampling points were selected following conditional Latin hypercube design using topographical parameters (digital elevation, slope, topographical wetness index, and Pennock landform classification). Gas samples were collected over a two-year crop rotation with corn (2019) and soybean (2020). Additional sampling was conducted at BF at spring thaw (2020). Time stability analysis using mean relative difference (MRD) and standard deviation of mean relative difference (SDRD) was performed to test the hypothesis that "simultaneous analysis of spatiotemporal variations in N₂O emissions could help to identify and characterize representative monitoring locations, hotspots, coldspots and areas with few hot and cold moments. Most of the hotspots were located at shoulder positions, coldspots, and cold moments at backslope, and representative monitoring points were located at leveled positions or localized depressions. Time stability analysis coupled with multivariate groping analysis supported our hypothesis and helped successfully identify hotspots, coldspots, and representative locations based on landform classification with few exceptions. However, inclusion of additional topographical (curvature, contributing area, aspect) and morphological parameters (texture, thickness of soil horizon, depth to bedrock, and water table) are suggested for consideration in future research to manage variable-rate fertilizer application and mitigate N₂O hotspots at landscape level.

Improvement of the performance of simultaneous nitrification denitrification and phosphorus removal (SNDPR) system by nitrite stress

This study investigated a new way to improve the performance of simultaneous nitrification denitrification and phosphorus removal (SNDPR) system by regularly changing the anaerobic/micro-aerobic/anoxic mode to the anaerobic/anoxic mode with 30 mg/L of nitrite dosing. The results indicated that the removal efficiency of total inorganic nitrogen and PO₄^3--P was improved from 75.44% and 85.14% to 98.89% and 98.17%, respectively. And the good performance of the SNDPR showed a long-time sustainability when the C/N ratio was 5. The results of microbial community illustrated that the abundance of the main nitrite-oxidizing bacteria (NOB), Nitrospira sp., dropped from 5.71% to 0.85% and the abundance of denitrifying polyphosphate-accumulating organisms (DPAOs), Pseudomonas sp. and Acinetobacter sp., increased by 5 times after nitrite stress. The high level of nitric oxide (NO) and free nitrite acid produced by addition of nitrite strongly suppressed the undesired organisms NOB and ordinary heterotrophic denitrifying organisms, and promoted the enrichment of DPAOs. The NO accumulated in the nitrite denitrification process could inhibit NOB and promote AOB. This study revealed that NO plays an important role in regulating the microbial community in the SNDPR system.

Microbial process-oriented understanding of stimulation of soil N2O emission following the input of organic materials

Although crop residue return increases upland soil emissions of nitrous oxide (N₂O), a potent greenhouse gas, the mechanisms responsible for the increase remain unclear. Here, we investigate N₂O emission pathways, gross nitrogen (N)-cycling rates, and associated N-cycling gene abundances in an upland soil following the addition of various organic material under aerobic incubation using a combination of ¹⁵N tracing technique, acetylene (C₂H₂) inhibition, and real-time PCR (qPCR) methods. Increased total N₂O emissions following organic material amendment was attributed to both increased nitrification-derived N₂O emissions, following increased ammonia-oxidizing bacteria (AOB)-amoA abundance, and denitrification-derived N₂O emissions, following increased nirS and decreased nosZ abundance. Increasing plant residue carbon (C)/N ratio decreased total N₂O emissions by decreasing the contribution of denitrification to N₂O emissions, potentially due to higher proportions of denitrified N emitted as N₂O than nitrified N emitted as N₂O. We further propose a novel conceptual framework for organic material input effects on denitrification-derived N₂O emissions based on the decomposable characteristics of the added organic material. For slowly decomposing organic materials (e.g., plant residue) with insufficient available C, NO₃^--N immobilization surpassed denitrification, resulting in gradual decrease in denitrification-derived N₂O emissions with an increase in mineralization of plant residue C losses. In contrast, available C provided by readily available C sources (e.g., glucose) seemed sufficient to support the co-occurrence of NO₃^--N immobilization and denitrification. Overall, for the first time, we offer a microbial process perspective of N₂O emissions following organic material input. The findings could facilitate the improvement of process-orientated models of N₂O emissions and the formulation of appropriate N₂O mitigation strategies for crop residue-amended soils.

QM/MM Simulations of Protein Crystal Reactivity Guided by MSOX Crystallography: A Copper Nitrite Reductase Case Study

The recently developed multiple structures from one crystal (MSOX) serial crystallography method can be used to provide multiple snapshots of the progress of enzymatic reactions taking place within a protein crystal. Such MSOX snapshots can be used as a reference for combined quantum mechanical/molecular mechanical (QM/MM) simulations of enzyme reactivity within the crystal. QM/MM calculations are used to identify details of reference states that cannot be directly observed by X-ray diffraction experiments, such as protonation and oxidation states. These reference states are then used as known fixed endpoints for the modeling of reaction paths. We investigate the mechanism of nitrite reduction in an Achromobacter cycloclastes copper nitrite reductase crystal using MSOX-guided QM/MM calculations, identifying the change in nitrite binding orientation with a change in copper oxidation state, and determining the reaction path to the final NO-bound MSOX structure. The results are compared with QM/MM simulations performed in a solvated environment.

Distribution of Denitrification among Haloarchaea: A Comprehensive Study

Microorganisms from the Halobacteria class, also known as haloarchaea, inhabit a wide range of ecosystems of which the main characteristic is the presence of high salt concentration. These environments together with their microbial communities are not well characterized, but some of the common features that they share are high sun radiation and low availability of oxygen. To overcome these stressful conditions, and more particularly to deal with oxygen limitation, some microorganisms drive alternative respiratory pathways such as denitrification. In this paper, denitrification in haloarchaea has been studied from a phylogenetic point of view. It has been demonstrated that the presence of denitrification enzymes is a quite common characteristic in Halobacteria class, being nitrite reductase and nitric oxide reductase the enzymes with higher co-occurrence, maybe due to their possible role not only in denitrification, but also in detoxification. Moreover, copper-nitrite reductase (NirK) is the only class of respiratory nitrite reductase detected in these microorganisms up to date. The distribution of this alternative respiratory pathway and their enzymes among the families of haloarchaea has also been discussed and related with the environment in which they constitute the major populations. Complete denitrification phenotype is more common in some families like Haloarculaceae and Haloferacaceae, whilst less common in families such as Natrialbaceae and Halorubraceae.

Electrochemical analysis of a microbial electrochemical snorkel in laboratory and constructed wetlands

Microbial electrochemical snorkel (MES) is a short-circuited microbial fuel cell applicable to water treatment that does not produce energy but requires lower cost for its implementation. Few reports have already described its water treatment capabilities but no deeper electrochemical analysis were yet performed. We tested various materials (iron, stainless steel and porous graphite) and configurations of snorkel in order to better understand the rules that will control in a wetland the mixed potential of this self-powered system. We designed a model snorkel that was studied in laboratory and on the field. We confirmed the development of MES by identifying anodic and cathodic parts, by measuring the current between them and by analyzing microbial ecology in laboratory and field experiments. An important application is denitrification of surface water. Here we discuss the influence of nitrate on its electrochemical response and denitrification performances. Introducing nitrate caused the increase of the mixed potential of MES and of current at a potential value relatively more positive than for nitrate-reducing biocathodes described in the literature. The major criteria for promoting application of MES in artificial wetland dedicated to mitigation of non-point source nitrate pollution from agricultural water are considered.

Activity and electron donor preference of two denitrifying bacterial strains identified by Raman gas spectroscopy

Human activities have greatly increased the input of reactive nitrogen species into the environment and disturbed the balance of the global N cycle. This imbalance may be offset by bacterial denitrification, an important process in maintaining the ecological balance of nitrogen. However, our understanding of the activity of mixotrophic denitrifying bacteria is not complete, as most research has focused on heterotrophic denitrification. The aim of this study was to investigate substrate preferences for two mixotrophic denitrifying bacterial strains, Acidovorax delafieldii and Hydrogenophaga taeniospiralis, under heterotrophic, autotrophic or mixotrophic conditions. This complex analysis was achieved by simultaneous identification and quantification of H₂, O₂, CO₂, ¹⁴N₂, ¹⁵N₂ and ¹⁵N₂O in course of the denitrification process with help of cavity-enhanced Raman spectroscopic (CERS) multi-gas analysis. To disentangle electron donor preferences for both bacterial strains, microcosm-based incubation experiments under varying substrate conditions were conducted. We found that Acidovorax delafieldii preferentially performed heterotrophic denitrification in the mixotrophic sub-experiments, while Hydrogenophaga taeniospiralis preferred autotrophic denitrification in the mixotrophic incubation. These observations were supported by stoichiometric calculations. The results demonstrate the prowess of advanced Raman multi-gas analysis to study substrate use and electron donor preferences in denitrification, based on the comprehensive quantification of complex microbial gas exchange processes.

Blooms of diatom and dinoflagellate associated with nutrient imbalance driven by cycling of nitrogen and phosphorus in anaerobic sediments in Johor Strait (Malaysia)

Coastal eutrophication is one of the pivotal factors driving occurrence of harmful algal blooms (HABs), whose underlying mechanism remained unclear. To better understand the nutrient regime triggering HABs and their formation process, the phytoplankton composition and its response to varying nitrogen (N) and phosphorus (P), physio-chemical parameters in water and sediment in Johor Strait in March 2019 were analyzed. Surface and sub-surface HABs were observed with the main causative species of Skeletonema, Chaetoceros and Karlodinium. The ecophysiological responses of Skeletonema to the low ambient N/P ratio such as secreting alkaline phosphatase, regulating cell morphology (volume; surface area/volume ratio) might play an important role in dominating the community. Anaerobic sediment iron-bound P release and simultaneous N removal by denitrification and anammox, shaped the stoichiometry of N and P in water column. The decrease of N/P ratio might shift the phytoplankton community into the dominance of HABs causative diatoms and dinoflagellates.

Realizing the role of N-acyl-homoserine lactone-mediated quorum sensing in nitrification and denitrification: A review

Nitrification and denitrification are crucial processes in the nitrogen cycle, a vital microbially driven biogeochemical cycle. N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) is widespread in bacteria and plays a key role in their physiological status. Recently, there has been an increase in research into how the AHL-mediated QS system is involved in nitrification and denitrification. Consequentially, the AHL-mediated QS system has been considered a promising regulatory approach in nitrogen metabolism processes, with high potential for real-world applications. In this review, the universal presence of QS in nitrifiers and denitrifiers is summarized. Many microorganisms taking part in nitrification and denitrification harbor QS genes, and they may produce AHLs with different chain lengths. The phenotypes and processes affected by QS in real-world applications are also reviewed. In wastewater bioreactors, QS could affect nitrogen metabolism efficiency, granule aggregation, and biofilm formation. Furthermore, methods commonly used to identify the existence and functions of QS, including physiological tests, genetic manipulation and omics analyses are discussed.

Ammonium-based aeration control improves nitrogen removal efficiency and reduces N2O emissions for partial nitritation-anammox reactors

This study deals with the effect of aeration control strategies on the nitrogen removal efficiency and nitrous oxide (N₂O) emissions in a partial nitritation-anammox reactor with granular sludge. More specifically, dissolved oxygen (DO) control, constant airflow and effluent ammonium (NH₄⁺) control strategies were compared through a simulation study. Particular attention was paid to the effect of flocs, which are deliberately or unavoidable present besides granules in this type of reactor. When applying DO control, DO setpoints had to be adjusted to the amount of flocs present in the reactor to maintain high nitrogen removal and reduce N₂O emissions, which is difficult to realize in practice because of variable floc fractions. Constant airflow rate control could maintain a good nitrogen removal efficiency independent of the floc fraction in the reactor, but failed in N₂O mitigation. Controlling aeration based on the effluent ammonium concentration results in both high nitrogen removal and relatively low N₂O emissions, also in the presence of flocs. Fluctuations in floc fractions caused significant upsets in nitrogen removal and N₂O emissions under DO control but had less effect at constant airflow and effluent ammonium control. Still, rapid and sharp drops in flocs led to a peak in N₂O emissions at constant airflow and effluent ammonium control. Overall, effluent ammonium control reached the highest average nitrogen removal and lowest N₂O emissions and consumed the lowest aeration energy under fluctuating floc concentrations.

Nitrogen removal and greenhouse gas fluxes from integrated buffer zones treating agricultural drainage water

Integrated buffer zones (IBZ) are novel mitigation measures designed to decrease the loading of nitrogen (N) transported by subsurface drainage systems from agricultural fields to streams. In IBZ, drainage water flows into a pond with free water surface followed by an inundated, vegetated filterbed. This design provides an environment favorable for denitrification and thus a decrease in nitrate concentration is expected as water flow through the IBZ. However, due to the establishment of anaerobic conditions, there is a risk for increasing emissions of the greenhouse gases nitrous oxide (N₂O) and methane (CH₄). In this year-long study, we evaluated the N removal efficiency along with the risk of N₂O and CH₄ emissions from two pilot-scale IBZs (IBZ1 and 2). The two IBZs had very different yearly removal efficiencies, amounting to 29% and 71% of the total N load at IBZ1 and 2, respectively. This was probably due to differences in infiltration rates to the filterbed, which was 22% and 81% of the incoming water at IBZ1 and 2, respectively. The site (IBZ2) with the highest removal efficiency was a net N₂O sink, while 0.9% of the removed nitrate was emitted as N₂O at IBZ1. Both IBZs were net sources of CH₄ but with different pathways of emission. In IBZ1 CH₄ was mainly lost directly to the atmosphere, while waterborne losses dominated in IBZ2. In conclusion, the IBZs were effective in removing N three years after establishment, and although the IBZs acted as greenhouse gas sources, especially due to CH₄, the emissions were comparable to those of natural wetlands and other drainage transport mitigation measures.

Biogeochemistry of Mediterranean Wetlands: A Review about the Effects of Water-Level Fluctuations on Phosphorus Cycling and Greenhouse Gas Emissions

Although Mediterranean wetlands are characterized by extreme natural water level fluctuations in response to irregular precipitation patterns, global climate change is expected to amplify this pattern by shortening precipitation seasons and increasing the incidence of summer droughts in this area. As a consequence, a part of the lake sediment will be exposed to air-drying in dry years when the water table becomes low. This periodic sediment exposure to dry/wet cycles will likely affect biogeochemical processes. Unexpectedly, to date, few studies are focused on assessing the effects of water level fluctuations on the biogeochemistry of these ecosystems. In this review, we investigate the potential impacts of water level fluctuations on phosphorus dynamics and on greenhouse gases emissions in Mediterranean wetlands. Major drivers of global change, and specially water level fluctuations, will lead to the degradation of water quality in Mediterranean wetlands by increasing the availability of phosphorus concentration in the water column upon rewetting of dry sediment. CO2 fluxes are likely to be enhanced during desiccation, while inundation is likely to decrease cumulative CO2 emissions, as well as N2O emissions, although increasing CH4 emissions. However, there exists a complete gap of knowledge about the net effect of water level fluctuations induced by global change on greenhouse gases emission. Accordingly, further research is needed to assess whether the periodic exposure to dry–wet cycles, considering the extent and frequency of the cycles, will amplify the role of these especial ecosystems as a source of these gases and thereby act as a feedback mechanism for global warming. To conclude, it is pertinent to consider that a better understanding about the effect of water level fluctuations on the biogeochemistry of Mediterranean wetlands will help to predict how other freshwater ecosystems will respond.

Nitrogen Fertilization. A Review of the Risks Associated with the Inefficiency of Its Use and Policy Responses

Nitrogen (N) is a key input to food production. Nearly half of N fertilizer input is not used by crops and is lost into the environment via emission of gases or by polluting water bodies. It is essential to achieve production levels, which enable global food security, without compromising environmental security. The N pollution level expected by 2050 is projected to be 150% higher than in 2010, with the agricultural sector accounting for 60% of this increase. In this paper, we review the status of the pollution from N fertilizers worldwide and make recommendations to address the situation. The analysis reviews the relationship between N fertilizer use, N use efficiency, no-point pollution, the role of farmer management practices, and policy approaches to address diffuse pollution caused by N fertilization. Several studies show a lack of information as one of the main hurdles to achieve changes in habits. The objective of this study is to highlight the gravity of the current global non-point pollution as well as the need for a communication effort to make farmers aware of the relationship between their activity and N pollution and, therefore, the importance of their fertilizer management practices.

Sediment Nutrient Flux Rates in a Shallow, Turbid Lake Are More Dependent on Water Quality Than Lake Depth

The bottom sediments of shallow lakes are an important nutrient sink; however, turbidity may alter the influence of water depth on sediment nutrient uptake by reducing light and associated oxic processes, or altering nutrient availability. This study assessed the relative influence of water quality vs. water depth on sediment nutrient uptake rates in a shallow agricultural lake during spring, when sediment and nutrient loading are highest. Nitrate and soluble reactive phosphorus (SRP) flux rates were measured from sediment cores collected across a depth and spatial gradient, and correlated to water quality. Overlying water depth and distance to shore did not influence rates. Both nitrate and SRP sediment uptake rates increased with greater Secchi depth and higher water temperature, and nitrate and SRP rates increased with lower water total N and total P, respectively. The importance of water temperature on N and P cycling was confirmed in an additional experiment; however, different patterns of nitrate reduction and denitrification suggest that alternative N2 production pathways may be important. These results suggest that water quality and temperature can be key drivers of sediment nutrient flux in a shallow, eutrophic, turbid lake, and water depth manipulation may be less important for maximizing spring runoff nutrient retention than altering water quality entering the lake.

Effects of Organic Fertilizers on the Soil Microorganisms Responsible for N2O Emissions: A Review

The use of organic fertilizers constitutes a sustainable strategy to recycle nutrients, increase soil carbon (C) stocks and mitigate climate change. Yet, this depends largely on balance between soil C sequestration and the emissions of the potent greenhouse gas nitrous oxide (N₂O). Organic fertilizers strongly influence the microbial processes leading to the release of N₂O. The magnitude and pattern of N₂O emissions are different from the emissions observed from inorganic fertilizers and difficult to predict, which hinders developing best management practices specific to organic fertilizers. Currently, we lack a comprehensive evaluation of the effects of OFs on the function and structure of the N cycling microbial communities. Focusing on animal manures, here we provide an overview of the effects of these organic fertilizers on the community structure and function of nitrifying and denitrifying microorganisms in upland soils. Unprocessed manure with high moisture, high available nitrogen (N) and C content can shift the structure of the microbial community, increasing the abundance and activity of nitrifying and denitrifying microorganisms. Processed manure, such as digestate, compost, vermicompost and biochar, can also stimulate nitrifying and denitrifying microorganisms, although the effects on the soil microbial community structure are different, and N₂O emissions are comparatively lower than raw manure. We propose a framework of best management practices to minimize the negative environmental impacts of organic fertilizers and maximize their benefits in improving soil health and sustaining food production systems. Long-term application of composted manure and the buildup of soil C stocks may contribute to N retention as microbial or stabilized organic N in the soil while increasing the abundance of denitrifying microorganisms and thus reduce the emissions of N₂O by favoring the completion of denitrification to produce dinitrogen gas. Future research using multi-omics approaches can be used to establish key biochemical pathways and microbial taxa responsible for N₂O production under organic fertilization.

Effect of inundation on greenhouse gas emissions from temperate coastal wetland soils with different vegetation types in southern Australia

Predicted sea level fluctuations and sea level rise with climate change will lead to inundation of coastal and estuarine soils. Coastal wetlands usually contain large amounts of organic matter, which can be potential sources of greenhouse gas emissions (GHGs; CO₂, CH₄, N₂O) during decomposition, but there are limited studies on the effects of sea level variation on GHGs in coastal wetlands. We measured the effect of brackish water inundation and wetting and drying cycles on GHG emissions from coastal wetland soil cores that supported four different vegetation types: Apium gravedens (AG), Leptospermum lanigerum (LL), Phragmites australis (PA) and Paspalum distichum (PD) from the estuarine floodplain of the Aire River in south-western Victoria, Australia. Intact soil cores were incubated under either dry, flooded, or a 14 day wet-dry cycle treatments for a total of 56 days at a constant temperature of 23 °C. CO₂, CH₄, and N₂O fluxes were investigated in closed chambers and measured with gas chromatography. In the dry treatment, a positive correlation was found between soil organic carbon (SOC) and CO₂ flux, and between SOC and CH₄ flux. Higher SOC is indicative of higher amounts of soil organic matter (SOM) which acts as a source of substrate for microbes to produce CO₂ or CH₄ emissions under aerobic or anaerobic conditions. The NO₂^- and NO₃^- concentrations were positively correlated with N₂O emissions in the wet-dry cycle treatment. NO₂^- and NO₃^- provide a supply of substrate for denitrification. The flooded treatment decreased cumulative CO₂ emissions by 34%, 25% and 14% at the LL, PA, PD sites, respectively, and decreased cumulative N₂O emissions by 42%, 39% and 43% at the AG, LL and PA sites, compared to the dry treatment. The wet-dry cycle treatment and dry treatment decreased cumulative CH₄ emissions for all vegetation types compared to the flooded treatment. The redox potential (Eh) was negatively correlated with CH₄ flux and positively correlated N₂O flux at all sites. This study highlights the significance of sea level fluctuations when estimating GHG flux from coastal and estuarine floodplains which are highly vulnerable to inundation, and the role of SOC and mineral N as important drivers affecting GHG flux.

Hot spots and hot moments of nitrogen removal from hyporheic and riparian zones: A review

The Earth is experiencing excessive nitrogen (N) input to its various ecosystems due to human activities. How to effectively and efficiently remove N from ecosystems has been, is and will be at the center of attention in N research. Hyporheic and riparian zones are widely acknowledged for their buffering capacity to reduce contaminants (especially N) transport downstream. However, these zones are usually misunderstood that they can remove N at all spots and at any moments. Here pathways of N removal from hyporheic and riparian zones are reviewed and summarized with an emphasize on their hot spots and hot moments. N is biogeochemically removed by denitrification, anammox, nitrifier denitrification, denitrifying anaerobic methane oxidation, Feammox and Sulfammox. Hot moments of N removal are mainly triggered by precipitation, fire and snowmelt. Finally, some research needs are outlined and discussed, such as developing approaches for multiscale sampling and monitoring, quantifying the effects of hot spots and hot moments at hyporheic and riparian zones and evaluating the impacts of human activities on hot spots and hot moments, to inspire more research on hot spots and hot moments of N removal. By this review, we hope to bring awareness of the heterogeneity of hyporheic and riparian zones to catchment managers and policy makers when tackling N pollution problems.

Denitrifying bacterial communities in surface-flow constructed wetlands during different seasons: characteristics and relationships with environment factors

Denitrification is an important part of the nitrogen cycle and the key step to removal of nitrogen in surface-flow wetlands. In this study, we explored space–time analysis with high-throughput sequencing to elucidate the relationships between denitrifying bacteria community structures and environmental factors during different seasons. Our results showed that along the flow direction of different processing units, there were dynamic changes in physical and chemical indicators. The bacterial abundance indexes (ACEs) in May, August, and October were 686.8, 686.8, and 996.2, respectively, whereas the Shannon-Weiner indexes were 3.718, 4.303, and 4.432, respectively. Along the flow direction, the denitrifying bacterial abundance initially increased and then decreased subsequently during the same months, although diversity tended to increase. The abundance showed similar changes during the different months. Surface flow wetlands mainly contained the following denitrifying bacteria genus: unclassified Bacteria (37.12%), unclassified Proteobacteria (18.16%), Dechloromonas (16.21%), unranked environmental samples (12.51%), unclassified Betaproteobacteria (9.73%), unclassified Rhodocyclaceae (2.14%), and Rhodanobacter (1.51%). During different seasons, the same unit showed alternating changes, and during the same season, bacterial community structures were influenced by the second genus proportion in different processing units. ACEs were strongly correlated with temperature, dissolved oxygen, and pH. Bacterial diversity was strongly correlated with temperature, electrical conductivity, pH, and oxidation reduction potential. Denitrifying bacteria are greatly affected by environmental factors such as temperature and pH.

Effects of dry-wet cycles on nitrous oxide emissions in freshwater sediments: a synthesis

Background

Sediments frequently exposed to dry-wet cycles are potential biogeochemical hotspots for greenhouse gas (GHG) emissions during dry, wet and transitional phases. While the effects of drying and rewetting on carbon fluxes have been studied extensively in terrestrial and aquatic systems, less is known about the effects of dry-wet cycles on N₂O emissions from aquatic systems. As a notable part of lotic systems are temporary, and small lentic systems can substantially contribute to GHG emissions, dry-wet cycles in these ecosystems can play a major role on N₂O emissions.

Methodology

This study compiles literature focusing on the effects of drying, rewetting, flooding, and water level fluctuations on N₂O emissions and related biogeochemical processes in sediments of lentic and lotic ecosystems.

Results

N₂O pulses were observed following sediment drying and rewetting events. Moreover, exposed sediments during dry phases can be active spots for N₂O emissions. The general mechanisms behind N₂O emissions during dry-wet cycles are comparable to those of soils and are mainly related to physical mechanisms and enhanced microbial processing in lotic and lentic systems. Physical processes driving N₂O emissions are mainly regulated by water fluctuations in the sediment. The period of enhanced microbial activity is driven by increased nutrient availability. Higher processing rates and N₂O fluxes have been mainly observed when nitrification and denitrification are coupled, under conditions largely determined by O₂ availability.

Conclusions

The studies evidence the driving role of dry-wet cycles leading to temporarily high N₂O emissions in sediments from a wide array of aquatic habitats. Peak fluxes appear to be of short duration, however, their relevance for global emission estimates as well as N₂O emissions from dry inland waters has not been quantified. Future research should address the temporal development during drying-rewetting phases in more detail, capturing rapid flux changes at early stages, and further explore the functional impacts of the frequency and intensity of dry-wet cycles.

Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments

A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93^T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93^T was capable of acetylenotrophic and diazotrophic growth, grew at 22-37 °C, pH 6.3-8.5 and in the presence of 10-45 g l^-1 NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93^T represented a member of the genus Syntrophotalea with highest 16S rRNA gene sequence similarities to Syntrophotalea acetylenica DSM 3246^T (96.6 %), Syntrophotalea carbinolica DSM 2380^T (96.5 %), and Syntrophotalea venetiana DSM 2394^T (96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93^T had low genome-wide average nucleotide identity (81-87.5 %) and <70 % digital DNA-DNA hybridization value with other members of the genus Syntrophotalea. The phylogenetic position of SFB93^T within the family Syntrophotaleaceae and as a novel member of the genus Syntrophotalea was confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species, Syntrophotalea acetylenivorans sp. nov., is proposed, with SFB93^T (=DSM 106009^T=JCM 33327^T=ATCC TSD-118^T) as the type strain.

Assessing and modeling biocatalysis in field denitrification beds reveals key influencing factors for future constructions

Environmental contamination with fertilizers is threatening biodiversity in many ecosystems due to nitrate-based eutrophication. One opportunity for a cost-efficient nitrate elimination are denitrification beds in which a microbial community thrives under anoxic conditions with polymeric plant material as a carbon and an electron source. Incoming nitrate is used as electron acceptor and reduced to molecular nitrogen. Projects realizing denitrification beds in field scale are sparse and robust data on their efficiency throughout the year mostly not available. This study analyzed the nitrate elimination efficiency and microbiology of a 216 m³ denitrification bed over the time course of more than three years. Phylogenetic as well as transcriptomic analysis revealed that the reactor contained a biofilm community growing on the surface of the wood chips and a planktonic community. Both differed in composition but their variance was affected only to a minor extend by seasonal temperature changes. Cellulose degradation was mainly conducted by the biofilm population while denitrification was mostly conducted by the planktonic community. Methanogens were detectable only to a very minor extend. Using online data from the nitrate concentration of in- and outflowing water as well as a hydrological model to predict the water inflow, it was possible to establish a process model that sufficiently describes the denitrification process. This model clearly indicates that the denitrification efficiency is mostly impacted by temperature and hydraulic retention time. It also suggests that the simple design of the denitrification bed most likely leads to different flow paths through the reactor depending on the volumetric flow rate. This study allows for the first time a robust estimation of the necessary reactor size for nitrate removal in a moderate continental climate setting. It also suggests how future denitrification beds could be improved for better performance.

Autotrophic denitrification in constructed wetlands: Achievements and challenges

The use of constructed wetlands for wastewater treatment is rapidly increasing worldwide due to their advantages of low operating and maintenance costs. Denitrification in constructed wetlands is dependent on the presence of organic carbon sources, and the shortage of organic carbon is the primary hurdle for nitrate removal. Therefore, the use of inorganic electronic donors has emerged as an alternative. This paper provides a comprehensive review of nitrate removal pathways using various inorganic electron donors and the performance and development of autotrophic denitrification in constructed wetlands. The main environmental parameters and operating conditions for nitrate removal in wetlands are discussed, and the challenges currently faced in the application of enhanced autotrophic denitrification wetlands are emphasized. Overall, this review illustrates the need for a deep understanding of the complex interrelationships among environmental and operational parameters and wetland substrates for improving the wastewater treatment performance of constructed wetlands.

Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution

Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O₂ and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.

Efficiency of mitigation measures targeting nutrient losses from agricultural drainage systems: A review

Diffusive losses of nitrogen and phosphorus from agricultural areas have detrimental effects on freshwater and marine ecosystems. Mitigation measures treating drainage water before it enters streams hold a high potential for reducing nitrogen and phosphorus losses from agricultural areas. To achieve a better understanding of the opportunities and challenges characterising current and new drainage mitigation measures in oceanic and continental climates, we reviewed the nitrate and total phosphorus removal efficiency of: (i) free water surface constructed wetlands, (ii) denitrifying bioreactors, (iii) controlled drainage, (iv) saturated buffer zones and (v) integrated buffer zones. Our data analysis showed that the load of nitrate was substantially reduced by all five drainage mitigation measures, while they mainly acted as sinks of total phosphorus, but occasionally, also as sources. The various factors influencing performance, such as design, runoff characteristics and hydrology, differed in the studies, resulting in large variation in the reported removal efficiencies.

Global nitrogen input on wetland ecosystem: The driving mechanism of soil labile carbon and nitrogen on greenhouse gas emissions

Greenhouse gas emissions from wetlands are significantly promoted by global nitrogen input for changing the rate of soil carbon and nitrogen cycling, and are substantially affected by soil labile carbon and nitrogen conversely. However, the driving mechanism by which soil labile carbon and nitrogen affect greenhouse gas emissions from wetland ecosystems under global nitrogen input is not well understood. Working out the driving factor of nitrogen input on greenhouse gas emissions from wetlands is critical to reducing global warming from nitrogen input. Thus, we synthesized 72 published studies (2144 paired observations) of greenhouse gas fluxes and soil labile compounds of carbon and nitrogen (ammonium, nitrate, dissolved organic carbon, soil microbial biomass nitrogen and carbon), to understand the effects of labile carbon and nitrogen on greenhouse gas emissions under global nitrogen input. Across the data set, nitrogen input significantly promoted carbon dioxide, methane and nitrous oxide emissions from wetlands. In particular, at lower nitrogen rates (<100 kg ha^-1·yr^-1) and with added ammonium compounds, freshwater wetland significantly promoted carbon dioxide and methane emissions. Peatland was the largest nitrous oxide source under these conditions. This meta-analysis also revealed that nitrogen input stimulated dissolved organic carbon, ammonium, nitrate, microbial biomass carbon and microbial biomass nitrogen accumulation in the wetland ecosystem. The variation-partitioning analysis and structural equation model were used to analyze the relationship between the greenhouse gas and labile carbon and nitrogen further. These results revealed that dissolved organic carbon (DOC) is the primary factor driving greenhouse gas emission from wetlands under global nitrogen input, whereas microbial biomass carbon (MBC) more directly affects greenhouse gas emission than other labile carbon and nitrogen.

Long-term effects of forest fires on soil greenhouse gas emissions and extracellular enzyme activities in a hemiboreal forest

Fire is the most important natural disturbance in boreal forests, and it has a major role regulating the carbon (C) budget of these systems. With the expected increase in fire frequency, the greenhouse gas (GHG) budget of boreal forest soils may change. In order to understand the long-term nature of the soil-atmosphere GHG exchange after fire, we established a fire chronosequence representing successional stages at 8, 19, 34, 65, 76 and 179 years following stand-replacing fires in hemiboreal Scots pine forests in Estonia. Changes in extracellular activity, litter decomposition, vegetation biomass, and soil physicochemical properties were assessed in relation to carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) emissions. Soil temperature was highest 8 years after fire, whereas soil moisture varied through the fire chronosequences without a consistent pattern. Litter decomposition and CO₂ efflux were still lower 8 years after fire compared with pre-fire levels (179 years after fire). Both returned to pre-fire levels before vegetation re-established, and CO₂ efflux was only strongly responsive to temperature from 19 years after fire onward. Recovery of CO₂ efflux in the long term was associated with a moderate effect of fire on enzyme activity, the input of above- and below-ground litter carbon, and the re-establishment of vegetation. Soil acted as a CH₄ sink and N₂O source similarly in all successional stages. Compared with soil moisture and time after fire, soil temperature was the most important predictor for both GHGs. The re-establishment of overstorey and vegetation cover (mosses and lichens) might have caused an increase in CH₄ and N₂O effluxes in the studied areas, respectively.

Cross-scale controls on the in-stream dynamics of nitrate and turbidity in semiarid agricultural waterway networks

Stream and riparian zone networks embedded in agricultural landscapes provide a potential intervention point to ameliorate the negative effects of agricultural runoff by reducing transport of nitrate (NO₃^-) and suspended sediments (SS) downstream. However, our ability to support and promote NO₃^- and SS attenuation is limited by our understanding of vegetative and hydrogeomorphic controls in realistic management contexts. In addition, agricultural landscapes are heterogenous on multiple management scales, from farm field to regional water management scales, and the effect of these heterogeneities and how they interact across scales to affect vegetative and hydrogeomorphic controls is poorly explored in many settings. This is especially true in irrigated agricultural settings, where stream and riparian networks are entwined with and sensitive to water management systems. To fill these gaps, we related the vegetative and hydrogeomorphic features of 67 waterway reaches across two water management districts in the California Central Valley to reach-scale NO₃^- and turbidity attenuation and district-scale water quality patterns. We found that in-stream NO₃^- attenuation was rare, but, when it did occur, it was promoted by shallow and wide riparian banks, low flows, and high channel-edge denitrification potential. Nitrate concentrations were consistently higher in upstream reaches compared to water district outlets, suggesting that while exports from the district were low, agricultural runoff may impair within-district water resources. Turbidity attenuation was highly variable and unrelated to vegetative or hydrogeomorphic features, suggesting that onfield controls are crucial to managing suspended sediments. We conclude that waterway networks have the potential to mitigate the effects of agricultural NO₃^- runoff in this setting, but that more effective monitoring and adoption of NO₃^- attenuating features is needed. Using our findings, we make specific management and monitoring recommendations at both reach and water district scales.

Poised potential is not an effective strategy to enhance bio-electrochemical denitrification under cyclic substrate limitations

Bio-electrochemical denitrification (BED) is a promising organic carbon-free nitrate remediation technology. However, the relationship between engineering conditions, biofilm community composition, and resultant functions in BED remains under-explored. This study used deep sequencing and variation partitioning analysis to investigate the compositional shifts in biofilm communities under varied poised potentials in the batch mode, and correlated these shifts to reactor-level functional differences. Interestingly, the results suggest that the proliferation of a key species, Thiobacillus denitrificans, and community diversity (the Shannon index), were almost equally important in explaining the reactor-to-reactor functional variability (e.g. variability in denitrification rates was 51% and 38% attributable to key species and community diversity respectively, with a 30% overlap), but neither was heavily impacted by the poised potential. The findings suggest that while enriching the key species may be critical in improving the functional efficiency of BED, poised potentials may not be an effective strategy to achieve the desired level of enrichment in substrate-limited real-world conditions.