Denitrification

Minimizing byproduct formation in bioelectrochemical denitrification with anammox bacteria

Autotrophic bioelectrochemical denitrification (BED) holds promise for nitrate remediation. However, the accumulation of byproducts such as NO2-, N2O, and NH4+, poses a significant challenge to effluent quality and climate adaptation. This study hypothesized that introducing anaerobic ammonium oxidation bacteria (anammox) to BED could alleviate this issue through synergy: a) anammox can utilize NH4+ and NO2- from BED without producing N2O, as seen in canonical denitrification, and b) BED can recycle NO3- from the anammox anabolic pathway. Results showed that Anammox_BED reduced NO2- accumulation by two-thirds, lowered the relative abundance of N2O by 80 %, and eliminated NO. Metagenomic analysis revealed that the anammox species Ca. Brocadia sapporoensis tripled in abundance in the bulk sludge. Meanwhile, Pseudomonas stutzeri and Bosea robiniae, species capable of reducing nitrate via extracellular electron transfer (EET) and supplying NO2- to anammox, halved in relative abundance, while the abundance of Stenotrophomonas acidaminiphila, a non-EET, ammonia assimilation species, doubled following anammox introduction. Metatranscriptomic analysis found upregulation of denitrification-related functional genes in Anammox_BED biofilm and survival- and motility- related genes in bulk sludge, possibly due to insufficient substrate. Overall, BED-Anammox successfully diverted the rate-limiting EET nitrite reduction towards anammox-driven nitrite utilization thereby mitigating the generation of unwanted intermediates.

Fungal fairy rings: history, ecology, dynamics and engineering functions

Fungal fairy rings (FFR) are fascinating natural phenomena that have intrigued people and scientists for centuries. These patterns, often represented by circular distributions of altered vegetation, are found in grasslands and forest habitats. Fairy rings occur when fungi grow radially in the soil, raising from a central point, progressively degrading organic matter and thus affecting vegetation. The observation of such spatial patterns allows mycologists to conduct an in-depth analysis of the role of fungi in ecosystems. This review presents the current knowledge and scientific advancement of the studies of FFRs. An historical appraisal from the most representative pioneer studies until recent works is presented in different scientific fields, including microbiology, chemistry, botany and ecology. Based on a deep analysis of bibliographic data, we synopsised different aspects of FFRs: i) history of studies, ii) taxonomy, iii) ecology (environmental conditions and biogeography), iv) classification of vegetation patterns, v) spatial dynamics, vi) role as ecosystem engineer (impact on soil chemistry, plants and microbiota). In conclusion, beside still open research areas requiring further investigation, a schematic functional model of fungal fairy rings is proposed, in which on one hand the dynamics of the fungal mycelium is explained by self-DNA accumulation and the build-up of autotoxicity. On the other hand, the effects of fungi on plants are related to the intermingled and differently spatially distributed effects of hydrophobicity, phytotoxicity and phytostimulation.

Quantification of denitrification rate in shallow groundwater using the single-well, push-pull test technique

Denitrification has been identified as a significant nitrate attenuation process in groundwater systems. Hence, accurate quantification of denitrification rates is consequently important for the better understanding and assessment of nitrate contamination of groundwater systems. There are, however, few studies that have investigated quantification of shallow groundwater denitrification rates using different analytical approaches or assuming different kinetic reaction models. In this study, we assessed different analytical approaches (reactant versus product) and kinetic reaction (zero-order and first-order) models analysing observations from a single-well, push-pull tests to quantify denitrification rates in shallow groundwater at two sites in the Manawatū River catchment, Lower North Island of New Zealand. Shallow groundwater denitrification rates analysed using the measurements of denitrification reactant (nitrate reduction) and zero-order kinetic models were quantified at 0.42-1.07 mg N L-1 h-1 and 0.05-0.12 mg N L-1 h-1 at the Palmerston North (PNR) and Woodville (WDV) sites, respectively. However, using first-order kinetic models, the denitrification rates were quantified at 0.03-0.09 h-1 and 0.002-0.012 h-1 at the PNR and WDV sites, respectively. These denitrification rates based on the measurements of denitrification reactant (nitrate reduction) were quantified significantly higher (6 to 60 times) than the rates estimated using the measurements of denitrification product (nitrous oxide production). However, the denitrification rate quantified based on the nitrate reduction may provide representative value of denitrification characteristics of shallow groundwater systems. This is more so when lacking practical methods to quantify all nitrogen species (i.e., total N, organic N, nitrite, nitrate, ammoniacal N, nitrous oxide, nitric oxide, and nitrogen gas) in a push-pull test. While estimates of denitrification rates also differed depending on the kinetic model used, both a zero-order and a first-order model appear to be valid to analyse and estimate denitrification rate from push-pull tests. However, a discrepancy in estimates of denitrification rates using either reactant or product and using zero- or first-order kinetics models may have implications in assessment of nitrate transport and transformation in groundwater systems. This necessitates further research and analysis for appropriate measurements and representation of spatial and temporal variability in denitrification characteristics of the shallow groundwater system.

Global Greenhouse Gas Emissions From Agriculture: Pathways to Sustainable Reductions

Agriculture serves as both a source and a sink of global greenhouse gases (GHGs), with agricultural intensification continuing to contribute to GHG emissions. Climate-smart agriculture, encompassing both nature- and technology-based actions, offers promising solutions to mitigate GHG emissions. We synthesized global data, between 1990 and 2021, from the Food and Agriculture Organization (FAO) of the United Nations to analyze the impacts of agricultural activities on global GHG emissions from agricultural land, using structural equation modeling. We then obtained predictive estimates of agricultural GHG emissions for the future period of 2022-2050 using deep-learning models. The FAO data show that, from 1990 to 2021, global livestock numbers, inorganic nitrogen (N) fertilizer use, crop residue, and irrigation area increased by 27%, 47%, 49%, and 37%, respectively. The increased livestock numbers contributed to the increases in CH4 and N2O emissions, while inorganic N fertilizer, crop residue, and irrigation mainly contributed to the increases in N2O emissions. Emissions of CO2 decreased because of a 29% reduction in net forest loss. As a result of the reduced deforestation emissions, the overall agricultural GHG emissions declined from 11.50 to 10.89 GtCO2eq from 1990 to 2021 despite the increases in livestock numbers, inorganic N fertilizer, crop residue, and irrigation. Looking ahead, our model predicts that if current agricultural trends persist, GHG emissions will rise to 11.82 ± 0.07 GtCO2eq in 2050. However, maintaining agricultural GHG emissions at the 2021 level through 2050 is possible if the rate of reduction in net forest loss is doubled. Furthermore, if the rate is tripled, agricultural GHG emissions can be limited to 9.85 ± 0.07 GtCO2eq in 2050. Our findings suggest that reductions in agricultural GHG emissions, alongside sustainable agricultural intensification and climate-smart agricultural practices, can be achieved through parallel efforts emphasizing accelerated forest conservation.

Biofilm and Extracellular Polymeric Substance (EPS) synergy: Revealing Staphylococcus's role in nitrate bioremediation

Staphylococcus species, traditionally associated with pathogenicity, are gaining attention for their role in environmental bioremediation, particularly nitrate reduction, which is crucial for mitigating eutrophication. In this study, denitrifying, biofilm-forming Staphylococcus strains were isolated from Dal Lake, India. Biofilm formation was quantified using a microtiter plate assay, and extracellular polymeric substances (EPS) were measured by dry weight. Statistical analysis revealed a strong positive correlation between EPS production and nitrate removal efficiency (r = 0.96, p < 0.001), with EPS accounting for 92% of the variance in nitrate reduction (R2 = 0.92). Among the isolates, Staphylococcus epidermidis exhibited the highest nitrate reduction at 87% (SD = 2.3%), followed by S. succinus at 83% (SD = 2.1%), S. equorum at 77% (SD = 2.5%), and Staphylococcus sp. at 70% (SD = 2.8%). The consistency of these findings was confirmed by boxplot analysis, and the regression model's robustness was validated by residual plots showing minimal systematic error. This research work provides the first evidence of the nitrate-reducing capabilities of these Staphylococcus species, underscoring their potential in sustainable bioremediation strategies for aquatic environments. The significant correlation between EPS production and nitrate reduction highlights the critical role of biofilms in enhancing microbial remediation processes. The study not only advances the understanding of Staphylococcus in non-pathogenic roles but also suggests that these strains could be pivotal in bioremediation technologies, potentially influencing future environmental management practices.

Synchronous monitoring agricultural water qualities and greenhouse gas emissions based on low-cost Internet of Things and intelligent algorithms

This study addressed the challenges of cost and portability in synchronous monitoring water quality and greenhouse gas emissions in paddy-dominated regions by developing a novel Internet of Things (IoT)-based monitoring system (WG-IoT-MS). The system, equipped with low-cost sensors and integrated intelligent algorithms, enabled real-time monitoring of dissolved N2O concentrations. Combined with an air-water gas exchange model, the system achieved efficient monitoring and simulation of CO2 and N2O emissions from agricultural water bodies while reducing monitoring costs by approximately 60 %. The proposed method was validated in paddy-dominated regions in Danyang, China. Results indicated the excellence of the dissolved N2O concentration model based on support vector regression, demonstrating accurate predictions within a concentration range of 2.003 to 13.247 μg/L. Notably, the model maintained acceptable predictive accuracy (R2 > 0.70) even when some variables were partially absent (with the number of missing variables < 2 and the missing proportion (MP) ≤ 50 %), making up for the data loss caused by sensor malfunctions. Furthermore, the model performed well (R2 > 0.80) when testing data sourced from paddy fields and lakes. Finally, CO2 and N2O emissions were successfully monitored, with the results validated using a floating chamber method (R2 > 0.70). The method provides crucial technical support for quantitative assessment of water quality and greenhouse gas emissions in paddy-dominated regions, laying a foundation for formulating effective emission reduction strategies.

Ultrasensitive Raman Gas Spectroscopy for Dinitrogen Sensing at the Parts-per-Billion Level

Sensing small changes in the concentration of dinitrogen (N2) is a difficult analytical task. As N2-sensing is crucial for nitrogen cycle research in general and studies of denitrification in particular, researchers went to great lengths to develop techniques like the gas-flow-soil-core method, which achieves a precision of 200 ppb at 20 ppm of N2. Here, we present a Raman gas spectroscopic technique based on high pressure, high laser power, and high-NA signal collection, which achieves a limit of detection (LoD) of 59 ppb N2 and a precision of 27 ppb at 10 ppm of N2. This improves the lowest LoD for N2 reported for Raman gas spectroscopy by 2 orders of magnitude. Furthermore, this constitutes an improvement in precision by 1 order of magnitude compared to the GC-MS-based gas-flow-soil-core method currently established in denitrification research. We show that the presented setup is both stable and tight enough to ensure highly sensitive, precise, and repeatable measurements of N2. As Raman gas spectroscopy is a versatile and comprehensive method, the described technique could be easily expanded to other relevant gases like nitrous oxide or to simultaneous multigas sensing. In summary, our method offers possibilities for N2-sensing and could eventually enable denitrification studies with increased sensitivity and a larger scope.

Forage conservation is a neglected nitrous oxide source

Agricultural activities are the major anthropogenic source of nitrous oxide (N 2 O ), an important greenhouse gas and ozone-depleting substance. However, the role of forage conservation as a potential source ofN 2 O has rarely been studied. We investigatedN 2 O production from the simulated silage of the three major crops-maize, alfalfa, and sorghum-used for silage in the United States, which comprises over 90% of the total silage production. Our findings revealed that a substantialN 2 O could be generated, potentially placing forage conservation as the third largestN 2 O source in the agricultural sector. Notably, the application of chlorate as an additive significantly reducedN 2 O production, but neither acetylene nor intermittent exposure to oxygen showed any impact. Overall, the results highlight that denitrifiers, rather than nitrifiers, are responsible forN 2 O production from silage, which was confirmed by molecular analyses. Our study reveals a previously unexplored source ofN 2 O and provides a crucial mechanistic understanding for effective mitigation strategies.

Nitrogen removal strategy for real swine wastewater by combining partial nitrification-denitrification process with anammox

Anammox process offers reduced operational cost and energy requirement compared to nitrification-denitrification methods due to lower biomass generation and no need for external carbon sources and aeration. High ammonia concetration and low biodegradable anaerobic digester of swaine wastewater provided an advantage for the growth of anammox microorangism. An anoxic/oxic (A/O) SBR and an anammox SBR were implemented parallelly to treat the same swine wastewater with partial nitrification/denitrification and partial nitrification/anammox process, respectively, and to compare their nitrogen removal efficiency. The nitrogen removal rates (NRRs) of the A/O SBR and anammox SBR were 0.054 and 0.26 kg-N/m3/day, respectively. The lower NRR of the A/O SBR could be attributed to insufficient biodegradable organic carbon sources in the denitrification process. The kinetic parameters obtained from the two SBRs were applied to estimate the time required for using the A/O process and partial nitrification/anammox process to treat the same amount of ammonia with the same reaction volume. Results showed that the A/O process required 3.3 times the reaction time of the partial nitrification/anammox process, suggesting that the partial nitrification/anammox process is a more efficient and economic nitrogen removal process for swine wastewater treatment. The next generation sequencing results revealed that Candidatus Brocadia, ranging from 10 to 23%, was the predominant anammox bacteria in the anammox SBR. More than 78.2 % of nitrite in the anammox SBR was removed through the anammox reaction.

Effect of mineral and organic fertilizer on N dynamics upon erosion-induced topsoil dilution

Erosion-induced topsoil dilution strongly affects cropland biogeochemistry and is associated with a negative effect on soil health and crop productivity. While its impact on soil C cycling has been widely recognized, there is little information about its impact on soil N cycling and N fertilizer dynamics. Here, we studied three factors potentially influencing N cycling and N fertilizer dynamics in cropping systems, namely: 1.) soil type, 2.) erosion-induced topsoil dilution and 3.) N fertilizer form, in a full-factorial pot experiment using canola plants. We studied three erosion affected soil types (Luvisol, eroded Luvisol, calcaric Regosol) and performed topsoil dilution in all three soils by admixing 20 % of the respective subsoil into its topsoil. N fertilizer dynamics were investigated using either mineral (calcium ammonium nitrate) or organic (biogas digestate) fertilizer, labeled with 15N. The fertilizer 15N recovery and the distribution of the fertilizer N in different soil fractions was quantified after plant maturity. Fertilizer N dynamics and utilization were influenced by all three factors investigated. 15N recovery in the plant-soil system was higher and fertilizer N utilization was lower in the treatments with diluted topsoil than in the non-diluted controls. Similarly, plants of the organic fertilizer N treatments took up significantly less fertilizer N in comparison to mineral fertilizer treatments. Both topsoil dilution and organic fertilizer application promoted 15N recovery and N accumulation in the soil fractions, with strong differences between soil types. Our study reveals an innovative insight: topsoil dilution due to soil erosion has a negligible impact on N cycling and dynamics in the plant-soil system. The crucial factors influencing these processes are found to be the choice of fertilizer form and the specific soil type. Recognizing these aspects is essential for a precise and comprehensive assessment of the environmental continuum, emphasizing the novelty of our findings.

The resting cyst of dinoflagellate Scrippsiella acuminata host bacterial microbiomes with more diverse trophic strategies under conditions typically observed in marine sediments

Variation in the condition of marine sediments provides selective preservation milieus, which act as a key determinant for the abundance and distribution of dinoflagellate resting cysts in natural sediments. Microbial degradation is an understudied biological factor of potential importance in the processes. However, gaps remain in our knowledge about the fundamental information of the bacterial consortia associated with dinoflagellate resting cysts both in laboratory cultures and in the field. Here we used Scrippsiella acuminata as a representative of cyst-producing dinoflagellates to delineate the diversity and composition of bacterial microbiomes co-existing with the laboratory-cultured resting cysts, and to explore possible impacts of low temperature, darkness, and anoxia (the mock conditions commonly observed in marine sediments) on the associated bacterial consortia. Bacterial microbiome with high diversity were revealed associated with S. acuminata at resting stage. The mock conditions could significantly shift bacterial community structure and exert notably inhibitory effects on growth-promoting bacteria. Resting cysts under conditions typically observed in marine sediments fostered bacterial microbiomes with more diverse trophic strategies, characteristic of prominently enriched anaerobic chemotrophic bacteria generating energy via respiration with several different terminal electron acceptors, which yielded more acidic milieu unfavorable for the preservation of calcareous resting cysts. Our findings suggest that there is complex and dynamic interaction between dinoflagellates resting cysts and the associated bacterial consortia in natural sediments. This intrinsic interaction may influence the maintenance and/or accumulation of dinoflagellate resting cysts with potential of germination and initiation blooms in the field.

Insight into a single-chamber air-cathode microbial fuel cell for nitrate removal and ecological roles

Bioelectrochemical systems are sustainable and potential technology systems in wastewater treatment for nitrogen removal. The present study fabricated an air-cathode denitrifying microbial fuel cell (DNMFC) with a revisable modular design and investigated metabolic processes using nutrients together with the spatiotemporal distribution characteristics of dominated microorganisms. Based on the detection of organics and solvable nitrogen concentrations as well as electron generations in DNMFCs under different conditions, the distribution pattern of nutrients could be quantified. By calculation, it was found that heterotrophic denitrification performed in DNMFCs using 56.6% COD decreased the Coulombic efficiency from 38.0% to 16.5% at a COD/NO3 --N ratio of 7. Furthermore, biological denitrification removed 92.3% of the nitrate, while the residual was reduced via electrochemical denitrification in the cathode. Correspondingly, nitrate as the electron acceptor consumed 16.7% of all the generated electrons, and the residual electrons were accepted by oxygen. Microbial community analysis revealed that bifunctional bacteria of electroactive denitrifying bacteria distributed all over the reactor determined the DNMFC performance; meanwhile, electroactive bacteria were mainly distributed in the anode biofilm, anaerobic denitrifying bacteria adhered to the wall, and facultative anaerobic denitrifying bacteria were distributed in the wall and cathode. Characterizing the contribution of specific microorganisms in DNMFCs comprehensively revealed the significant role of electroactive denitrifying bacteria and their cooperative relationship with other functional bacteria.

Nutrient concentration, loads and retention in a semiarid micro-estuary: The relative contribution of baseflow and flood events

Estuaries are a significant source of nutrients to the marine environment. The magnitude of this source is a function of nutrients load reaching the estuary and removal (attenuation) within estuaries. Most estuarine research is conducted in large estuaries, which do not reflect the processes in small estuaries in urban and semi-arid regions where flood water is a substantial portion of the annual discharge and the estuarine baseflow is often low and dominated by wastewater. To improve the understanding of nutrient attenuation and load into the Mediterranean, we conducted high-resolution nutrient sampling in the eutrophic Alexander micro-estuary as a test case. We sampled once per month during baseflows (years 2014-2019) and hourly during floods (years 2016-2018). The concentrations of inorganic nutrients (phosphorous (P) and nitrogen (N)) were extremely high during baseflows. Dissolved ammonium and particulate P were the only nutrients that were in the estuary (by 55 % and 30 %, respectively). Floods were rare, occurring ~4 % of the time, but contributed 62 % of the annual water discharge of the Alexander micro-estuary (14.7 ± 3.8 106 m3 y-1). The concentration of all dissolved nutrients decreased during floods but was higher than expected (DIN 584 ± 50 μmol L-1, phosphate 21 ± 2 μmol L-1), accounting for 42 % and 55 % of the overall annual DIN (123.5 ± 44.9-ton yr-1) and P (6.7 ± 1.9 ton yr-1) loads to sea, respectively. The N:P ratios were 16 and 34 during baseflow and flood events, respectively. Previously, nutrient loads were calculated by multiplying baseflow-measured concentrations by the total water volume of baseflow and floods. Our calculations, based on high-resolution sampling, revealed lower annual loads of P and N to the sea that were 56 % and 89 % of previous estimates, which is a considerable difference in an oligotrophic system such as the eastern Mediterranean.

Decreasing denitrification rates poses a challenge to further decline of nitrogen concentration in Lake Taihu, China

Nitrogen (N) concentrations in many lakes have decreased substantially in recent years due to external load reduction to mitigate harmful algal blooms. However, little attention has been paid to the linkage between the lakes' nitrogen removal efficiency and improved water quality in lakes, especially the variation of denitrification rate (DNR) under decreasing N concentrations. To understand the efficiency of N removal under improving water quality and its influence on the N control targets in Lake Taihu, a denitrification model based on in situ experimental results was developed and long-term (from 2007 to 2022) water quality and meteorological observations were used to estimate DNR and relate it to the amount of N removal (ANR) from the lake. The concentration of total nitrogen (TN) in Lake Taihu decreased from 3.28 mg L-1 to 1.41 mg L-1 from 2007 to 2022 but the reduction showed spatial heterogeneity. The annual mean DNR decreased from 45.6 μmol m-2 h-1 to 4.2 μmol m-2 h-1, and ANR decreased from 11.85×103 t yr-1 to 1.17×103 t yr-1 during the study years. N budget analysis suggested that the amount of N removed by denitrification accounted for 23.3 % of the external load in 2007, but decreased to only 4.0 % in 2022. Thus, the contribution of N removal by internal N cycling decreased significantly as water quality improved. Notably, the proportion of ANR in winter to total ANR increased from 14 % in 2007 to 23 % in 2022 due to warming. This could potentially lead to N deficiencies in spring and summer, thus limiting the availability of N to phytoplankton. A TN concentration of less than 1.0 mg L-1 in the lake and 1.5 mg L-1 in the inflowing lake zones in spring contribute to local N-limitation in Lake Taihu for cyanobacteria control. Our study revealed a general pattern that N removal efficiency decreases with improved water quality, which is instructive for eutrophic lakes in nitrogen management.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

Fluorine materials scavenge excess carbon dioxide and promote Escherichia coli growth

Fluorinated solvents have been used as oxygen carriers in closed microbial cultures to sustain aerobic conditions. However, the growth-promoting effects of fluorinated solvents remain unclear. Therefore, this study aimed to elucidate the mechanism by which fluorinated solvents promote microbial growth and to explore alternative materials that can be easily isolated after culture. Escherichia coli and HFE-7200, a fluorinated solvent, were used to explore factors other than oxygen released by fluorinated solvents that promote microbial growth. E. coli growth was promoted in gas-permeable cultures, and HFE-7200 alleviated medium acidification. Gas chromatography confirmed that HFE-7200 functioned as a scavenger of carbon dioxide produced by E. coli metabolism. Because fluorinated solvents can dissolve various gases, they could scavenge metabolically produced toxic gases from microbial cultures. Furthermore, using polytetrafluoroethylene, a solid fluorine material, results in enhanced bacterial growth. Such solid materials can be easily isolated and reused for microbial culture, suggesting their potential as valuable technologies in food production and biotechnology.

Comprehensive multi-gas study by means of fiber-enhanced Raman spectroscopy for the investigation of nitrogen cycle processes

The extensive use of synthetic fertilizers has led to a considerable increase in reactive nitrogen input into agricultural and natural systems, resulting in negative effects in multiple ecosystems, the so-called nitrogen cascade. Since the global population relies on fertilization for food production, synthetic fertilizer use needs to be optimized by balancing crop yield and reactive nitrogen losses. Fiber-enhanced Raman spectroscopy (FERS) is introduced as a unique method for the simultaneous quantification of multiple gases to the study processes related to the nitrogen cycle. By monitoring changes in the headspace gas concentrations, processes such as denitrification, nitrification, respiration, and nitrogen fixation, as well as fertilizer addition were studied. The differences in concentration between the ambient and prepared process samples were evident in the Raman spectra, allowing for differentiation of process-specific spectra. Gas mixture concentrations were quantified within a range of low ppm to 100% for the gases N2, O2, CO2, N2O, and NH3. Compositional changes were attributed to processes of the nitrogen cycle. With help of multivariate curve resolution, it was possible to quantify N2O and CO2 simultaneously. The impact of fertilizers on N-cycle processes in soil was simulated and analyzed for identifying active processes. Thus, FERS was proven to be a suitable technique to optimize fertilizer composition and to quantify N2O and NH3 emissions, all with a single device and without further sample preparation.

Soil N2 O emissions from specialty crop systems: A global estimation and meta-analysis

Nitrous oxide (N2 O) exacerbates the greenhouse effect and thus global warming. Agricultural management practices, especially the use of nitrogen (N) fertilizers and irrigation, increase soil N2 O emissions. As a vital sector of global agriculture, specialty crop systems usually require intensive input and management. However, soil N2 O emissions from global specialty crop systems have not been comprehensively evaluated. Here, we synthesized 1137 observations from 114 published studies, conducted a meta-analysis to evaluate the effects of agricultural management and environmental factors on soil N2 O emissions, and estimated global soil N2 O emissions from specialty crop systems. The estimated global N2 O emission from specialty crop soils was 1.5 Tg N2 O-N year-1 , ranging from 0.5 to 4.5 Tg N2 O-N year-1 . Globally, soil N2 O emissions exponentially increased with N fertilizer rates. The effect size of N fertilizer on soil N2 O emissions generally increased with mean annual temperature, mean annual precipitation, and soil organic carbon concentration but decreased with soil pH. Global climate change will further intensify the effect of N fertilizer on soil N2 O emissions. Drip irrigation, fertigation, and reduced tillage can be used as essential strategies to reduce soil N2 O emissions and increase crop yields. Deficit irrigation and non-legume cover crop can reduce soil N2 O emissions but may also lower crop yields. Biochar may have a relatively limited effect on reducing soil N2 O emissions but be effective in increasing crop yields. Our study points toward effective management strategies that have substantial potential for reducing N2 O emissions from global agricultural soils.

Mechanism of denitrification in subsurface-dammed Ryukyu limestone aquifer, southern Okinawa Island, Japan

Denitrification crucially regulates the attenuation of groundwater nitrate and is unlikely to occur in a fast-flowing aquifer such as the Ryukyu limestone aquifer in southern Okinawa Island, Japan. However, evidences of denitrification have been observed in several wells within this region. This study analyzed environmental isotopes (δ15NNO3 and ẟ18ONO3) to derive the rationale for denitrification at this site. Additionally, the presence of two subsurface dams in the study area may influence the processes involved in nitrate attenuation. Herein, we analyzed 150 groundwater samples collected spatially and seasonally to characterize the variations in the groundwater chemistry and stable isotopes during denitrification. The values of δ15NNO3 and δ18ONO3 displayed a progressive trend up to +59.7 ‰ and + 21 ‰, respectively, whereas the concentrations of NO3--N decreased to 0.1 mg L-1. In several wells, the enrichment factors of δ15NNO3 ranged from -6.6 to -2.1, indicating rapid denitrification, and the δ15NNO3 to δ18ONO3 ratios varied from 1.3:1 to 2:1, confirming the occurrence of denitrification. Denitrification intensively proceeds under conditions of depleted dissolved oxygen concentrations (<2 mg L-1), sluggish groundwater flow with longer residence times, high concentrations of dissolved organic carbon (>1.2 mg L-1), and low groundwater levels during the dry season with precipitation rates of <100 mm per month (Jun-Sep). SF6 analysis indicated the exclusive occurrence of denitrification in specific wells with groundwater residence times exceeding 30 years. These wells are located in close proximity to the major NE-SW fault system in the Komesu area, where the hydraulic gradient was below 0.005. Detailed geological and lithological investigations based on borehole data revealed that subsurface dams did not cause denitrification while the major NE-SW fault system uplifted the impermeable basement rock of the Shimajiri Group, creating a lithological gap at an equivalent depth that ultimately formed a sluggish groundwater area, promoting denitrification.

Nitric Oxide in Fungi: Production and Function

Nitric oxide (NO) is synthesized in all kingdoms of life, where it plays a role in the regulation of various physiological and developmental processes. In terms of endogenous NO biology, fungi have been less well researched than mammals, plants, and bacteria. In this review, we summarize and discuss the studies to date on intracellular NO biosynthesis and function in fungi. Two mechanisms for NO biosynthesis, NO synthase (NOS)-mediated arginine oxidation and nitrate- and nitrite-reductase-mediated nitrite reduction, are the most frequently reported. Furthermore, we summarize the multifaceted functions of NO in fungi as well as its role as a signaling molecule in fungal growth regulation, development, abiotic stress, virulence regulation, and metabolism. Finally, we present potential directions for future research on fungal NO biology.

Isotopomeric Peak Assignment for N2O in Cross-Labeling Experiments by Fiber-Enhanced Raman Multigas Spectroscopy

Human intervention in nature, especially fertilization, greatly increased the amount of N2O emission. While nitrogen fertilizer is used to improve nitrogen availability and thus plant growth, one negative side effect is the increased emission of N2O. Successful regulation and optimization strategies require detailed knowledge of the processes producing N2O in soil. Nitrification and denitrification, the main processes responsible for N2O emissions, can be differentiated using isotopic analysis of N2O. The interplay between these processes is complex, and studies to unravel the different contributions require isotopic cross-labeling and analytical techniques that enable tracking of the labeled compounds. Fiber-enhanced Raman spectroscopy (FERS) was exploited for sensitive quantification of N2O isotopomers alongside N2, O2, and CO2 in multigas compositions and in cross-labeling experiments. FERS enabled the selective and sensitive detection of specific molecular vibrations that could be assigned to various isotopomer peaks. The isotopomers 14N15N16O (2177 cm-1) and 15N14N16O (2202 cm-1) could be clearly distinguished, allowing site-specific measurements. Also, isotopomers containing different oxygen isotopes, such as 14N14N17O, 14N14N18O, 15N15N16O, and 15N14N18O could be identified. A cross-labeling showed the capability of FERS to disentangle the contributions of nitrification and denitrification to the total N2O fluxes while quantifying the total sample headspace composition. Overall, the presented results indicate the potential of FERS for isotopic studies of N2O, which could provide a deeper understanding of the different pathways of the nitrogen cycle.

Performance analysis of microbial fuel cell - membrane bioreactor with reduced graphene oxide enhanced polypyrrole conductive ceramic membrane: Wastewater treatment, membrane fouling and microbial community under high salinity

The application of membrane bioreactor (MBR) in high salinity wastewater treatment was mainly hindered by membrane fouling. Microbial fuel cell (MFC)-MBR coupling system was established to alleviate membrane fouling and save energy. Reduced graphene oxide/polypyrrole ceramic membrane (rGO/PPy CM) with high conductivity and stability was innovatively placed in MFC-MBRs as both cathode and filter, with PPy CM, rGO/PPy CM and CM placed in other reactors. MFC-MBR (rGO/PPy) and MFC-MBR (PPy) achieved higher pollutant removal efficiencies (90.73 % and 90.45 % for TOC, 87.22 % and 86.56 % for NH4+-N, respectively) and superior anti-fouling performance (1.86 and 1.93 kPa/d for average membrane fouling rates) than both conventional MBRs (CMBRs). The stable voltage generation was around 287 and 242 mV, respectively. Through high throughput sequencing, electric field showed a positive correlation with the abundance and activity of most dominant phylum (Bacteroidetes, Chloroflexi, Actinobacteria, and Firmicutes) and functional genes (amoA, hao, narG, napA, nirK, norB, and nosZ), thereby improving pollutant removal efficiency. The higher conductivity of rGO/PPy CM resulted in enhanced electric field intensity, leading to superior performance of anti-fouling and pollutant removal. This study inventively explored the effects of conductive membrane property on electricity generation performance, microbial community, pollutant removal and membrane fouling, providing theoretical support for the selection of electrode materials in MFC-MBR.

Modeling Path Importance for Effective Alzheimer's Disease Drug Repurposing

Recently, drug repurposing has emerged as an effective and resource-efficient paradigm for AD drug discovery. Among various methods for drug repurposing, network-based methods have shown promising results as they are capable of leveraging complex networks that integrate multiple interaction types, such as protein-protein interactions, to more effectively identify candidate drugs. However, existing approaches typically assume paths of the same length in the network have equal importance in identifying the therapeutic effect of drugs. Other domains have found that same length paths do not necessarily have the same importance. Thus, relying on this assumption may be deleterious to drug repurposing attempts. In this work, we propose MPI (Modeling Path Importance), a novel network-based method for AD drug repurposing. MPI is unique in that it prioritizes important paths via learned node embeddings, which can effectively capture a network's rich structural information. Thus, leveraging learned embeddings allows MPI to effectively differentiate the importance among paths. We evaluate MPI against a commonly used baseline method that identifies anti-AD drug candidates primarily based on the shortest paths between drugs and AD in the network. We observe that among the top-50 ranked drugs, MPI prioritizes 20.0% more drugs with anti-AD evidence compared to the baseline. Finally, Cox proportional-hazard models produced from insurance claims data aid us in identifying the use of etodolac, nicotine, and BBB-crossing ACE-INHs as having a reduced risk of AD, suggesting such drugs may be viable candidates for repurposing and should be explored further in future studies.

Do NO, N2O, N2 and CO2 fluxes differ in soils sourced from cropland and varying riparian buffer vegetation? An incubation study

Riparian buffers are expedient interventions for water quality functions in agricultural landscapes. However, the choice of vegetation and management affects soil microbial communities, which in turn affect nutrient cycling and the production and emission of gases such as nitric oxide (NO), nitrous oxide (N2O), nitrogen gas (N2) and carbon dioxide (CO2). To investigate the potential fluxes of the above-mentioned gases, soil samples were collected from a cropland and downslope grass, willow and woodland riparian buffers from a replicated plot scale experimental facility. The soils were re-packed into cores and to investigate their potential to produce the aforementioned gases via potential denitrification, a potassium nitrate (KNO3 -) and glucose (labile carbon)-containing amendment, was added prior to incubation in a specialized laboratory DENItrification System (DENIS). The resulting NO, N2O, N2 and CO2 emissions were measured simultaneously, with the most NO (2.9 ± 0.31 mg NO m-2) and N2O (1413.4 ± 448.3 mg N2O m-2) generated by the grass riparian buffer and the most N2 (698.1 ± 270.3 mg N2 m-2) and CO2 (27,558.3 ± 128.9 mg CO2 m-2) produced by the willow riparian buffer. Thus, the results show that grass riparian buffer soils have a greater NO3 - removal capacity, evidenced by their large potential denitrification rates, while the willow riparian buffers may be an effective riparian buffer as its soils potentially promote complete denitrification to N2, especially in areas with similar conditions to the current study.

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.

Bacterial denitrification drives elevated N2O emissions in arid southern California drylands

Soils are the largest source of atmospheric nitrous oxide (N2O), a powerful greenhouse gas. Dry soils rarely harbor anoxic conditions to favor denitrification, the predominant N2O-producing process, yet, among the largest N2O emissions have been measured after wetting summer-dry desert soils, raising the question: Can denitrifiers endure extreme drought and produce N2O immediately after rainfall? Using isotopic and molecular approaches in a California desert, we found that denitrifiers produced N2O within 15 minutes of wetting dry soils (site preference = 12.8 ± 3.92 per mil, δ15Nbulk = 18.6 ± 11.1 per mil). Consistent with this finding, we detected nitrate-reducing transcripts in dry soils and found that inhibiting microbial activity decreased N2O emissions by 59%. Our results suggest that despite extreme environmental conditions-months without precipitation, soil temperatures of ≥40°C, and gravimetric soil water content of <1%-bacterial denitrifiers can account for most of the N2O emitted when dry soils are wetted.

Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses

Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.

Abundance of Oligoflexales bacteria is associated with algal symbiont density, independent of thermal stress in Aiptasia anemones

Many multicellular organisms, such as humans, plants, and invertebrates, depend on symbioses with microbes for metabolic cooperation and exchange. Reef-building corals, an ecologically important order of invertebrates, are particularly vulnerable to environmental stress in part because of their nutritive symbiosis with dinoflagellate algae, and yet also benefit from these and other microbial associations. While coral microbiomes remain difficult to study because of their complexity, the anemone Aiptasia is emerging as a simplified model. Research has demonstrated co-occurrences between microbiome composition and the abundance and type of algal symbionts in cnidarians. However, whether these patterns are the result of general stress-induced shifts or depletions of algal-associated bacteria remains unclear. Our study aimed to distinguish the effect of changes in symbiont density and thermal stress on the microbiome of symbiotic Aiptasia strain CC7 by comparing them with aposymbiotic anemones, depleted of their native symbiont, Symbiodinium linucheae. Our analysis indicated that overall thermal stress had the greatest impact on disrupting the microbiome. We found that three bacterial classes made up most of the relative abundance (60%-85%) in all samples, but the rare microbiome fluctuated between symbiotic states and following thermal stress. We also observed that S. linucheae density correlated with abundance of Oligoflexales, suggesting these bacteria may be primary symbionts of the dinoflagellate algae. The findings of this study help expand knowledge on prospective multipartite symbioses in the cnidarian holobiont and how they respond to environmental disturbance.

CO2, CH4, and N2O emissions from dredged material exposed to drying and zeolite addition under field and laboratory conditions

Dredging, the removal of sediment from water courses, is generally conducted to maintain their navigability and to improve water quality. Recent studies indicate that dredging can significantly reduce aquatic greenhouse gas (GHG) emissions. These studies, however, do not consider the potential emission from the dredged material (sludge) in the depot. In addition, it is unknown if and how GHG emissions from sludge depots can be reduced. Here we present spatiotemporal variations of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes, as well as environmental variables from a sludge depot located in the Netherlands. Measurements were conducted monthly from the time the depot was filled until the sludge was dry and the depot was abolished. We also experimentally assessed the GHG mitigation potential of 1) keeping the sludge permanently inundated, and 2) the addition of different amounts of zeolite to increase sludge nitrogen binding capacity to reduce N2O emissions. In the depot and in the laboratory, a decrease in moisture content coincided with increased CO2 and N2O emissions while CH4 emissions decreased. We observed that permanent inundation reduced emissions (∼4 times less CO2-eq than in drying sludge). Adding zeolite lowered N2O fluxes from permanently inundated sludge but did not reduce total GHG emissions. During the depot's operational period, average CO2, CH4, and N2O fluxes were 5078, 27, and 5 mg m-2 d-1, respectively. GHG emissions from drying sludge occurred mainly in the form of CO2 (73% of the total CO2-eq emissions), with average GHG emission rates comparable to those reported for ditches and ponds. We estimate that approximately 14 tons of CO2-eq were emitted from the 0.011 km2 depot, which contained ∼20,000 m3 of sludge, during its entire operational period, and we argue that more studies are needed, considering different sludge origins, to expand our understanding of sludge depots.

Novel slow-release carbon source improves anodic denitrification and electricity generation efficiency in microbial fuel cells

MFC anodic denitrification is more suitable for the coexistence of organic matter and nitrate in actual sewage, but the traditional carbon source has some problems such as high cost and difficulty of dosage control in MFC. Herein, corncob and polycaprolactone (PCL) were mechanically pulverized and mixed in the system of polyvinyl alcohol and sodium alginate, and cross-linked to prepare slow-release carbon source fillers (CPSP), which were added to the MFC anolyte to realize the coupling of solid-phase denitrification and anodic denitrification. Results showed the start-up period of MFC experimental group (MFC-C) with CPSP was slightly longer than the control group (MFC-0), but MFC-C's maximum output voltage (648.4 mV) and power density (2738 mW/m3) could be increased by 5% and 15% higher than that of MFC-0 (P < 0.05). The degradation process of MFC substrate in unit cycle was mainly divided into nitrogen removal stage (0-8 h) and electricity generation stage (8-48 h). The NO3--N and COD degradation and power generation kinetic processes of MFC conformed to the Han-Levenspiel model. Kinetics experiments showed CPSP can improve the affinity and tolerance of MFC to NO3--N, also it can alleviate the pressure of electron competition in anolyte and improve coulombic efficiency. In addition, microbial communities were significantly changed under the effect of CPSP (P < 0.001). Meanwhile, CPSP can promote the synthesis of denitrification functional genes. This study provides a new strategy to improve the performance of MFC by the addition of novel denitrification carbon source.

Modeling Path Importance for Effective Alzheimer's Disease Drug Repurposing

Recently, drug repurposing has emerged as an effective and resource-efficient paradigm for AD drug discovery. Among various methods for drug repurposing, network-based methods have shown promising results as they are capable of leveraging complex networks that integrate multiple interaction types, such as protein-protein interactions, to more effectively identify candidate drugs. However, existing approaches typically assume paths of the same length in the network have equal importance in identifying the therapeutic effect of drugs. Other domains have found that same length paths do not necessarily have the same importance. Thus, relying on this assumption may be deleterious to drug repurposing attempts. In this work, we propose MPI (Modeling Path Importance), a novel network-based method for AD drug repurposing. MPI is unique in that it prioritizes important paths via learned node embeddings, which can effectively capture a network's rich structural information. Thus, leveraging learned embeddings allows MPI to effectively differentiate the importance among paths. We evaluate MPI against a commonly used baseline method that identifies anti-AD drug candidates primarily based on the shortest paths between drugs and AD in the network. We observe that among the top-50 ranked drugs, MPI prioritizes 20.0% more drugs with anti-AD evidence compared to the baseline. Finally, Cox proportional-hazard models produced from insurance claims data aid us in identifying the use of etodolac, nicotine, and BBB-crossing ACE-INHs as having a reduced risk of AD, suggesting such drugs may be viable candidates for repurposing and should be explored further in future studies.

Treatment by enhanced denitrification of forecasted nitrate concentrations under different climate change scenarios

Climate change has a decisive influence on future water resources and, consequently, on future nitrate (NO3-) concentrations. Due to decreasing water resources, in addition to decreasing and finite NO3- degradation capacities of the aquifers, higher NO3- concentrations are expected in the future. Likewise, NO3- pollution is expected to become more frequent. However, enhanced denitrification by addition of organic carbon (C) as an electron donor is a promising treatment method. This study describes the first model using NO3- projections based on climate projections, combined with the treatment method of enhanced denitrification. The exemplary study area is the Lodshof water catchment which is located in the Lower Rhine Embayment. The model illustrates the considerable potential of enhanced denitrification as an effective treatment. The expected increase in NO3- concentrations by the end of the 21st century, resulting from climate chance and a decreasing water resource, can be reduced by 38-58% in this model. In all projections, the limit value of 50 mg/L can be complied by this treatment. A projection with 20% lower NO3- input and the described treatment highlights the effectivity of combining measures to be able to manage the NO3- problem. Furthermore, this publication critically discusses the transfer of denitrification rates from laboratory experiments to the field scale and finally into models like this.

Study of the key biotic and abiotic parameters influencing ammonium removal from wastewaters by Fe3+-mediated anaerobic ammonium oxidation (Feammox)

The release of ammonia (as NH4+) into water bodies causes serious environmental problems. Therefore, the removal of ammonia from wastewater effluents has become a worldwide concern. New autotrophic biological alternatives for ammonia removal could reduce the limitations of conventional organic carbon-dependent nitrification-denitrification methods. Here, the potential of anaerobic ammonium oxidation coupled to Fe3+ reduction (a process known as Feammox) is studied in wastewater treatment plants of the yeast and beer production industry, not related to ammonium or iron treatment. This process is presented as a viable option to improve the efficiency of ammonia removal from wastewater. The results of this study show that enrichments under Feammox conditions achieved removals of 28.19-32.25% of the total NH4+. The highest rates of ammonium removal and Fe3+ reduction were achieved using FeCl3 as iron source and pH = 7.0. Different environmental conditions for the enrichments were studied and it was found that the use of sodium acetate as a carbon source and an incubation temperature of 35 °C presented higher rates of iron reduction and higher increase in nitrate concentration, related to ammonium oxidative processes. Likewise, the presence of relevant species of the iron and nitrogen cycles as Ferrovum myxofaciens, Geobacter spp, Shewanella spp, Albidiferax ferrireducens and Anammox was verified, supporting the findings of this study. These results provide information that may be relevant to the potential applicability of Feammox to treat wastewater with high ammonia load and could help develop cost-effective and environmentally friendly methods for ammonium removal in wastewater treatment plants.

Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater-A Review

Nitrate (NO3-) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3- have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas (N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3--removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3- in several field studies. NO3- removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3- to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3- pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3- from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3- in WBR, and perspectives to enhance WBR performance in the future.

Extreme low-flow conditions in a dual-chamber denitrification bioreactor contribute to pollution swapping with low landscape-scale impact

Denitrification bioreactors are an effective edge-of-field conservation practice for nitrate (NO₃) reduction from subsurface drainage. However, these systems may produce other pollutants and greenhouse gases during NO₃ removal. Here a dual-chamber woodchip bioreactor system experiencing extreme low-flow conditions was monitored for its spatiotemporal NO₃ and total organic carbon dynamics in the drainage water. Near complete removal of NO₃ was observed in both bioreactor chambers in the first two years of monitoring (2019-2020) and in the third year of monitoring in chamber A, with significant (p < 0.01) reduction of the NO₃-N each year in both chambers with 8.6-11.4 mg NO₃-N L^-1 removed on average. Based on the NO₃ removal observed, spatial monitoring of sulfate (SO₄), dissolved methane (CH₄), and dissolved nitrous oxide (N₂O) gases was added in the third year of monitoring (2021). In 2021, chambers A and B had median hydraulic residence times (HRTs) of 64 h and 39 h, respectively, due to varying elevations of the chambers, with drought conditions making the differences more pronounced. In 2021, significant production of dissolved CH₄ was observed at rates of 0.54 g CH₄-C m^-3 d^-1 and 0.07 g CH₄-C m^-3 d^-1 in chambers A and B, respectively. In chamber A, significant removal (p < 0.01) of SO₄ (0.23 g SO₄ m^-3 d^-1) and dissolved N₂O (0.21 mg N₂O-N m^-2 d^-1) were observed, whereas chamber B produced N₂O (0.36 mg N₂O-N m^-2 d^-1). Considering the carbon dioxide equivalents (CO₂e) on an annual basis, chamber A had loads (~12,000 kg CO₂e ha^-1 y^-1) greater than comparable poorly drained agricultural soils; however, the landscape-scale impact was small (<1 % change in CO₂e) when expressed over the drainage area treated by the bioreactor. Under low-flow conditions, pollution swapping in woodchip bioreactors can be reduced at HRTs <50 h and NO₃ concentrations >2 mg N L^-1.

Anoxic granular activated sludge process for simultaneous removal of hazardous perchlorate and nitrate

An airtight, anoxic bubble-column sequencing batch reactor (SBR) was developed for the rapid cultivation of perchlorate (ClO₄^-) and nitrate (NO₃^-) reducing granular sludge (GS) in this study. Feast/famine conditions and shear force selection pressures in tandem with a short settling time (2-min) as a hydraulic section pressure resulted in the accelerated formation of anoxic granular activated sludge (AxGS). ClO₄^- and NO₃^- were efficiently (>99.9%) reduced over long-term (>500-d) steady-state operation. Specific NO₃^- reduction, ClO₄^- reduction, chloride production, and non-purgeable dissolved organic carbon (DOC) oxidation rates of 5.77 ± 0.54 mg NO₃^--N/g VSS·h, 8.13 ± 0^.74 mg ClO₄^-/g VSS·h, 2.40 ± 0.₄0 mg Cl^-/g VSS·h, and 16.0 ± 0.06 mg DOC/g VSS·h were recorded within the reactor under steady-state conditions, respectively. The AxGS biomass cultivated in this study exhibited faster specific ClO₄^- reduction, NO₃^- reduction, and DOC oxidation rates than flocculated biomass cultivated under similar conditions and AxGS biomass operated in an up-flow anaerobic sludge blank (UASB) bioreactor receiving the same influent loading. EPS peptide identification revealed a suite of extracellular catabolic enzymes. Dechloromonas species were present in high abundance throughout the entirety of this study. This is one of the initial studies on anoxic granulation to simultaneously treat hazardous chemicals and adds to the science of the granular activated sludge process.

Size and temperature drive nutrient retention potential across water bodies in China

Lentic water bodies, including lakes, reservoirs, and wetlands, retain excess nutrients in runoff from agricultural and urban activities, and protect downstream water bodies from eutrophication. To develop effective nutrient mitigation strategies, it is important to understand the controls on nutrient retention in lentic systems and what drives variability between different systems and geographical regions. Efforts to synthesize water body nutrient retention at the global scale are biased toward studies from North America and Europe. Numerous studies published in Chinese Language journals exist in the extensive China National Knowledge Infrastructure (CNKI), but are missing from global synthesis due to their absence in English language journal databases. We address this gap by synthesizing data from 417 waterbodies in China to assess hydrologic and biogeochemical drivers of nutrient retention. In this study, we found median retention of 46 and 51% for nitrogen and phosphorus, respectively, across all water bodies in our national synthesis, and on average, wetlands retain more nutrients than lakes or reservoirs. The analysis of this dataset highlights the influence of water body size on first-order nutrient removal rate constants, as well as how regional temperature variations affect nutrient retention in water bodies. The dataset was used to calibrate the HydroBio-k model, which explicitly considers the effect of residence times and temperature on nutrient retention. Application of the HydroBio-k model across China reveals patterns of nutrient removal potential, where regions with a higher density of small water bodies retain more nutrients than others, such that regions like the Yangtze River Basin with a greater proportion of smaller water bodies have greater retention rates. Our results emphasize the importance of lentic systems and their function in nutrient removal and water quality improvement, as well as the drivers and variability of these functions at the landscape scale.

Extended pilot test of a cross-injection in situ denitrification system for pre-emptive treatment of municipal well water

Elevated groundwater nitrate concentrations have been linked to deleterious health and environmental effects. A significant source of the nitrate is nitrogen fertilizers applied to agricultural landscapes. Beneficial Management Practices (BMPs), including the optimization of fertilizer use and selective crop rotations, have proven to be effective in some cases. The city of Woodstock in southern Ontario relies on public wells for all of its municipal supply. Several of the wells have experienced chronic increases in nitrate concentrations exceeding the maximum allowable limit of 10 mg/L N-NO₃^-. While BMPs are established, an interim reduction plan based on enhanced in situ denitrification (Cross Injection System, CIS) in a 15 m thick zone of high nitrate mass flux within the aquifer zone was evaluated. Based in the results of preliminary acetate injection experiments, a C:N ratio of 2.35, (approximately 260 mg acetate/L), was selected to optimize the denitrification reaction. Injections were performed for six hours a day every day for a period of approximately two months. Dissolved oxygen (DO) and nitrate concentrations recorded over time indicated that reduction of both commenced within a few days of the beginning of the acetate injections and reduced levels were maintained for the remainder of the two-month injection period. Denitrification occurred throughout the profile although nitrate reduction was the highest in the lower groundwater velocity zones. An overall reduction of nitrate of 50% was achieved through the treated section of the aquifer. It is estimated that an upscaled treatment system utilizing a treatment width of only 70 m would be sufficient to reduce the nitrate concentrations to below the drinking water limit demonstrating the potential for the CIS method to functions as an interim groundwater nitrate reduction strategy.

Development of overlying water aeration system powered by sediment-microbial-fuel-cell for nutrient suppression

Sediment microbial fuel cells (SMFCs) represent a burgeoning technology that allows the remediation of sediments, such as nutrient suppression, while concurrently generating electricity. However, there is a limitation in that the nutrient suppression effect is restricted to a narrow range near the electrode. To address this issue, we developed an SMFC-aeration system, which intermittently aerates the overlying water with the power of SMFCs, thereby enhancing the nutrient suppression effect of SMFCs. The SMFC-aeration system achieved stable charge/discharge cycles through a capacitor-based circuit and aerated the overlying water. The dissolved NH₄⁺ and NO₂^- concentrations in the overlying water decreased. Suppression in the dissolved NH₄⁺ concentration near the anodes was also noticed compared to a consortium that employed only SMFCs. These findings were brought about by the synergistic effect of the SMFC-aeration system, which enabled the remediation of sediments and overlying water. To our knowledge, this is the first report on the intermittent operation of pumps by SMFCs, the increase of DO, and nutrient suppression. The SMFC-aeration system holds great potential as an environmental remediation method in closed-water areas in the future.

Redirecting carbon to recover VFA to facilitate biological short-cut nitrogen removal in wastewater treatment: A critical review

Wastewater treatment plants (WWTPs) are facing a great challenge to transition from energy-intensive to carbon-neutral and energy-efficient systems. Biological nutrient removal (BNR) can be severely impacted by carbon limitation, particularly for wastewater with a low carbon-to-nitrogen (C/N) ratio, which can significantly increase the operational costs. Waste activated sludge (WAS) is a valuable byproduct of WWTPs, as it contains high levels of organic matter that can be utilized to improve BNR management by recovering and reusing the fermentative volatile fatty acids (VFAs). This review provides a comprehensive examination of the recovery and reuse of VFAs in wastewater management, with a particular focus on advancing the preferable biological short-cut nitrogen removal process for carbon-insufficient municipal wastewaters. First, the method of carbon redirection for recovering VFAs was reviewed. Carbon could be captured through the two-stage A/B process or via sludge fermentation with different sludge pretreatment and process control strategies to accelerate sludge hydrolysis and inhibit methanogens to enhance VFA production. Second, VFAs can support the metabolism of autotrophic N-cycling microorganisms involved in wastewater treatment, such as AOB, NOB, anammox, and comammox bacteria. However, VFAs can also cause inhibition at high concentrations, leading to the partition of AOB and NOB; and can promote partial denitrification as an efficient carbon source for heterotrophic denitrifiers. Third, the lab- and pilot-scale engineering practices with different configurations (i.e., A²O, SBR, UASB) were summarized that have shown the feasibility of utilizing the fermentate to achieve superior nitrogen removal performance without the need for external carbon addition. Lastly, the future perspectives on leveraging the relationships between mainstream and sidestream, nitrogen and phosphorus, autotrophs and heterotrophs were given for sustainable and efficient BNR management.

Biofilter-constructed wetland-trophic pond system: A new strategy for effective sewage treatment and agricultural irrigation in rural area

Artificial ecosystems with high biological complexity are generally considered to be efficient in metabolizing substances and resistant to temperature shock. In this study, a novel near-natural system (BCT system), which consisted of simple biofilter, constructed wetland and trophic biology pond, was conducted to treat rural sewage in situ for irrigation into farmland. Water quality related to carbon and nutrients and microbial community were analyzed along the system to reveal the effect of each unit. The annual average removals of BCT system for TN, NH₄⁺-N, TP and COD could reach 46.53%, 52.18%, 41.48%, and 53.21%, respectively. There was no significant decrease for removal efficiencies from high temperature period (HTP, ≥15 °C) to low temperature period (LTP, <15 °C). In LTP, the trophic pond (TRP) removed 34.85% of TN, 33.93% of NH₄⁺-N, 13.71% of TP and 18.77% of COD, while the removal efficiencies of constructed wetland fluctuated greatly. The TRP facilitated the BCT system to maintain the removal capability during low temperature period. The relative abundance of denitrification functional genes in TRP increased nearly tenfold from HTP to LTP. The effluent quality from the system can meet the agricultural irrigation standards, demonstrating the effect of BCT system on sewage treatment and agricultural irrigation in rural area.

Modified microbiology through enhanced denitrification by addition of various organic substances-temperature effect

Worldwide, the environmental nitrate (NO₃^-) problem is increasingly coming into focus. These increases in NO₃^- concentration result mainly from agricultural inputs and are further exacerbated by decreasing and finite geogenic NO₃^- degradation capacity in aquifers. Thus, treatment methods are becoming more and more important. In this study, the effects of enhanced denitrification with addition of organic carbon (C) on thereby autochthonous occurring microbiology and compared at room temperature as well as 10 °C were investigated. Incubation of bacteria and fungi was carried out using natural sediments without degradation capacity and groundwater with high NO₃^- concentrations. Addition of the four applied substrates (acetate, glucose, ascorbic acid, and ethanol) results in major differences in microbial community. Cooling to 10 °C changes the microbiology again. Relative abundances of bacteria are strongly influenced by temperature, which is probably the explanation for different denitrification rates. Fungi are much more sensitive to the milieu change with organic C. Different fungi taxa preferentially occur at one of the two temperature approaches. Major modifications of the microbial community are mainly observed whose denitrification rates strongly depend on the temperature effect. Therefore, we assume a temperature optimum of enhanced denitrification specific to each substrate, which is influenced by the microbiology.

A. Jorand F, Barrière F, Etienne M. Challenges and Applications of Nitrate-Reducing Microbial Biocathodes

Bioelectrochemical systems which employ microbes as electrode catalysts to convert chemical energy into electrical energy (or conversely), have emerged in recent years for water sanitation and energy recovery. Microbial biocathodes, and especially those reducing nitrate are gaining more and more attention. The nitrate-reducing biocathodes can efficiently treat nitrate-polluted wastewater. However, they require specific conditions and they have not yet been applied on a large scale. In this review, the current knowledge on nitrate-reducing biocathodes will be summarized. The fundamentals of microbial biocathodes will be discussed, as well as the progress towards applications for nitrate reduction in the context of water treatment. Nitrate-reducing biocathodes will be compared with other nitrate-removal techniques and the challenges and opportunities of this approach will be identified.

Emission dynamics of greenhouse gases regulated by fluctuation of water level in river-connected wetland

The application of reservoirs in the upper reaches of rivers will change the hydrological rhythm of river-connected wetlands in the lower reaches, causing changes in the distribution of wetland vegetation. The differences of carbon and nitrogen sequestration and emission potential in different vegetations may lead to the dynamics of greenhouse gas emissions from wetlands during hydrological periods. For a wetland connected to the Yangzi River, China, the dynamic changes of vegetation and water areas were identified by remote sensing, and the water level, the emission fluxes of greenhouse gases and the functional bacteria of carbon and nitrogen in soil were measured in-situ. Compared with drought period, the area of phragmites zone in flooding period increased by 28.2%, while the areas of carex and phalaris zones decreased by 42.9%. The carbon and nitrogen accumulation in the soil of phragmites zone is the highest, while the cumulative amount of phalaris is the lowest. The emission fluxes of CH₄ and N₂O in mud/water and various vegetations were positively correlated with water level and reached the maximum during flooding period. Although the global warming potential of mud/water was highest than that of vegetations, carex zone had the highest warming potential among vegetation zones. CH₄ contributes 8-37 times as much as N₂O to global warming potential in the wetland. The increase of flooding time promoted the emissions of CH₄ and N₂O in the wetland. The anaerobic condition caused by flooding stimulated the activities of denitrifying and methanogenic bacteria, thus increasing the emission of greenhouse gases. The sequestrations and emissions of carbon and nitrogen regulated by a reservoir in the upstream suggest that the operation of water conservancies should be considered to alleviate the greenhouse gas emission from river-connected wetland.

Nitrate removal rates, isotopic fractionation, and denitrifying bacteria in a woodchip-based permeable reactive barrier system: a long-term column experiment

This study evaluated the effectiveness of using organic carbon materials (i.e., woodchips) to remove nitrate from groundwater. The results of our flow-through column experiment, which was conducted over 1.6 years, suggested that denitrifying bacteria reduce nitrate by using it as an electron acceptor and woodchips as an electron donor. The nitrate removal rates were sufficiently high (0.39-1.04 mmol L-1 day-1) during the operation of the column. Denitrification process was supported by fractionation of nitrogen and oxygen isotopes (δ15N and δ18O), with the δ15N and δ18O values enriched from 7.4‰ and 22.3‰ to 21.2‰ and 30.4‰, respectively. Enrichment factors ([Formula: see text]) for 15 N and 18O were calculated using the Rayleigh fractionation model, with values of - 13.2‰ for ε15N and - 7.1‰ for ε18O. The fractionation ratio of 15 N to 18O was 1.9:1, confirming denitrification. The most abundant bacterial genera in the soil used for inoculation were Enterobacter (86.7%), Nitrospira (1.8%), and Arthrobacter (1.5%), while those in the column effluent were Macrococcus (37.1%), Escherichia (14.7%), and Shigella (14.6%), indicating that bacterial communities changed in response to geochemical conditions in the column. This study suggests that nitrate in groundwater can be effectively removed using woodchip-based passive treatment systems and that information on isotopic fractionation and denitrifying bacteria can be key tools to understand denitrification.

Metagenomic analysis of Fe(II)-oxidizing bacteria for Fe(III) mineral formation and carbon assimilation under microoxic conditions in paddy soil

Microbially mediated Fe(II) oxidation is prevalent and thought to be central to many biogeochemical processes in paddy soils. However, we have limited insights into the Fe(II) oxidation process in paddy fields, considered the world's largest engineered wetland, where microoxic conditions are ubiquitous. In this study, microaerophilic Fe(II) oxidizing bacteria (FeOB) from paddy soil were enriched in gradient tubes with FeS, FeCO₃, and Fe₃(PO₄)₂ as iron sources to investigate their capacity for Fe(II) oxidation and carbon assimilation. Results showed that the highest rate of Fe(II) oxidation (k = 0.836 mM d^-1) was obtained in the FeCO₃ tubes, and cells grown in the Fe₃(PO₄)₂ tubes yielded maximum assimilation amounts of ¹³C-NaHCO₃ of 1.74% on Day 15. Amorphous Fe(III) oxides were found in all the cell bands with iron substrates as a result of microbial Fe(II) oxidation. Metagenomics analysis of the enriched microbes targeted genes encoding iron oxidase Cyc2, oxygen-reducing terminal oxidase, and ribulose-bisphosphate carboxylase, with results indicated that the potential Fe(II) oxidizers include nitrate-reducing FeOB (Dechloromonas and Thiobacillus), Curvibacter, and Magnetospirillum. By combining cultivation-dependent and metagenomic approaches, our results found a number of FeOB from paddy soil under microoxic conditions, which provide insight into the complex biogeochemical interactions of iron and carbon within paddy fields. The contribution of the FeOB to the element cycling in rice-growing regions deserves further investigation.

Biohydrogen production potential with sulfate and nitrate removal by heat-pretreated enriched sulfate-reducing microorganisms-based bioelectrochemical system

In this study, heat-pretreated sulfate-reducing bacteria (SRBs) were evaluated for simultaneous sulfate and nitrate removal in a bioelectrochemical system (BES). The effect of the applied potential of 20 mV to SRBs was evaluated at a sulfate concentration of 3 g/L and/or nitrate concentration of 0.5 g/L supplemented before heat pretreatment for sulfate and nitrate removal. The highest H₂ production of 2.24 ± 0.04 mM/L in heat-pretreated culture was observed in the presence of sulfate at an applied potential of 20 mV (BHE-S). Simultaneous reduction of sulfate and nitrate was significant in BESs supplemented with either sulfate or nitrate during heat-shock pretreatment of the culture. The highest SO₄^2- removal of 88.91 ± 0.8% was found in culture heat pretreated with NO₃^- and applied with 20 mV potential (BHE-N). The kinetics of heat-pretreated culture showed higher R² and ultimate potential for H₂ on the continuous application of 20 mV potential.

Simultaneous heterotrophic nitrification and aerobic denitrification potential of Paenibacillus sp. strain GLM-08 isolated from lignite mine waste and its role ammonia removal from mine waste water

Paenibacillus sp. strain GLM-08 was isolated from a lignite mine waste site in the Barmer basin, Rajasthan, India. The strain is efficient in heterotrophic nitrification and aerobic denitrification. This bacterium could remove approximately more than 95% of NH₄⁺, NO₃^-, and NO₂^- in 24 h. The average nitrogen (N) removal rate of the strain was found to be 4.775 mg/L/H, 5.66 mg/L/H, and 5.01 mg/L/H for NH₄⁺, NO₃^-, and NO₂^-, respectively. Bioaugmentation of mine wastewater with Paenibacillus sp. strain GLM-08 demonstrated N removal of 86.6% under conditions of a high load of NH₄⁺. The presence of potential genetic determinants (nxrB, nirS, and nosZ) having role in heterotrophic nitrification and aerobic denitrification was confirmed by PCR based analysis. The findings show that this bacterium performs simultaneous nitrification and denitrification and has a high nitrogen removal efficiency indicating the potential application of the strain in the treatment of wastewater.

Summer greenhouse gas fluxes in different types of hemiboreal lakes

Lakes are considered important regulators of atmospheric greenhouse gases (GHG). We estimated late summer open water GHG fluxes in nine hemiboreal lakes in Estonia classified under different lake types according to the European Water Framework Directive (WFD). We also used the WFD typology to provide an improved estimate of the total GHG emission from all Estonian lakes with a gross surface area of 2204 km² representing 45,227 km² of hemiboreal landscapes (the territory of Estonia). The results demonstrate largely variable CO₂ fluxes among the lake types with most active emissions from Alkalitrophic (Alk), Stratified Alkalitrophic (StratAlk), Dark Soft and with predominant binding in Coastal, Very Large, and Light Soft lakes. The CO₂ fluxes correlated strongly with dissolved CO₂ saturation (DCO₂) values at the surface. Highest CH₄ emissions were measured from the Coastal lake type, followed by Light Soft, StratAlk, and Alk types; Coastal, Light Soft, and StratAlk were emitting CH₄ partly as bubbles. The only emitter of N₂O was the Alk type. We measured weak binding of N₂O in Dark Soft and Coastal lakes, while in all other studied lake types, the N₂O fluxes were too small to be quantified. Diversely from the common viewpoint of lakes as net sources of both CO₂ and CH₄, it turns out from our results that at least in late summer, Estonian lakes are net sinks of both CO₂ alone and the sum of CO₂ and CH₄. This is mainly caused by the predominant CO₂ sink function of Lake Peipsi forming ¾ of the total lake area and showing negative net emissions even after considering the Global Warming Potential (GWP) of other GHGs. Still, by converting CH₄ data into CO₂ equivalents, the combined emission of all Estonian lakes (8 T C day^-1) is turned strongly positive: 2720 T CO₂ equivalents per day.

Nitrogen deposition stimulated winter nitrous oxide emissions from bare sand more than biological soil crusts in cold desert ecosystem

Dryland ecosystems are often nitrogen-limited, and small nitrogen inputs may produce large responses to dryland ecological processes, such as gaseous nitrogen emission. The effect of increased anthropogenic nitrogen deposition on N₂O and NO emissions in desert ecosystems is unclear, especially in non-growing seasons when the surface is covered with snow. In this study, nitrogen applications were performed on biological soil crusts (lichen crust and moss crust, bare sand for control) in the Gurbantunggut Desert, Northwest China. We measured the fluxes of N₂O and NO and related nitrogen cycle functional gene abundances in winter for three-years period. Nitrogen addition significantly affected N₂O emissions and increased the abundances of key functional gene for nitrogen cycle, while it only slightly influenced NO emissions. These effects of nitrogen addition depended on composition of biological soil crusts. For bare sand and lichen crust, nitrogen addition significantly increased N₂O emissions, whereas for moss crust, only a negligible effect was observed. Meanwhile, significant differences in nitrogen cycle functional gene abundances were found among different composition of biological soil crusts. Abundance of amoA, narG, and nosZ genes were highly related to N₂O and NO emissions. Thus, our results indicate that gaseous nitrogen emissions were generally increased by nitrogen addition through their effects on related functional microbial groups. The effects were regulated by composition of biological soil crusts which can buffer the effects of increasing nitrogen addition during winter.