Denitrification

Relationship between denitrification and anammox rates and N2 production with substrate consumption and pH in a riparian zone

Denitrification and anaerobic ammonium oxidation (anammox) are the key processes to quantitatively remove nitrate (NO3-) and balance the nitrogen (N) budget of the ecosystem. In this paper, a slurry-based 15N tracer approach was used to study the correlation and quantitative relation of substrate consumption and pH with rates of denitrification and anammox in a riparian zone. The results showed that the fastest rates of 0.93 µg N h-1 and 0.32 µg N h-1 for denitrification (Denitrif-N2) and anammox (Denitrif-N2), respectively. N2 produced by denitrification occupied 74.04% and produced by anammox occupied 25.96% of the total N2, proving denitrification is the dominant process to remove NO3-. The substrate content (NO3-, NH4+ and TOC) and pH varied during incubation and were significantly correlated with Dentrif-N2 and Anammox-N2. Nitrate and TOC as the substrates of denitrification demonstrated a significant correlation with Anammox-N2, which was associated with the products of denitrification involved in the anammox process. This proved a coupling of denitrification and anammox. A quantitative relationship was observed between Dentrif-N2 and Anammox-N2 in the range of 2.75-2.90 when TOC, NH4+ and NO3- consumption per unit mass or pH changed per unit. Nitrogen mass balance analysis showed that 1 mg N substrate (NO3-+NH4+) consumption in the denitrification and anammox can produce 1.05 mg N2 with a good linear relationship (r2 = 0.9334). This could be related to other processes that produced extra N2 in denitrification and anammox system.

Nitrate removal and environmental side-effects controlled by hydraulic residence time in woodchip bioreactors treating cold agricultural drainage water

Denitrifying woodchip bioreactors (WBRs) remove nitrate (NO 3 - ) from agricultural drainage water at field-scale, but their efficacy at cold temperatures remains uncertain. This study shows how hydraulic residence time (HRT) controls NO 3 - removal and environmental side-effects of WBRs at low water temperature under pilot-scale conditions with controlled operation of nine WBRs (94 dm3). Hydraulic properties were assessed by a bromide tracer test, and NO 3 - removal, emissions of nitrous oxide (N2O) and methane (CH4), and losses of dissolved organic carbon (DOC) were measured at HRTs of 5-30 h. Inlet NO 3 - concentrations were increasingly reduced at higher HRTs. The relationship between HRT and the efficiency (%) of NO 3 - removal was linear (R a d j 2  = 0.94), while the relationship between HRT and NO 3 - reduction rates (NRR) was logistic (R a d j 2  = 0.88). Gaseous emissions of N2O were equally low at HRTs of 10-30 h, but higher at 5 h (P < 0.05). Methane fluxes were small, but with consistent emissions at HRTs of 20-30 h and uptake at 5-15 h. HRT had limited effect on effluent DOC concentrations, but strong effect on mass losses that were five-fold higher (320 mg L-1) at the HRT of 5 h than at 30 h. In summary, at cold temperatures HRTs of ≤ 20 h resulted in suboptimal NRR, accelerating DOC losses, and increased risk of N2O losses at least below a threshold HRT of 5-10 h. HRTs of 20-30 h gave maximal NRR, smallest losses of DOC and N2O, but an increased risk of CH4 emissions.

Dynamic modelling of N2 O emissions from a full-scale granular sludge partial nitritation-anammox reactor

Partial nitration-anammox is a resource-efficient pathway for nitrogen removal from wastewater. However, the advantages of this nitrogen removal technology may be counter-acted by the emission of N₂ O, a potent greenhouse gas. In this study, mathematical modelling was applied to analyse N₂ O formation and emission dynamics and to develop N₂ O mitigation strategies for a one-stage partial nitritation-anammox granular sludge reactor. Dynamic model calibration for such a full-scale reactor was performed, applying a 1-dimensional biofilm model and including several N₂ O formation pathways. Simultaneous calibration of liquid phase concentrations and N₂ O emissions leads to improved model fit compared to their consecutive calibration. The model could quantitatively predict the average N₂ O emissions and qualitatively characterize the N₂ O dynamics, adjusting only seven parameter values. The model was validated with N₂ O data from an independent data set at different aeration conditions. Nitrifier nitrification was identified as the dominating N₂ O formation pathway. Off-gas recirculation as a potential N₂ O emission reduction strategy was tested by simulation and showed indeed some improvement, be it at the cost of higher aeration energy consumption. This article is protected by copyright. All rights reserved.

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.

Diurnal variability in soil nitrous oxide emissions is a widespread phenomenon

Manual measurements of nitrous oxide (N₂ O) emissions with static chambers are commonly practised. However, they generally do not consider the diurnal variability of N₂ O flux, and little is known about the patterns and drivers of such variability. We systematically reviewed and analysed 286 diurnal data sets of N₂ O fluxes from published literature to (i) assess the prevalence and timing (day or night peaking) of diurnal N₂ O flux patterns in agricultural and forest soils, (ii) examine the relationship between N₂ O flux and soil temperature with different diurnal patterns, (iii) identify whether non-diurnal factors (i.e. land management and soil properties) influence the occurrence of diurnal patterns and (iv) evaluate the accuracy of estimating cumulative N₂ O emissions with single-daily flux measurements. Our synthesis demonstrates that diurnal N₂ O flux variability is a widespread phenomenon in agricultural and forest soils. Of the 286 data sets analysed, ~80% exhibited diurnal N₂ O patterns, with ~60% peaking during the day and ~20% at night. Contrary to many published observations, our analysis only found strong positive correlations (R > 0.7) between N₂ O flux and soil temperature in one-third of the data sets. Soil drainage property, soil water-filled pore space (WFPS) level and land use were also found to potentially influence the occurrence of certain diurnal patterns. Our work demonstrated that single-daily flux measurements at mid-morning yielded daily emission estimates with the smallest average bias compared to measurements made at other times of day, however, it could still lead to significant over- or underestimation due to inconsistent diurnal N₂ O patterns. This inconsistency also reflects the inaccuracy of using soil temperature to predict the time of daily average N₂ O flux. Future research should investigate the relationship between N₂ O flux and other diurnal parameters, such as photosynthetically active radiation (PAR) and root exudation, along with the consideration of the effects of soil moisture, drainage and land use on the diurnal patterns of N₂ O flux. The information could be incorporated in N₂ O emission prediction models to improve accuracy.

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.

Simultaneous removal of nitrate and phosphate in groundwater using Ca-citrate complex

Eutrophication can be caused by excessive input of nutrients, such as nitrate and phosphate, to surface water. Nutrients in groundwater can enter surface water by means of base flow, requiring treatment before they reach surface water bodies. While some studies have attempted to remove nitrate and phosphate, methods for simultaneous removal in groundwater have rarely been reported. In this study, we propose an innovative treatment method to simultaneously remove nitrate and phosphate in groundwater based on an injection of Ca-citrate complex. A total of five batch experiments with different conditions were conducted to identify the removal mechanisms of nitrate and phosphate and to evaluate the use of alternative organic materials, such as lactate. The results showed that Ca-citrate complex can remove nitrate and phosphate simultaneously. Nitrate was removed through denitrification by denitrifying bacteria which used citrate as a carbon source. The removal mechanisms for phosphate were precipitation of phosphate minerals (e.g., hydroxyapatite) and adsorption. The results also showed that reactive materials based on Ca-lactate complex were able to remove nitrate and phosphate. This study suggests that nitrate and phosphate in groundwater can simultaneously be removed using organic-based calcium complexes, proposing a promising remedial method to alleviate potential eutrophication in surface water as well as groundwater contamination.

Effect of Denitrifying Bacterial Biomass and Carbon Sources on Nitrate Removal

Denitrification based on immobilized microbial cellulose may offer an economical replacement for conventional treatment for nitrate removal. The environmental and bacterial biomass may influence the rate of biological denitrification processes. This study aimed to investigate the factors that affect denitrification rates, including carbon sources, pH, and bacterial inoculum. Different inoculum biomass of Pseudomonas aeruginosa and various carbon sources of glucose, sucrose, and cellulose with different concentrations were tested to assimilate 100 mg/L of KNO3 as nitrate source. Additionally, five additional inoculations, five different incubation time, and seven different pH levels were studied. The Pseudomonas aeruginosa isolates used different mineral media with three carbon sources, glucose, sucrose, and cellulose, with different concentrations at different rates to denitrify nitrate. The highest denitrification rate was with glucose after 18 hrs and was after 24 hrs when sucrose and cellulose were used, respectively. The bacterial biomass denitrification level was the highest, between 0.8% and 1% of OD600=1. Nitrate removal by Pseudomonas aeruginosa was the highest at pH 7, 8, and 9. This report suggests that when glucose is used as a carbon source, at neutral to alkaline pH, and 1% of denitrifying bacterial biomass, the highest level of biological denitrification process may be achieved.

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.

Contrasting subsurface denitrification characteristics under temperate pasture lands and its implications for nutrient management in agricultural catchments

Subsurface denitrification plays a key role in the reduction or 'attenuation' of nitrate contamination of groundwater and surface waters. We investigated subsurface denitrification characteristics in the vadose zone and shallow groundwater at four sites under pastoral farming in the Manawatū River catchment, located in the lower part of North Island, New Zealand. The denitrification potential of the vadose zone was determined by the laboratory incubation assays measuring the denitrifying enzyme activity (DEA) in soil samples collected from different soil horizons (up to 2.1 m below ground surface), whereas denitrification rates in shallow groundwaters were measured in situ by single-well, push-pull tests conducted in piezometers installed at multiple depths at the study sites. Soils and underlying geology, defining hydrogeologic settings, appear to influence the spatial variability of subsurface denitrification characteristics at the study sites. Where the vadose zone is thin and composed of coarse-textured soils, percolation of nitrate was evident in observed high nitrate-nitrogen concentrations (>5 mg L^-1) in oxic and young shallow groundwaters, but low nitrate-nitrogen concentrations (<0.05 mg L^-1) were observed in the reduced shallow groundwater found underneath the fine textured soils and/or a thick vadose zone. This was confirmed by the push-pull tests measuring denitrification rates from 0.08 to 1.07 mg N L^-1 h^-1 in the reduced shallow groundwaters (dissolved oxygen or DO < 0.5 mg L^-1), while negligible in the oxic groundwaters (DO > 5 mg L^-1) found at the study sites. These contrasting subsurface denitrification characteristics determine the ultimate delivery of nitrate losses from agricultural soils to receiving waters, where the fine textured thick vadose zone and reducing groundwater conditions offer nitrate reduction in the subsurface environment.

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.

Functional microorganisms and enzymes related nitrogen cycle in the biofilm performing simultaneous nitrification and denitrification

Simultaneous nitrification and denitrification (SND) is a potential energy-saving process in wastewater treatment while the nitrogen removal mechanism is still unclear due to the lack of information about the functional microbes and enzymes. Sequencing batch biofilm reactors were implemented to achieve efficient SND. Eight nitrogen removal related microorganisms out of the top abundant 20 microbial community and reference species were used to construct a phylogenetic tree. Functional enzymes and modules analysis were investigated to reveal the SND pathway: in the aerobic part of the biofilm, ammonia oxidation was catalyzed by complete ammonia oxidizers while in the inner anoxic part, denitrification, dissimilatory nitrate reduction (DNRA) and nitrogen fixation (NF) cooperated to stimulate nitrate removal. These results provide a practical aeration control strategy to achieve SND and indicate that DNRA and NF are important nitrogen removal pathways that should not be ignored in the SND mechanism.

Spatial Distribution of Integrated Nitrate Reduction across the Unsaturated Zone and the Groundwater Body in Germany

Nitrate pollution in groundwater and its mitigation strategies is currently a topic of controversial debate in Germany, and the demand for harmonised approaches for the implementation of regulations is increasing. Important factors that need to be considered when planning mitigation measures are the nitrogen inputs into water bodies and the natural nitrate reduction capacity. The present study introduces a nationwide, harmonised and simplified approach for estimating nitrate reduction as an integral quantity across the unsaturated zone and the groundwater body. The nitrate reduction rates vary from 0% to 100%, and are on average 57%, with high values in the north of Germany and low values in the south. Hydrogeological characteristics are associated with the estimated nitrate reduction rates, whereby the influence of aquifer type and redox conditions are particularly relevant. The nitrate reduction rates are substantially higher in porous aquifers and under anaerobic conditions than in fractured, consolidated aquifers and under aerobic conditions. This contribution presents a harmonised conceptual approach to derive the nitrate reduction rate at a 1 km × 1 km resolution. This information can be used when planning and designing mitigation measures to meet the groundwater nitrate limits.

Synchronous Nutrient Controlled-Release of Greenhouse Gases During Mineralization of Sediments from Different Lakes

Lake sediments, as an important emission source of nutrients and greenhouse gases, play a crucial role during the biogeochemical cycle processes. However, the impact mechanisms of different nutrient levels on greenhouse gas emission from lakes are still insufficient. In this study, the sediments from eight shallow lakes in the middle and lower reaches of the Yangtze River were cultured to study the release characteristics of greenhouse gases more than one month. Results showed that the greenhouse gases during the mineralization processes of sediments were mainly released to the atmosphere instead of being dissolved in the overlying water. The released concentrations of CH₄ and CO₂ were as high as 1 × 10³ μmol L^-1 in the later stage of the experiment, while the concentration of N₂O was relatively low with a maximal value of about 10 μmol L^-1. In addition, all the lake sediments displayed a nutrient release to the overlying water, where the concentrations of TC, TOC, TN, NH₄⁺-N and TP were up to 173.0, 102.7, 36.7, 30.8 and 6.34 mg L^-1, respectively. The nutrient levels of different lake sediments are symmetrical to the released nutrients concentrations in the overlying water. The further statistical analysis illustrated a synchronous nutrient controlled-release of greenhouse gases, that is, the higher the levels of nutrients in the sediments, the higher the concentrations of greenhouse gases released. These findings provide a better understanding that the control of endogenous nutrient levels of sediments is extremely important for lacustrine management, which can play a positive role in mitigating the greenhouse gas emissions from lake sediments.

Investigating the role of organic carbon amendments and microbial denitrification gene abundance in nitrogen removal from experimental agricultural drainage ditches with low-grade weirs

Low-grade weirs placed within agricultural drainage ditches in the Lower Mississippi Alluvial Valley can be used as a management practice to enhance nitrogen removal. The addition of organic carbon amendments within ditches that contain weirs could further increase nitrogen removal. Through repeated trials, changes in NO 3 - -N concentration between inflow and outflow were variable in the ditch without weirs, while only decreases in concentration were observed in ditches with weirs. Significant differences in NO 3 - -N concentrations were observed between treatments, with greater removal of NO 3 - -N observed in dissolved organic carbon treatments compared to control and particulate organic carbon treatments. At medium- and high-flow rates, respectively, dissolved organic carbon treatments resulted in greater NO 3 - -N concentration decreases of 31.6% and 27.1% compared to 19% and 11.6% in particulate organic carbon treatments and 18.6% and 17.2% in control treatments. Significant effects of weirs and sampling date on nirS, nirK, nosZ, and 16S rRNA gene abundances were observed. Observed increases in NO 3 - -N removal with organic carbon amendments, provides support for continued investigation on improving the efficacy of organic carbon amendments as a best management practice for NO 3 - -N removal in agricultural drainage ditches. PRACTITIONER POINTS: Dissolved organic carbon amendments increased nitrate-nitrogen removal. Only decreases in nitrate-nitrogen concentration were observed in ditches with weirs. Increasing flow rate did not affect nitrate-nitrogen removal. Abundance of denitrification-performing microbes likely did not affect N removal. Lack of anaerobic soil conditions and short residence time reduced nitrate-N removal.

Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment

Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.

The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle

Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N₂O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.

Characterization of Denitrifying Community for Application in Reducing Nitrogen: a Comparison of nirK and nirS Gene Diversity and Abundance

Studies have shown that the addition of biochar to agricultural soils has the potential to mitigate climate change by decreasing nitrous oxide (N₂O) emissions resulting from denitrification. Rice paddy field soils have been known to have strong denitrifying activity, but the response of microbes to biochar for weakening denitrification in rice paddy field soils is not well known. In this work, compared with the chemical fertilizer alone, the chemical fertilizer + 20 t hm^-2 biochar fertilizer slightly decreased denitrifying the nitrite reductase activity (S-NiR) and N₂O emission without statistic difference, whereas the chemical fertilizer + 40 t hm^-2 biochar significantly boosted them. The abundance of nir-denitrifiers contributed to S-NiR and N₂O emission, especially nirS-denitrifiers, rather than the variation of community structure. Pearson correlation analysis showed that NO₂^--N was a key factor for controlling the abundance of nir-denitrifiers, S-NiR and N₂O emission. The biochar addition fertilization treatments strongly shaped the community structure of nirK-denitrifiers, while the community structure of nirS-denitrifiers remained relatively stable. In addition, Paracoccus and Sinorhizobium were revealed to be as the predominant lineage of nirS- and nirK-containing denitrifiers, respectively. Distance-based redundancy analysis (db-RDA) showed that changes in the nir-denitrifier community structure were significantly related to soil organic carbon, NO₃^--N, and total phosphorus. Our findings suggest that, although the nirS- and nirK-denitrifiers are both controlling nitrite reductase, their responses to biochar addition fertilization treatments showed significant discrepancies of diversity, abundance, and contribution to N₂O and S-NiR in a paddy soil.

The Structure and Diversity of Nitrogen Functional Groups from Different Cropping Systems in Yellow River Delta

The Yellow River Delta (YRD) region is an important production base in Shandong Province. It encompasses an array of diversified crop systems, including the corn-wheat rotation system (Wheat-Corn), soybean-corn rotation system (Soybean-Corn), fruits or vegetables system (Fruit), cotton system (Cotton) and rice system (Rice). In this study, the communities of ammonia oxidizer-, denitrifier- and nitrogen (N)-fixing bacteria in those cropping systems were investigated by Illumina Miseq sequencing. We found that Rice soil exhibited significantly higher diversity indices of investigated N-cycling microbial communities than other crop soils, possibly due to its high soil water content. Wheat-Corn soils had higher abundances of nitrification gene amoA and denitrification genes nirK and nirS, and exhibited higher soil potential nitrification rate (PNR), compared with Soybean-Corn, Cotton and Fruit soils. Consistently, redundancy analysis (RDA) showed that soil water content (SWC), electrical conductivity (EC), and total nitrogen (TN) were the most important influencing factors of the diversity and structure of the investigated N-cycling microbial.

Hydrilla verticillata-Sulfur-Based Heterotrophic and Autotrophic Denitrification Process for Nitrate-Rich Agricultural Runoff Treatment

Hydrilla verticillata-sulfur-based heterotrophic and autotrophic denitrification (HSHAD) process was developed in free water surface constructed wetland mesocosms for the treatment of nitrate-rich agricultural runoff with low chemical oxygen demand/total nitrogen (C/N) ratio, whose feasibility and mechanism were extensively studied and compared with those of H. verticillata heterotrophic denitrification (HHD) mesocosms through a 273-day operation. The results showed that the heterotrophic and autotrophic denitrification can be combined successfully in HSHAD mesocosms, and achieve satisfactory nitrate removal performance. The average NO₃^--N removal efficiency and denitrification rate of HSHAD were 94.4% and 1.3 g NO₃^--N m^-3·d^-1 in steady phase II (7-118 d). Most nitrate was reduced by heterotrophic denitrification with sufficient organic carbon in phase I (0-6 d) and II, i.e., the C/N ratio exceeded 4.0, and no significant difference of nitrate removal capacity was observed between HSHAD and HHD mesocosms. During phase III (119-273 d), sulfur autotrophic denitrification gradually dominated the HSHAD process with the C/N ratio less than 4.0, and HSHAD mesocosms obtained higher NO₃^--N removal efficiency and denitrification rate (79.1% and 1.1 g NO₃^--N m^-3·d^-1) than HHD mesocosms (65.3% and 1.0 g NO₃^--N m^-3·d^-1). As a whole, HSHAD mesocosms removed 58.8 mg NO₃^--N more than HHD mesocosms. pH fluctuated between 6.9-9.0 without any pH buffer. In general, HSHAD mesocosms were more stable and efficient than HHD mesocosms for NO₃^--N removal from agricultural runoff during long-term operation. The denitrificans containing narG (1.67 × 10⁸ ± 1.28 × 10⁷ copies g^-1 mixture-soil^-1), nirS (8.25 × 10⁷ ± 8.95 × 10⁶ copies g^-1 mixture-soil^-1), and nosZ (1.56 × 10⁶ ± 1.60 × 10⁵ copies g^-1 mixture-soil^-1) of litter bags and bottoms in HSHAD were higher than those in HHD, which indicated that the combined heterotrophic and autotrophic denitrification can increase the abundance of denitrificans containing narG, nirS, and nosZ, thus leading to better denitrification performance.

Effects of water level and vegetation on nitrate dynamics at varying sediment depths in laboratory-scale wetland mesocosms

Recent increases in the frequency of extreme floods and droughts associated with climate change can affect fluctuating groundwater or wetland water levels and wetland plant growth, and consequently cause redox condition changes in nitrogen dynamics in wetland sediments. Here, we studied the fate of nitrate (NO₃^-), dissolved organic carbon (DOC), and the microbial characteristics at different sediment depths in response to water levels (i.e., 5 or 2.5 cm) above the sediment surface and in the presence or absence of plants (Phragmites communis Trin) for four months in three wetland mesocosms. Results showed that mesocosm A (MA) with a high water level (5 cm above the surface) and plants had significantly higher DOC concentrations (17.57 ± 8.22 mg/L) in sediment that were actively consumed by microorganisms than other mesocosms with low water level (MB) and without plant (MC) (8.77 ± 2.38 mg/L and 7.87 ± 2.72 mg/L in MB and MC, respectively). Consequently, the most of influent NO₃^- (20 mg-N/L) dramatically reduced in the vicinity of plant roots (-20 to -15 cm sediment depth) where active denitrification was expected in MA. Moreover, the functional genes involved in denitrification such as narG (2.4 × 10⁸ -3.5 × 10⁸ copies·g^-1) and nirS (5.6 × 10⁶-1.1 × 10⁷ copies·g^-1) were more abundant in this mesocosm. The profile of the microbial community structure at the class level revealed that Alphaproteocbacteria (MA: 14.19 ± 1.19%; MB: 14.01 ± 0.51%; MC: 15.21 ± 2.76%) and Actinobacteria (MA: 8.21 ± 1.91%; MB: 13.91 ± 2.13%; MC: 11.75 ± 3.43%) were predominant in all three mesocosms. Interestingly, the clustered heatmap supported the obvious difference in microbial composition of MA from other mesocosms showing relatively more abundant Clostridia (6.71 ± 1.54%) and Deltaproteobacteria (7.05 ± 0.68%). These results can provide an insight to understand the biogeochemical nitrogen cycle associated with climate change in wetland systems.

Can multiple harvests of plants improve nitrogen removal from the point-bar soil of lake?

Point bar areas around lakes can provide ecological service functions. For example, plants growing on point bars absorb and remove nutrients from the soil and water. However, if the point-bar plants are unregulated, in the fall and winter, plant debris will decompose, releasing nutrients that then enter the water body and cause eutrophication. Therefore, any harvesting should be managed. But how to harvest plants and how often to harvest them, and there is little research on these. In this study, the point bar at Qingcaosha Reservoir was used to study the effects of three plant harvesting modes (M1: unharvested; M2: one harvest in the fall; and M3: one harvest in summer and one in the fall) on the removal of nitrogen (N) from point-bar soil. The largest amount of N was removed by the plants when the M3 mode was used (26.93 g/m²). However, the M2 mode removed the most N from the soil during the plant growth season (81.62 g/m²), which implied that the nitrification and denitrification effects of soil microorganisms make the largest contribution to N removal from this point-bar soil. The nitrification and denitrification activity of microorganisms was higher for M2 than for M1 and M3 in the following year. Additionally, summer harvesting (M3) had a negative effect on nitrification efficiency in the current season because anaerobic bacteria in the soil significantly increased and nitrifying bacteria significantly decreased after harvesting. However, after a period of recovery, the number of microbial nitrifiers increased again and nitrification activity rose in the following year. The reduction in oxygen supply after harvesting may be the main reason for low nitrification in the current season, but it was beneficial to nitrification and denitrification in the following year because there was luxuriant plant growth. Therefore, when considering both the current season and the following year, harvesting should not be too frequent and one harvest in the fall (M2) led to the largest removal of N from the soil.

Land Use, Not Stream Order, Controls N2O Concentration and Flux in the Upper Mara River Basin, Kenya

Anthropogenic activities have led to increases in nitrous oxide (N2O) emissions from river systems, but there are large uncertainties in estimates due to lack of data in tropical rivers and rapid increase in human activity. We assessed the effects of land use and river size on N2O flux and concentration in 46 stream sites in the Mara River, Kenya, during the transition from the wet (short rains) to dry season, November 2017 to January 2018. Flux estimates were similar to other studies in tropical and temperate systems, but in contrast to other studies, land use was more related to N2O concentration and flux than stream size. Agricultural stream sites had the highest fluxes (26.38 ± 5.37 N2O-N μg·m-2·hr-1) compared to both forest and livestock sites (5.66 ± 1.38 N2O-N μg·m-2·hr-1 and 6.95 ± 2.96 N2O-N μg·m-2·hr-1, respectively). N2O concentrations in forest and agriculture streams were positively correlated to stream carbon dioxide (CO2-C(aq)) but showed a negative correlation with dissolved organic carbon, and the dissolved organic carbon:dissolved inorganic nitrogen ratio. N2O concentration in the livestock sites had a negative relationship with CO2-C(aq) and a higher number of negative fluxes. We concluded that in-stream chemoautotrophic nitrification was likely the main biogeochemical process driving N2O production in agricultural and forest streams, whereas complete denitrification led to the consumption of N2O in the livestock stream sites. These results point to the need to better understand the relative importance of nitrification and denitrification in different habitats in producing N2O and for process-based studies.

An Electron-Balance Based Approach to Predict the Decreasing Denitrification Potential of an Aquifer

Numerical models for reactive transport can be used to estimate the breakthrough of a contaminant in a pumping well or at other receptors. However, as natural aquifers are highly heterogeneous with unknown spatial details, reactive transport predictions on the aquifer scale require a stochastic framework for uncertainty analysis. The high computational demand of spatially explicit reactive-transport models hampers such analysis, thus motivating the search for simplified estimation tools. We suggest performing an electron balance between the reactants in the infiltrating solution and in the aquifer matrix to obtain the hypothetical time of dissolved-reactant breakthrough at a receptor if the reaction with the matrix was instantaneous. This time we denote as the advective breakthrough time for instantaneous reaction (τ_inst ). It depends on the amount of the reaction partner present in the matrix, the mass flux of the dissolved reactant, and the stoichiometry. While the shape of the reactive-species breakthrough curve depends on various kinetic parameters, the overall timing scales with τ_inst . We calculate the latter by particle tracking. The effort of computing τ_inst is so low that stochastic calculations become feasible. We apply the concept to a two-dimensional test case of aerobic respiration and denitrification. A detailed spatially explicit reactive-transport model includes microbial dynamics. Scaling the time of local breakthrough curves observed at individual points by τ_inst decreased the variability of electron-donor breakthrough curves significantly. We conclude that the advective breakthrough time for instantaneous reaction is efficient in estimating the time over which an aquifer retains its degradation potential.

Proto-dolomite formation in microbial consortia dominated by Halomonas strains

Microbes can be found in hypersaline environments forming diverse populations with complex ecological interactions. Microbes in such environments were found to be involved in the formation of minerals including dolomite, a mineral of economic importance and whose origin has been long-debated. Various reports on in vitro experiments using pure cultures provided evidence for the microbial role in dolomite formation. However, culturing experiments have been limited in scope and do not fully address the possible interactions of the naturally occurring microbial communities; consequently, the ability of microbes as a community to form dolomite has been investigated in this study. Our experiments focused on examining the microbial composition by culturing aerobic heterotrophs from the top hypersaline sediments of Al-Khiran sabkha in Kuwait, a modern dolomite-forming environment. The objectives of this study were to assess the ability of two microbial consortia to form dolomite using enrichment culture experiments, mineralogy, and metagenomics. Proto-dolomite was formed by a microbial community dominated by Halomonas strains whereby degradation of the extracellular polymeric substances (EPS) was observed and the pH changed from 7.00 to 8.58. Conversely, proto-dolomite was not observed within a microbial community dominated by Clostridiisalibacter in which EPS continuously accumulated and the pH slightly changed from 7.00 to 7.29.

Phosphorus availability and plants alter soil nitrogen retention and loss

Availability of phosphorus (P) can directly and/or indirectly affect nitrogen (N) retention and loss from soil by stimulating microbial and plant root activities. However, it is not clear how P availability and plant presence interact on nitrous oxide (N₂O) emission and nitrate (NO₃^-) leaching in soil. A mesocosm experiment was conducted to investigate the effect of P addition (0, 10 and 20 mg P kg^-1) with and without plant presence (Phalaris aquatica, C3 grass) on N₂O emission, NO₃^- leaching and ¹⁵N recovery. Our results showed large variation in N₂O emission with significant increases after leaching events. We observed that initially low but later (after 53 days of sowing) high levels of P addition increased N₂O emission rates, possibly by stimulating nitrifiers and/or denitrifiers in soil. Plant presence decreased N₂O emission at times when plants reduced water and NO₃^- in the soil, but increased N₂O emission at times when both water and NO₃^- in the soil were abundant, and where plants may have stimulated denitrification through supply of labile organic C. Furthermore, an increase in net N mineralization, possibly due to increased decomposition stimulated by root derived C, may also have contributed to the higher cumulative N₂O emission with plant presence. P addition increased ¹⁵N recovery in soil, but reduced it in leachates, suggesting increased ¹⁵N fixation in microbial biomass. Our results showed that both P addition and plant presence stimulated N loss as N₂O, but also increased N retention in the soil-plant system and thus reduced N loss through leaching.

Denitrification performance and microbial diversity of immobilized bacterial consortium treating nitrate micro-polluted water

A heterotrophic denitrification process using bacterial consortium immobilized by polyurethane foams carriers to treat nitrate micro-polluted water was investigated. Nitrate reduction and nitrite accumulation were studied under several factors including initial COD/NO₃^--N concentration ratio, initial pH, initial NO₂^--N/NO₃^--N concentration ratio and inlet NO₃^--N concentration. Batch denitrification experiments showed that nitrate was completely removed at 5 h without nitrite accumulation under the optimum conditions of COD/NO₃^--N concentration ratio of 5.0-5.5 and initial pH of 7.2 ± 0.1. High initial NO₂^--N/NO₃^--N ratio enhanced denitrification rate mainly by accelerating nitrite reduction. Denitrification processes followed zero-order reaction kinetics at different initial NO₃^--N concentrations and obtained higher denitrification rate at higher inlet nitrate. High-throughput sequencing results showed that microbial community structure differed between the surface and interior space of polyurethane foams carriers while the dominant population in the inner zone of carriers was Pseudoxanthomonas.

NO3 - removal efficiency in field denitrification beds: key controlling factors and main implications

Nitrate pollution is a growing environmental threat that affects both ground- and surface-water. The typically used technique for nitrate elimination in wastewater treatment plants cannot be applied for all water streams as it necessitates a highly developed technical infrastructure. Field denitrification beds comprise one strategy to treat surface water containing high nitrate loads, which typically is due to the increasing agricultural land use. Here, the water passes through a basin containing a cheap carbon material as electron donor that provides the environmental niche for a complex microbial biocenosis. The microorganisms catalyse the hydrolysis of the polymeric organic carbon substrate and a variety of fermentative and respiratory pathways that are in the end supposed to lead to an efficient denitrification process. This review article integrates our current knowledge on environmental and operating parameters of and within denitrification beds including biotic and abiotic factors influencing the nitrate removal efficiency. Steering of these two factors can allow to minimise pollution swapping and the formation of greenhouse gases.

Nitrification and denitrification processes for mitigation of nitrous oxide from waste water treatment plants for biovalorization: Challenges and opportunities

Nitrous oxide (N₂O) is a potent greenhouse gas. Even though its emissions is much lesser than CO₂ but its global warming potential (GWP) is 298 times more than CO₂. N₂O emissions from wastewater treatment plants was caused due to incomplete nitrification or incomplete denitrification catalyzed by ammonia-oxidizing bacteria and heterotrophic denitrifiers. Low dissolved oxygen, high nitrite accumulation, change in optimal pH or temperature, fluctuation in C/N ratio, short solid retention time and non-availability of Cu ions were responsible for higher N₂O leakage. Regulation of enzyme metabolic pathways involved in N₂O production and reduction has also been reviewed. Sequential bioreactors, bioscrubbers, membrane biofilters usage have helped microbial nitrification-denitrification processes in succumbing N₂O production in wastewater treatment plants. Reduction of N₂O negativity has been studied through its valorization for the formation of value added products such as biopolymers has led to biorefinery approaches as an upcoming mitigation strategy.

Denitrifying Bacteria Active in Woodchip Bioreactors at Low-Temperature Conditions

Woodchip bioreactor technology removes nitrate from agricultural subsurface drainage by using denitrifying microorganisms. Although woodchip bioreactors have demonstrated success in many field locations, low water temperature can significantly limit bioreactor efficiency and performance. To improve bioreactor performance, it is important to identify the microbes responsible for nitrate removal at low temperature conditions. Therefore, in this study, we identified and characterized denitrifiers active at low-temperature conditions by using culture-independent and -dependent approaches. By comparative 16S rRNA (gene) analysis and culture isolation technique, Pseudomonas spp., Polaromonas spp., and Cellulomonas spp. were identified as being important bacteria responsible for denitrification in woodchip bioreactor microcosms at relatively low temperature conditions (15°C). Genome analysis of Cellulomonas sp. strain WB94 confirmed the presence of nitrite reductase gene nirK. Transcription levels of this nirK were significantly higher in the denitrifying microcosms than in the non-denitrifying microcosms. Strain WB94 was also capable of degrading cellulose and other complex polysaccharides. Taken together, our results suggest that Cellulomonas sp. denitrifiers could degrade woodchips to provide carbon source and electron donors to themselves and other denitrifiers in woodchip bioreactors at low-temperature conditions. By inoculating these denitrifiers (i.e., bioaugmentation), it might be possible to increase the nitrate removal rate of woodchip bioreactors at low-temperature conditions.

Nitrogen variations during the ice-on season in the eutrophic lakes

Nitrogen accumulation in sediments, and the subsequent migration and transformations between sediment and the overlying water, plays an important role in the lake nitrogen cycle. However, knowledge of these processes are largely confined to ice-free seasons. Recent research under ice has mainly focused on the water eco-environmental effects during winter. Sediment N accumulation during the ice-on season and its associated eco-environmental impacts have never been systematically investigated. To address these knowledge gaps, we chose Wuliangsu Lake in China as a case study site, taking advantage of the spatial disparity between the 13 semi-separated sub-lakes. Based on samples of 35 sampling sites collected before, in the middle, and at the end of ice-on season separately, we performed a quantitative analysis of under-ice lake N accumulation and water-sediment N exchange by analyzing N fraction variations. Hierarchical Cluster Analysis and Relevance Analysis were used to help elucidate the main causes and implications of under-ice N variation. Our results clearly show that existing studies have underestimated the impact of under-ice N accumulation on the lake ecology throughout year: 1) Sediment N accumulated 2-3 times more than that before winter; 2) residual nitrogen (Res-N) contributed to the majority of the accumulated sediment N and was mainly induced by the debris of macrophytes; 3) total available nitrogen (TAN) was the most easily exchanged fractions between sediment and water, and it mainly affected the water environment during winter; 4) the Res-N accumulation during the ice-on season may have a strong impact on the eco-environment in the subsequent seasons. Our research is valuable for understanding the mechanism of internal nutrient cycle and controlling the internal nitrogen pollution, especially in shallow seasonally-frozen lakes that have long suffered from macrophyte-phytoplankton co-dominated eutrophication.

In Situ Denitrification in Saturated Riparian Buffers

Excess NO leaching from the agricultural Midwest via tile drainage water has contributed to both local drinking water and national Gulf of Mexico benthic hypoxia concerns. Both in-field and edge-of-field practices have been designed to help mitigate NO flux to surface waters. Edge-of-field practices focus on maximizing microbial denitrification, the conversion of NO to N gas. This study assessed denitrification rates from two saturated riparian buffers (SRBs) for 2 yr and a third SRB for 1 yr, for a total of five sample years. These SRBs were created by diverting NO-rich tile drainage water into riparian buffers soils. The SRBs in this study removed between 27 and 96% of the total diverted NO load. Measured cumulative average denitrification rate for each SRB sample year accounted for between 3.7 and 77.3% of the total NO removed. Both the cumulative maximum and 90% confidence interval denitrification rates accounted for all of the NO removed by the SRBs in three of the five sample years, indicating that denitrification can be a dominant NO removal mechanism in this edge-of-field practice. When adding the top 20 cm of each core to the cumulative denitrification rates for each SRB, denitrification accounted for between 33 and over 100% of the total NO removed. Buffer age (time since establishment) was speculated to enhance denitrification rates, and there was a trend of the soil closer to the surface making up the majority of the total denitrification rate. Finally, both NO and C could limit denitrification in these SRBs.

Mulch-Derived Organic Carbon Stimulates High Denitrification Fluxes from Agricultural Ditch Sediments

Reactive N is an essential input for healthy, vibrant crop production, yet excess N is often transported off field via agricultural ditches to downstream receiving ecosystems, where it can cause negative impacts to human health, biodiversity loss, as well as eutrophication and resultant hypoxia. Denitrification, the transformation of reactive N to unreactive N gas, within agricultural ditches has potential to reduce impacts to downstream ecosystems but requires substantial organic C substrates. We used a flow-through intact core experiment to test the effects of low-cost management options including a common agricultural amendment, gypsum, and an overlying hardwood mulch layer on promoting denitrification within agricultural ditch sediments. We found significantly higher denitrification potentials in mulch (11.2 mg N-N m h) and mulch-gypsum cores (9.2 mg N-N m h) than in gypsum (1.3 mg N-N m h) or control cores (0.6 mg N-N m h). Higher denitrification rates corresponded with high dissolved organic C (DOC) fluxes within the mulch and mulch-gypsum treatments (72.8-115.2 mg m h) and were ultimately able to remove 65 to 69% of N loads. Results indicate DOC from overlying mulch additions to agricultural ditches significantly increase denitrification in intact cores and suggest that the addition of DOC sources in agricultural ditches may contribute a simple, low-cost option to reduce reactive N export and improve ecological outcomes within aquatic agroecosystems.

Anammox granule as new inoculum for start-up of anaerobic sulfide oxidation (ASO) process and its reverse start-up

The feasibility of implementing anaerobic ammonium oxidation (anammox) granules to start up high-loading anaerobic sulfide oxidation (ASO) in an upflow anaerobic sludge bed (UASB) reactor was investigated. An innovation method of the reverse start-up of anammox was also validated. Firstly, the reactor was operated to treat sulfide-rich wastewaters into which nitrite was introduced as an electron acceptor. An high-rate performance with sulfide and nitrate removal rates of 105.5 ± 0.11 kg S m^-3 d^-1 and 28.45 ± 3.40 kg N m^-3 d^-1, respectively, was accomplished. Sulfurovum were enriched with the increase of the substrate load and then conquered Candidatus Kuenenia to be the predominant bacteria. Excitation-emission matrix (EEM) spectroscopy showed that the intensities of fluorescence decreased and protein-like substrates were the main components associated with the process of start-up. FT-IR analysis found that the main functional groups indicator were O-H groups. Secondly, the reverse start-up of anammox (achieving 90% TN removal) was achieved immediately when the substrate changed. 16S rRNA analysis indicated the successfully enrichment of anammox bacteria (Candidatus Kuenenia). These results suggest that anammox granules can act as inoculum of high-loading ASO process and the reverse start-up provides a new perspective for the fast initiation of anammox process.

Denitrification and the controlling factors in Yunnan Plateau Lakes (China): Exploring the role of enhanced internal nitrogen cycling by algal blooms

Denitrification plays an important role in nitrogen (N) removal in freshwater ecosystems. This internal process regulates the fluctuations of N concentration, especially for lakes with high nutrients concentrations and long residence time. Lakes in Yunnan plateau (southwestern China) provide typical cases, while studies in this region have been rare. Therefore, we studied denitrification of two lakes (Lake Dianchi in hypereutrophic state and Lake Erhai in mesotrophic) in this region. We used acetylene inhibition technique to quantify potential denitrification rate (PDR) of these lakes in April and August, 2015 and 2016. PDR of the sediments ranged 0-1.21 μmol/(N·m²·hr), and that of overlying water ranged 0-0.24 μmol/(N·L·hr). Then, we used Least Angle Regression to determine the controlling factors for denitrification. Nutrients controlled PDR from two aspects: providing essential nitrogen sources; and affecting the richness and metabolism of denitrifying bacteria. In April, both aspects limited PDR; while only nitrogen sources limited PDR in August, due to depleted nitrate and enhanced denitrifying bacteria activity. Ammonia was most significant to denitrification, indicating that nitrate from nitrification transported to the bottom of well-mixed lake provide major N source by denitrification. The high PDR and low nitrate concentrate in August were evidence of an enhanced internal N cycling by algal blooms.

Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium

Respiratory ammonification and denitrification are two evolutionarily unrelated dissimilatory nitrogen (N) processes central to the global N cycle, the activity of which is thought to be controlled by carbon (C) to nitrate (NO3 -) ratio. Here we find that Intrasporangium calvum C5, a novel dual-pathway denitrifier/respiratory ammonifier, disproportionately utilizes ammonification rather than denitrification when grown under low C concentrations, even at low C:NO3 - ratios. This finding is in conflict with the paradigm that high C:NO3 - ratios promote ammonification and low C:NO3 - ratios promote denitrification. We find that the protein atomic composition for denitrification modules (NirK) are significantly cost minimized for C and N compared to ammonification modules (NrfA), indicating that limitation for C and N is a major evolutionary selective pressure imprinted in the architecture of these proteins. The evolutionary precedent for these findings suggests ecological importance for microbial activity as evidenced by higher growth rates when I. calvum grows predominantly using its ammonification pathway and by assimilating its end-product (ammonium) for growth under ammonium-free conditions. Genomic analysis of I. calvum further reveals a versatile ecophysiology to cope with nutrient stress and redox conditions. Metabolite and transcriptional profiles during growth indicate that enzyme modules, NrfAH and NirK, are not constitutively expressed but rather induced by nitrite production via NarG. Mechanistically, our results suggest that pathway selection is driven by intracellular redox potential (redox poise), which may be lowered when resource concentrations are low, thereby decreasing catalytic activity of upstream electron transport steps (i.e., the bc1 complex) needed for denitrification enzymes. Our work advances our understanding of the biogeochemical flexibility of N-cycling organisms, pathway evolution, and ecological food-webs.

Linking abundance and community of microbial N2O-producers and N2O-reducers with enzymatic N2O production potential in a riparian zone

As aquatic-terrestrial ecotones, riparian zones are hotspots not only for denitrification but also for nitrous oxide (N₂O) emission. Due to the potential role of nosZ II in N₂O mitigation, emerging studies in terrestrial ecosystems have taken this newly reported N₂O-reducer into account. However, our knowledge about the interactions between denitrification activities and both N₂O-producers and reducers (especially for nosZ II) in aquatic ecosystems remains limited. In this study, we investigated spatiotemporal distributions of in situ N₂O flux, potential N₂O production rate, and potential denitrification rate, as well as of the related genes in a riparian zone of Baiyangdian Lake. Real-time quantitative PCR (qPCR) and high-throughput sequencing targeted functional genes were used to analyze the denitrifier communities. Results showed that great differences in microbial activities and abundances were observed between sites and seasons. Waterward sediments (constantly flooded area) had the lowest N₂O production potential in both seasons. Not only the environmental factors (moisture content, NH₄⁺ content and TOM) but also the community structure of N₂O-producers and N₂O-reducers (nirK/nirS and nosZ II/nosZ I ratios) could affect the potential N₂O production rate. The abundance of the four functional genes in the winter was higher than in the summer, and the values all peaked at the occasionally flooded area in the winter. The dissimilarity in community composition was mainly driven by moisture content. Altogether, we propose that the N₂O production potential was largely regulated by the community structure of N₂O-producers and N₂O-reducers in riparian zones. Increasing the constantly flooded area and reducing the occasionally flooded area of lake ecosystems may help reduce the level of denitrifier-produced N₂O.

Effects of Urban Stormwater Control Measures on Denitrification in Receiving Streams

Urban areas are increasingly adopting the use of ecologically-based technologies for stormwater management to mitigate the effects of impervious surface runoff on receiving water bodies. While stormwater control measures (SCMs) reduce runoff, their ability to influence ecosystem function in receiving streams is not well known. To understand the effect of SCMs on net ecosystem function in stream networks, we measured sediment denitrification in four streams across a gradient of urban and suburban residential development in Charlotte, NC. We evaluated the influence of SCM inputs on actual (DNF) and potential (DEA) denitrification activity in stream sediments at the SCM-stream confluence to quantify microbial processes and the environmental factors that control them. DNF was variable across sites, ranging from 0–6.60 mg-N·m−2·h−1 and highly correlated with in-stream nitrate (NO3-N) concentrations. Sites with a greater impervious area showed a pattern of significantly higher DEA rates upstream of the SCM compared to downstream, while sites with less imperviousness showed the opposite trend. We hypothesize that this is because of elevated concentrations of carbon and nitrogen provided by pond and wetland outflows, and stabilization of the benthic habitat by lower peak discharge. These results suggest that SCMs integrated into the watershed have the potential to create cascading positive effects on in-stream nutrient processing and thereby improve water quality; however, at higher levels of imperviousness, the capacity for SCMs to match the scale of the impacts of urbanization likely diminishes.

Multi-Parameter Laser Imaging Reveals Complex Microscale Biofilm Matrix in a Thick (4,000 μm) Aerobic Methanol Oxidizing Community

Although methanol has frequently been used as an inexpensive supplementary carbon source to support treatment processes, knowledge of the resultant microbial biofilms, their 3D architecture, microenvironments, exopolymer chemistry and populations remains limited. We supplied methanol as a supplementary carbon source to biofilms developing in rotating annular reactors. Analysis of circulation waters (1.0 l d^-1) indicated that dissolved organic carbon was reduced by 25%, NO₃-nitrogen by 95%, and total phosphorus by 70%. Analyses of populations using culture based techniques and fluorescence in situ hybridization indicated enrichment of nitrifiers, denitrifiers, and methylotrophic bacteria relative to reference biofilms not receiving methanol. The biofilms that developed were up to 4,000 μm thick. Staining with fluor conjugated lectins in combination with nucleic acid stains, revealed the presence of discrete bacterial cells inside complex globular polymeric structures. These structures were in turn surrounded by an interstitial polymer containing a variety of bacterial cell types. The globular structures bound FITC-conjugated lectins, from Canavalia ensiformis and Ulex europeaus. The FITC-lectin of Phaseolus vulgaris bound the surface of the globular structures and more generally within the matrix. Chemical analyses of the polymer paralleled the results of lectin analyses indicating that the dominant neutral sugars were glucose, galactose, mannose, rhamnose, with fucose and ribose as minor constituents. Amino sugars were not detected. Dual channel imaging with pH sensitive probes indicated that pH gradients from pH 4 to 7 occurred across the globular microcolonies. Critically for the maintenance of aerobic conditions throughout the thick biofilm it was extensively penetrated by a fine fissure network revealed by the location of fluorescent latex microbeads as detected by confocal laser scanning microscopy. Microelectrode studies confirmed the absence of any detectable Eh gradients within the biofilm. However, mobility of various size-fractionated fluorescent probes indicated that the basal region was only penetrated by the lowest molecular weight probes with a hydrated radius of 2.2 nm or less. These observations indicate the selection of a unique, thick (>4,000 μm) microbial community in which a self-organized architecture promotes the maintenance of optimal conditions and metabolism throughout the biofilm community.

Spatial and temporal variations in the geochemistry of shallow groundwater contaminated with nitrate at a residential site

The concentrations of nitrate (NO₃^-), major ions, and dissolved inorganic carbon (DIC) and the stable carbon isotopes of DIC (δ¹³C_DIC) in shallow groundwater below a 45 × 60 m residential property was investigated over a period of 38 months. Our aim was to identify the processes which control the spatial and temporal distribution of NO₃^- in the shallow groundwater and assess water-rock interactions linked to denitrification. Groundwater sampled quarterly from eight locations showed an average NO₃^- concentration of 36.8 mg/L and a range between 0.1 and 214.9 mg/L compared to the US EPA maximum contaminant level of 10 mg/L. Heterogeneity in nitrate distribution was from residential application of N-based fertilizers offsite and from onsite application on flower beds and for lawn care. The temporal behavior of nitrate at all eight groundwater locations was markedly different and independent of seasonal hydrologic variations. Nitrate attenuation was spatially controlled by heterogeneous denitrification and rain dilution near roof drains. Groundwater locations with active denitrification were characterized by higher DIC concentrations and lower δ¹³C_DIC from organic carbon mineralization and by higher ionic concentrations from weathering of aquifer minerals. The variation in the relative standard deviations (RSD) of the measured parameters over space (RSD-s) and time (RSD-t) was highest for NO₃^- associated with variable spatiotemporal input and lowest for pH, pCO₂, and δ¹³C_DIC indirectly controlled by denitrification. Denitrification induced mineral weathering products such as DIC, Ca²⁺, Mg²⁺, and HCO₃^- showed medium to high RSD-s and RSD-t. The RSD-s and RSD-t were positively correlated (R² = 0.85) with the RSD-s showing approximately twofold higher magnitude than RSD-t due to greater variability between monitoring wells locations than variability at each groundwater location over time. Nitrate contamination and denitrification represent important long-term driver of aquifer weathering and changes in groundwater geochemistry below residential communities.

The Functioning of a Water Body Within a Fluvio-Lacustrine System as an Effect of Excessive Nitrogen Loading—The Case of Lake Symsar and its Drainage Area (Northeastern Poland)

Generally, in water ecosystems, it is assumed that rivers play a transport role. In turn, lakes have accumulation properties. However, in fluvio-lacustrine systems, each water body located on a river track can disrupt naturally occurring processes. One such process is the nitrogen cycle. An analysis of the nitrogen cycle, at both the global and local levels, is of extreme significance in view of the progressive degradation of aquatic ecosystems. In this study, we attempted to show that the specific properties of reservoirs located in river–lake systems contribute to an adequate reaction of these reservoirs to situations involving an excessive pollution load. Despite the intensive exchange of water in lakes, they were mainly shown to have an accumulation function. In particular, in those located in the lower part of the system, the total nitrogen load transported outside the example reservoir decreased by 4.3%. The role of these reservoirs depends on the morphometric, hydrologic, and meteorological conditions. The actual loading of the water body was shown to be more than double the permitted critical loading. The creation of conditions similar to those occurring in river–lake systems by, for example, delaying the outflow of water, may favor the protection of surface water from the last element of the system, because this limits the transport of pollutants. This study of the functioning and evolution of lakes’ fluvio-lacustrine systems, including the balance of the nutrient load, enables the prediction of the aquatic ecosystem’s responses in the future and their changes.

Acetylenotrophy: a hidden but ubiquitous microbial metabolism?

Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.

Estimating N2 O processes during grassland renewal and grassland conversion to maize cropping using N2 O isotopocules

RATIONALE

Enhanced nitrous oxide (N₂ O) emissions can occur following grassland break-up for renewal or conversion to maize cropping, but knowledge about N₂ O production pathways and N₂ O reduction to N₂ is very limited. A promising tool to address this is the combination of mass spectrometric analysis of N₂ O isotopocules and an enhanced approach for data interpretation.

METHODS

The isotopocule mapping approach was applied to field data using a δ¹⁵ N^sp_N2O and δ¹⁸ O_N2O map to simultaneously determine N₂ O production pathways contribution and N₂ O reduction for the first time. Based on the isotopic composition of N₂ O produced and literature values for specific N₂ O pathways, it was possible to distinguish: (i) heterotrophic bacterial denitrification and/or nitrifier denitrification and (ii) nitrification and/or fungal denitrification and the contribution of N₂ O reduction.

RESULTS

The isotopic composition of soil-emitted N₂ O largely resembled the known end-member values for bacterial denitrification. The isotopocule mapping approach indicated different effects of N₂ O reduction on the isotopic composition of soil-emitted N₂ O for the two soils under study. Differing N₂ O production pathways in different seasons were not observed, but management events and soil conditions had a significant impact on pathway contribution and N₂ O reduction. N₂ O reduction data were compared with a parallel ¹⁵ N-labelling experiment.

CONCLUSIONS

The field application of the isotopocule mapping approach opens up new prospects for studying N₂ O production and consumption of N₂ O in soil simultaneously based on mass spectrometric analysis of natural abundance N₂ O. However, further studies are needed in order to properly validate the isotopocule mapping approach.

Dramatic source-sink transition of N2O in the water level fluctuation zone of the Three Gorges Reservoir during flooding-drying processes

Biogeochemical cycling of nitrous oxide (N₂O), a significant greenhouse gas (GHG), can influence global climate change. The production and emission of N₂O mediated by hydrological regimes is particularly active in water level fluctuation zones (WLFZs). However, the hydrological mechanisms affecting N₂O transformation and production across the water-sediment micro-interface remain unclear. In this study, intact sediment cores from the WLFZs of the Three Gorges Reservoir (TGR) were incubated for 24 days in a laboratory microcosm to identify the effects of the flooding-drying processes on the yield and emission of N₂O. Results showed a source-sink transition of N₂O in the first 1.5 days during the flooding period, with the water column subsequently acting as a sink relative to the atmosphere in the following experimental period. The source-sink transition was ascribed to changes in oxygen concentration in the water column and sediment regulation of NO₃^--N transformation, resulting in denitrification and N₂O production. Preliminary estimates on the mass budget of N₂O in a typical WLFZs of the TGR showed slight emission fluxes, ranging from 13.08 to 43.08 μmol m^-2 from flooding period to drying process. Although these N₂O emissions were relatively low, the emission peak detected during the initial period (first 1.5 days) of the flooding phase provides important knowledge on the mitigation of GHG emissions from hydropower sources, which should be incorporated into future reservoir operations.

Controls on denitrification potential in nitrate-rich waterways and riparian zones of an irrigated agricultural setting

Denitrification, the microbial conversion of NO₃^- to N gases, is an important process contributing to whether lotic and riparian ecosystems act as sinks for excess NO₃^- from agricultural activities. Though agricultural waterways and riparian zones have been a focus of denitrification research for decades, almost none of this research has occurred in the irrigated agricultural settings of arid and semiarid climates. In this study, we conducted a broad survey of denitrification potential in riparian soils and channel sediments from 79 waterway reaches in the irrigated agricultural landscape of California's Central Valley. With this approach, we sought to capture the wide range of variation that arose from diverse waterway management and fluctuating flow conditions, and use this variation to identify promising management interventions. We explored associations of denitrification potentials with surface water NO₃^- -N, organic matter, flow conditions, vegetation cover, near-channel riparian bank slope, and channel geomorphic features using generalized linear mixed models. We found strong associations of sediment denitrification potentials with reach flow conditions, which we hypothesize was the result of variation in microbial communities' tolerance to dry-wet cycles. Denitrification potentials in riparian soils, in contrast, did not appear affected by flow conditions, but instead were associated with organic matter, vegetation cover, and bank slope in the riparian zone. These results suggest a strong need for further work on how denitrification responds to varying flow conditions and dry-wet cycles in non-perennial lotic ecosystems. Our findings also demonstrate that denitrifier communities respond to key features of waterway management, which can therefore be leveraged to control denitrification through a variety of management actions.

Mitigation of nitrous oxide emissions from acidic soils by Bacillus amyloliquefaciens, a plant growth-promoting bacterium

Nitrous oxide (N₂ O) is a long-lived greenhouse gas that can result in the alteration of atmospheric chemistry and cause accompanying changes in global climate. To date, many techniques have been used to mitigate the emissions of N₂ O from agricultural fields, which represent one of the most important sources of N₂ O. In this study, we designed a greenhouse pot experiment and a microcosmic serum bottle incubation experiment using acidic soil from a vegetable farm to study the effects of Bacillus amyloliquefaciens (BA) on plant growth and N₂ O emission rates. The addition of BA to the soil promoted plant growth enhanced the soil pH and increased the total nitrogen (TN) contents in the plants. At the same time, it decreased the concentrations of ammonium (NH₄⁺ ), nitrate (NO₃^- ) and TN in the soil. Overall, the addition of BA resulted in a 50% net reduction of N₂ O emissions compared with the control. Based on quantitative PCR and the network analysis of DNA sequencing, it was demonstrated that BA partially inhibited the nitrification process through the significant reduction of ammonia oxidizing bacteria. Meanwhile, it enhanced the denitrification process, mainly by increasing the abundance of N₂ O-reducing bacteria in the treatment with BA. The results of our microcosm experiment provided evidence that strongly supported the above findings under more strictly controlled laboratory conditions. Taken together, the results of our study evidently demonstrated that BA has dual effects on the promotion of plant growth and the dramatic reduction of greenhouse emissions, thus suggesting the possibility of screening beneficial microbial organisms from the environment that can promote plant growth and mitigate greenhouse trace gases.

Multi-scale measurements show limited soil greenhouse gas emissions in Kenyan smallholder coffee-dairy systems

Efforts have been made in recent years to improve knowledge about soil greenhouse gas (GHG) fluxes from sub-Saharan Africa. However, data on soil GHG emissions from smallholder coffee-dairy systems have not hitherto been measured experimentally. This study aimed to quantify soil GHG emissions at different spatial and temporal scales in smallholder coffee-dairy farms in Murang'a County, Central Kenya. GHG measurements were carried out for one year, comprising two cropping seasons, using vented static chambers and gas chromatography. Sixty rectangular frames were installed on two farms comprising the three main cropping systems found in the area: 1) coffee (Coffea arabica L.); 2) Napier grass (Pennisetum purpureum); and 3) maize intercropped with beans (Zea mays and Phaseolus vulgaris). Within these fields, chambers were allocated on fertilised and unfertilised locations to capture spatial variability. Cumulative annual fluxes in coffee plots ranged from 1 to 1.9kgN₂O-Nha^-1, 6.5 to 7.6MgCO₂-Cha^-1 and ^-3.4 to -2.2kgCH₄-Cha^-1, with 66% to 94% of annual GHG fluxes occurring during rainy seasons. Across the farm plots, coffee received most of the N inputs and had 56% to 89% higher emissions of N₂O than Napier grass, maize and beans. Within farm plots, two to six times higher emissions were found in fertilised hotspots - around the perimeter of coffee trees or within planted maize rows - than in unfertilised locations between trees, rows and planting holes. Background and induced soil N₂O emissions from fertiliser and manure applications in the three cropping systems were lower than hypothesized from previous studies and empirical models. This study supplements methods and underlying data for the quantification of GHG emissions at multiple spatial and temporal scales in tropical, smallholder farming systems. Advances towards overcoming the dearth of data will facilitate the understanding of synergies and tradeoffs of climate-smart approaches for low emissions development.