Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE

Organic acids released by submerged macrophytes with damaged leaves alter the denitrification microbial community in rhizosphere

Submerged macrophytes have important impacts on the denitrification and anaerobic ammonia-oxidizing (anammox) processes. Leaf damage in these plants probably changes the rhizosphere environment, affecting organic acid release and denitrifying bacteria. However, there is a lack of comprehensive understanding of the specific changes. This study investigated these changes in the rhizosphere of Potamogeton crispus with four degrees of leaf excision. When 0 %, 30 %, 50 % and 70 % of leaves were excised, the concentrations of total organic acid were 31.45, 32.67, 38.26, and 35.16 mg/L, respectively. The abundances of nirS-type denitrifying bacteria were 2.10 × 1010, 1.59 × 1010, 2.54 × 1010, and 4.67 × 1010 copies/g dry sediment, respectively. The abundances of anammox bacteria were 7.58 × 109, 4.59 × 109, 3.81 × 109, and 3.90 × 109 copies/g dry sediment, respectively. The concentration of total organic acids and the abundance of two denitrification microorganisms in the rhizosphere zone were higher than those in the root zone and non-rhizosphere zone. With increasing leaf damage, the number of OTUs in the Pseudomonas genus of nirS-type denitrifying bacteria first increased and then decreased, while that of the Thauera genus was relatively stable. The overall increase in the OTU number of anammox bacteria indicated that leaf damage promotes root exudates release, thereby leading to an increase in their diversity. The co-occurrence network revealed that the two denitrification microorganisms had about 60.52 % positive connections in rhizosphere while 64.73 % negative connections in non-rhizosphere. The abundance and community composition of both denitrification microorganisms were positively correlated with the concentrations of various substances such as oxalic acid, succinic acid, total organic acids and NO2--N. These findings demonstrate that submerged plant damage has significantly impacts on the structure of denitrification microbial community in the rhizosphere, which may alter the nitrogen cycling process in the deposit sediment. SYNOPSIS: This study reveals leaf damage of macrophyte changed the rhizosphere denitrification microbial community, which is helpful to further understand the process of nitrogen cycle in water.

Effects of O2 on accumulation of nitrous and elemental sulfur and microbial community structure in double short-cut sulfur autotrophic denitrification system

Understanding the effect of O2 on the accumulation characteristics of NO2--N and S0 in the sulfur autotrophic denitrification (DSSADN) system is crucial for enhancing the denitrification efficiency of partial nitrification-anammox using DSSADN. The results revealed that in an environment without O2 entry, the NO2--N accumulation efficiency (NiAE) and S0 accumulation efficiency (S0AE) of the DSSADN system reached 89.40 % and 93.41 %, respectively. Once system entered O2, ORP value kept increasing. When ORP increased to -59.9 mV (DO = 0.1 mg/L), soxB and nirK gene expression rose and as well NiAE and S0AE continuously decreased to 48.13 % and 29.35 %. When ORP was above 30.9 mV (DO >0.2 mg/L) but below 81.0 mV (DO<0.4 mg/L), narG gene expression reduced and the relatively high sqr gene expression allowed NiAE and S0AE remained at 45.08 % and 33.31 %. O2 promoted the synergistic effect of Thiobacillus and Azoarcus without the proliferation of nitrite oxidizing bacteria.

Biological treatment of N-methylpyrrolidone, cyclopentanone, and diethylene glycol monobutyl ether distilled residues and their effects on nitrogen removal in a full-scale wastewater treatment plant

Manufacturing processes in semiconductor and photonics industries involve the use of a significant amount of organic solvents. Recycle and reuse of these solvents produce distillate residues and require treatment before being discharged. This study aimed to evaluate the performance of the biological treatment system in a full-scale wastewater treatment plant that treats wastewater containing distillate residues from the recycling of electronic chemicals. Batch experiments were conducted to investigate the optimal operational conditions for the full-scale wastewater treatment plant. To achieve good nitrogen removal efficiency with effluent ammonia and nitrate concentrations below 20 mg N/L and 50 mg N/L, respectively, it was suggested to control the ammonia concentration and pH of the influent below 500 mg N/L and 8.0, respectively. In addition, the biodegradability of N-methylpyrrolidone, diethylene glycol monobutyl ether, and cyclopentanone distillate residues from the electronic chemicals manufacturing process were evaluated under aerobic, anoxic, and anaerobic conditions. N-methylpyrrolidone and cyclopentanone distillate residues were suggested to be treated under anoxic condition. However, substrate inhibition occurred when using cyclopentanone distillate residue as a carbon source with chemical oxygen demand (COD) levels higher than 866 mg/L and nitrate levels higher than 415 mg N/L. Under aerobic condition, the COD from both N-methylpyrrolidone and cyclopentanone distillate residues could be easily degraded. Nevertheless, a negative effect on nitrification was observed, with a prolonged lag time for ammonia oxidation as the initial COD concentration increased. The specific ammonia oxidation rate and nitrate production rate decreased under high COD concentration contributed by N-methylpyrrolidone and cyclopentanone distillate residues. Furthermore, the biodegradability of diethylene glycol monobutyl ether distillate residue was found to be low under aerobic, anoxic, and anaerobic conditions. With respect to the abundance of nitrogen removal microorganisms in the wastewater treatment plant, results showed that Comammox may have an advantage over ammonia oxidizing bacteria under high pH conditions. In addition, Comammox may have higher resistance to environmental changes. Dominance of Comammox over ammonia oxidizing bacteria under high ammonia condition was first reported in this study.

Pyric herbivory decreases soil denitrification despite increased nitrate availability in a temperate grassland

Pyric herbivory, the combination of controlled burning and targeted grazing, is an effective strategy for restoring abandoned, shrub-encroached rangelands to open ecosystems. This practice may impact soil nitrogen pools by altering soil nitrification and denitrification rates, and may lead to an increase of nitrogen losses through nitrate leaching and N-gas emissions. This research, located in the south-western Pyrenees, investigated the effects of pyric herbivory on soil nitrification and denitrification potentials and mineral nitrogen content in a gorse-encroached temperate rangeland six months after the burning was implemented. The study included three treatments: high-severity burning plus grazing, low-severity burning plus grazing, and unburned and ungrazed areas (control). We measured soil nitrification and denitrification potentials (net and gross), the limitation of denitrifiers by nitrogen or organic carbon, and the abundance of nitrite- and nitrous oxide-reducing bacteria. Additional soil and vegetation data complemented these measurements. Results showed that pyric herbivory did not significantly affect nitrification potential, which was low and highly variable. However, it decreased gross denitrification potential and nitrous oxide reduction to dinitrogen in high-severely burned areas compared to the control. Denitrification rates directly correlated with microbial biomass nitrogen, soil organic carbon, soil water content and abundance of nirS-harbouring bacteria. Contrary to the expected, soil nitrate availability did not directly influence denitrification despite being highest in burned areas. Overall, the study suggests that pyric herbivory does not significantly affect mid-term nitrification rates in temperate open ecosystems, but may decrease denitrification rates in intensely burned areas. These findings highlight the importance of assessing the potential impacts of land management practices, such as pyric herbivory, on soil nutrient cycling and ecosystem functioning.

Machine Learning-Assisted Optimization of Mixed Carbon Source Compositions for High-Performance Denitrification

Appropriate mixed carbon sources have great potential to enhance denitrification efficiency and reduce operational costs in municipal wastewater treatment plants (WWTPs). However, traditional methods struggle to efficiently select the optimal mixture due to the variety of compositions. Herein, we developed a machine learning-assisted high-throughput method enabling WWTPs to rapidly identify and optimize mixed carbon sources. Taking a local WWTP as an example, a mixed carbon source denitrification data set was established via a high-throughput method and employed to train a machine learning model. The composition of carbon sources and the types of inoculated sludge served as input variables. The XGBoost algorithm was employed to predict the total nitrogen removal rate and microbial growth, thereby aiding in the assessment of the denitrification potential. The predicted carbon sources exhibited an enhanced denitrification potential over single carbon sources in both kinetic experiments and long-term reactor operations. Model feature analysis shows that the cumulative effect and interaction among individual carbon sources in a mixture significantly enhance the overall denitrification potential. Metagenomic analysis reveals that the mixed carbon sources increased the diversity and complexity of denitrifying bacterial ecological networks in WWTPs. This work offers an efficient method for WWTPs to optimize mixed carbon source compositions and provides new insights into the mechanism behind enhanced denitrification under a supply of multiple carbon sources.

Enhanced nitrogen removal by an isolated aerobic denitrifying strain in a vertical-flow constructed wetland

The addition of bacterial agents is an effective method for improving nitrogen removal from wetlands. Herein, an aerobic denitrifier, RC-15, was added to a vertical-flow constructed wetland (CW), and the presence of functional genes and microbial communities was investigated at different CW depths. For the RC-15-treated CW, the removal of NO3- and TN during the process was significantly greater than in the control. Quantitative PCR revealed that nirS is a dominant denitrifying gene for treating WWTP tailwater. Moreover, the presence of the RC-15 strain significantly enhanced the abundance of the napA gene and nirK gene in the CWs. The napA gene was concentrated in the upper layer of the CWs, and the nirK gene was concentrated in the middle and bottom layers. Compared to the control, the addition of the bacterial agent Trial resulted in a more diverse denitrification pathway, a greater abundance of 16Sr RNA, and a greater number of denitrifying strains. According to the microbial community analysis, Proteobacteria and Chloroflexi dominated denitrification in the CWs. Greater abundances of Thauera, Aeromonas and Ardenticatenales were found at the genus level, indicating that these genera have potential applications in future nitrogen removal projects.

Mineral and organic fertilisation influence ammonia oxidisers and denitrifiers and nitrous oxide emissions in a long-term tillage experiment

Nitrous oxide (N2O) emissions from different agricultural systems have been studied extensively to understand the mechanisms underlying their formation. While a number of long-term field experiments have focused on individual agricultural practices in relation to N2O emissions, studies on the combined effects of multiple practices are lacking. This study evaluated the effect of different tillage [no-till (NT) vs. conventional plough tillage (CT)] in combination with fertilisation [mineral (MIN), compost (ORG), and unfertilised control (CON)] on seasonal N2O emissions and the underlying N-cycling microbial community in one maize growing season. Rainfall events after fertilisation, which resulted in increased soil water content, were the main triggers of the observed N2O emission peaks. The highest cumulative emissions were measured in MIN fertilisation, followed by ORG and CON fertilisation. In the period after the first fertilisation CT resulted in higher cumulative emissions than NT, while no significant effect of tillage was observed cumulatively across the entire season. A higher genetic potential for N2O emissions was observed under NT than CT, as indicated by an increased (nirK + nirS)/(nosZI + nosZII) ratio. The mentioned ratio under NT decreased in the order CON > MIN > ORG, indicating a higher N2O consumption potential in the NT-ORG treatment, which was confirmed in terms of cumulative emissions. The AOB/16S ratio was strongly affected by fertilisation and was higher in the MIN than in the ORG and CON treatments, regardless of the tillage system. Multiple regression has revealed that this ratio is one of the most important variables explaining cumulative N2O emissions, possibly reflecting the role of bacterial ammonia oxidisers in minerally fertilised soil. Although the AOB/16S ratio aligned well with the measured N2O emissions in our experimental field, the higher genetic potential for denitrification expressed by the (nirK + nirS)/(nosZI + nosZII) ratio in NT than CT was not realized in the form of increased emissions. Our results suggest that organic fertilisation in combination with NT shows a promising combination for mitigating N2O emissions; however, addressing the yield gap is necessary before incorporating it in recommendations for farmers.

Biostimulation with oxygen and electron donors supports micropollutant biodegradation in an experimentally simulated nitrate-reducing aquifer

The availability of suitable electron donors and acceptors limits micropollutant natural attenuation in oligotrophic groundwater. This study investigated how electron donors with different biodegradability (humics, dextran, acetate, and ammonium), and different oxygen concentrations affect the biodegradation of 15 micropollutants (initial concentration of each micropollutant = 50 μg/L) in simulated nitrate reducing aquifers. Tests mimicking nitrate reducing field conditions showed no micropollutant biodegradation, even with electron donor amendment. However, 2,4-dichlorophenoxyacetic acid and mecoprop were biodegraded under (micro)aerobic conditions with and without electron donor addition. The highest 2,4-dichlorophenoxyacetic acid and mecoprop biodegradation rates and removal efficiencies were obtained under fully aerobic conditions with amendment of an easily biodegradable electron donor. Under microaerobic conditions, however, amendment with easily biodegradable dissolved organic carbon (DOC) inhibited micropollutant biodegradation due to competition between micropollutants and DOC for the limited oxygen available. Microbial community composition was dictated by electron acceptor availability and electron donor amendment, not by micropollutant biodegradation. Low microbial community richness and diversity led to the absence of biodegradation of the other 13 micropollutants (such as bentazon, chloridazon, and carbamazepine). Finally, adaptation and potential growth of biofilms interactively determined the location of the micropollutant removal zone relative to the point of amendment. This study provides new insight on how to stimulate in situ micropollutant biodegradation to remediate oligotrophic groundwaters as well as possible limitations of this process.

Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments

In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).

Removal efficiency and abundance of nitrogen cycling microorganism in three bio-matrix materials to treat swine wastewater

A bio-matrix material (BMM) system is used to pretreat swine wastewater and reduce the nitrogen (N) concentration to the tolerance range of plants in constructed wetlands. In this study, rice straw (RS), wheat straw (WS), and corn stalk (CS) were applied to treat pollutants from swine wastewater, respectively. This one year-long field experiment make up for the lack of long-term experiments and mechanistic investigations of BMM. The pollutant removal efficiency, degradation process of crop straw, and the abundance of nitrogen cycling genes were determined in different BMM systems. The results showed that the removal efficiency of COD, TN, NH4+, and NO3- was the best in the initial 6 months. Furthermore, RS and WS exhibited favorable annual removal efficiency of TN and NH4+, which were 32.81% and 32.99%, 35.3% and 34.97%, respectively. Moreover, the removal efficiency of COD was 30.81% in three BMM systems. Meanwhile, it was found that the dry matter (DM) degradation of crop straws was fast in the first 4-5 months. The degradation rates of cellulose, hemicellulose, and lignin were 94.19%, 94.36%, and 87.32%, respectively, in 1 year. The abundance of nitrogen cycling genes significantly increased by adding BMM, compared with CK (P < 0.05). This showed the abundance of the hzsB gene in RS was the highest, while nirK, nirS, AOA, and AOB were the highest in WS. The addition of RS and WS was better than that of CS in promoting the abundance of nitrogen cycling microorganisms. The results indicated that adding BMM could enhance the anaerobic ammonia oxidation, nitrification, and denitrification. This study not only extends our comprehension of BMM mechanisms in swine wastewater treatment but also serves as a guiding light for numerous farms in similar climate regions.

Regulation of nitrite-dependent anaerobic methane oxidation bacteria by available phosphorus and microbial communities in lake sediments of cold and arid regions

As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH4 consumption in lake sediments. However, there is a dearth of knowledge regarding the effects of anthropogenic activities on N-DAMO bacteria in lakes in the cold and arid regions. Sediment samples were collected from five sampling areas in Lake Ulansuhai at varying depth ranges (0-20, 20-40, and 40-60 cm). The ecological characterization and niche differentiation of N-DAMO bacteria were investigated using bioinformatics and molecular biology techniques. Quantitative PCR confirmed the presence of N-DAMO bacteria in Lake Ulansuhai sediments, with 16S rRNA gene abundances ranging from 1.72 × 104 to 5.75 × 105 copies·g-1 dry sediment. The highest abundance was observed at the farmland drainage outlet with high available phosphorus (AP). Anthropogenic disturbances led to a significant increase in the abundance of N-DAMO bacteria, though their diversity remained unaffected. The heterogeneous community of N-DAMO bacteria was affected by interactions among various environmental characteristics, with AP and oxidation-reduction potential identified as the key drivers in this study. The Mantel test indicated that the N-DAMO bacterial abundance was more readily influenced by the presence of the denitrification genes (nirS and nirK). Network analysis revealed that the community structure of N-DAMO bacteria generated numerous links (especially positive links) with microbial taxa involved in carbon and nitrogen cycles, such as methanogens and nitrifying bacteria. In summary, N-DAMO bacteria exhibited sensitivity to both environmental and microbial factors under various human disturbances. This study provides valuable insights into the distribution patterns of N-DAMO bacteria and their roles in nitrogen and carbon cycling within lake ecosystems.

Single and Combined Effects of Phenanthrene and Silver Nanoparticles on Denitrification Processes in Coastal Marine Sediments

The increasing production and utilization of polycyclic aromatic hydrocarbons (PAHs) and commercial silver nanoparticles (AgNPs) have raised concerns about their potential environmental release, with coastal sediments as a substantial sink. To better understanding the effects of these contaminants on denitrification processes in coastal marine sediments, a short-term exposure simulation experiment was conducted. We investigated the effects of single and combined contamination of phenanthrene (Phe) and AgNPs on denitrification processes in a coastal marine sediment. Results showed that all contaminated treatment groups had different degrees of inhibitory effect on denitrification activity, denitrifying enzyme activity, total bacteria count and denitrifying genes. The inhibitory effect sequence of each treatment group was combined treatment > AgNPs treatment > Phe treatment. Moreover, the inhibitory effects of denitrifying genes were much larger than that of total bacteria count, indicating that the pollutants had specific toxic effects on denitrifying bacteria. The sequence of sensitivity of three reduction process to pollutants was N2O > NO2- > NO3-. All contaminated treatment groups could increase NO3-, NO2- and N2O accumulation. Furthermore, according to the linear relationship between functional gene or reductase and denitrification process, we also found that the abundance of denitrifying genes could better predict the influence of Phe and AgNPs on sediment denitrification than the denitrifying bacterial diversity. In addition, at the genus level, the community structure of nirS- and nosZ-type denitrifying bacteria changed dramatically, while changes at the phylum level were comparatively less pronounced. Single and combined contamination of Phe and AgNPs could reduce the dominance of Pseudomonas, which may lead to a potential slow-down in the degradation of Phe and inhibition of denitrification, especially the combined contamination. Overall, our study revealed that combined contamination of Phe and AgNPs could lead to an increase in NO3-, NO2- and N2O accumulation in coastal sediment, which poses a risk of eutrophication in coastal areas, exacerbates the greenhouse effect and has adverse effects on global climate change.

Mycorrhizosphere bacteria inhibit greenhouse gas emissions from microplastics contaminated soil by regulating soil enzyme activities and microbial community structure

Microplastics (MPs) accumulation in terrestrial ecosystems can affect greenhouse gases (GHGs) production by altering microbial and soil structure. Presently, research on the MPs effect on plants is not consistent, and underlying molecular mechanisms associated with GHGs are yet unknown. For the first time, we conducted a microcosm study to explore the impact of MPs addition (Raw vs. aged) and Trichoderma longibrachiatum and Bacillus subtilis inoculation (Sole vs. combination) on GHGs emission, soil community structure, physiochemical properties, and enzyme activities. Our results indicated that the addition of aged MPs considerably enhanced the GHGs emissions (N2O (+16%) and CO2 (+21%), respectively), C and N cycling gene expression, microbial biomass carbon, and soil physiochemical properties than raw MPs. However, the soil microbial community structure and enzyme activities were enhanced in raw MPs added treatments, irrespective of the MPs type added to soil. However, microbial inoculation significantly reduced GHGs emission by altering the expression of C and N cycling genes in both types of MPs added treatments. The soil microbial community structure, enzymes activities, physiochemical properties and microbial biomass carbon were enhanced in the presence of microbial inoculation in both type of MPs. Among sole and combined inoculation of Trichoderma and Bacillus subtilis, the co-applied Trichoderma and Bacillus subtilis considerably reduced the GHGs emission (N2O (-64%) and CO2 (-61%), respectively) by altering the expression of C and N cycling genes regardless of MPs type used. The combined inoculation also enhanced soil enzyme activities, microbial community structure, physiochemical properties and microbial biomass carbon in both types of MPs treatment. Our findings provide evidence that polyethylene MPs likely pose a high risk of GHGs emission while combined application of Trichoderma and Bacillus subtilis significantly reduced GHGs emission by altering C and N cycling gene expression, soil microbial community structure, and enzyme activities under MPs pollution in a terrestrial ecosystem.

Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.

Effects of multi-plant harvesting on nitrogen removal and recovery in constructed wetlands

The harvesting of plants is considered an effective method for nutrient recovery in constructed wetlands (CWs). However, excessive plant harvesting can lead to a decrease in plant biomass. It remains unclear what harvesting frequency can optimize plant nutrient uptake and pollutant removal. In this study, CWs planted with Myriophyllum aquaticum were constructed, and three different frequencies of plant harvesting (high: 45 days/time; low: 90 days/time; none: CK) were set to investigate nitrogen removal and its influencing mechanism, as well as the capacity for plant nutrient recovery. The results showed that the average removal efficiencies of ammonia nitrogen (NH4+-N) at 45 days/time, 90 days/time, and CK were 90.3%, 90.8%, and 88.3% respectively, while the corresponding total nitrogen (TN) were 61.2%, 67.4%, and 67.4%. Dissolved oxygen (DO) concentration and water temperature were identified as the main environmental factors affecting nitrogen removal efficiency. Low harvest frequency (90 days/time) increased DO concentration and NH4+-N removal efficiency without impacting TN removal. Additionally, TN recovery from plants under high and low harvest was found to be approximately 9.21-9.32 times higher than that from no harvest conditions. The above studies indicated that a harvest frequency of every 90 days was one appropriate option for M. aquaticum, which not only increased NH4+-N removal efficiencies but also facilitated more efficient nitrogen recovery from the wetland system.

Diversity, community structure, and abundance of nirS-type denitrifying bacteria on suspended particulate matter in coastal high-altitude aquaculture pond water

Denitrifying bacteria harboring the nitrate reductase S (nirS) gene convert active nitrogen into molecular nitrogen, and alleviate eutrophication in aquaculture water. Suspended particulate matter (SPM) is an important component of aquaculture water and a carrier for denitrification. SPM with different particle sizes were collected from a coastal high-altitude aquaculture pond in Maoming City, China. Diversity, community structure, abundance of nirS-type denitrifying bacteria on SPM and environmental influencing factors were studied using high-throughput sequencing, fluorescence quantitative PCR, and statistical analysis. Pseudomonas, Halomonas, and Wenzhouxiangella were the dominant genera of nirS-type denitrifying bacteria on SPM from the ponds. Network analysis revealed Pseudomonas and Halomonas as the key genera involved in the interaction of nirS-type denitrifying bacteria on SPM in the ponds. qPCR indicated a trend toward greater nirS gene abundance in progressively larger SPM. Dissolved oxygen, pH, temperature, and SPM particle size were the main environmental factors influencing changes in the nirS-type denitrifying bacterial community on SPM in coastal high-altitude aquaculture pond water. These findings increase our understanding of the microbiology of nitrogen cycle processes in aquaculture ecosystem, and will help optimize aquatic tailwater treatment strategies.

Effect of tillage state of paddy soils with heavy metal pollution on the nosZ gene of N2O reductase

Paddy soils are an important source of atmospheric nitrous oxide (N2O). However, numerous studies have focused on N2O production during the soil tillage period, neglecting the N2O production during the dry fallow period. In this study, we conducted an incubation experiment using the acetylene inhibition technique to investigate N2O emission and reduction rates of paddy soil profiles (0-1 m) from Guangdong Province and Jinlin Province in China, with different heavy-metal pollution levels. The abundance and community structures of denitrifying bacteria were determined via quantitative-PCR and Illumina MiSeq sequencing of nosZ, nirK, and nirS genes. Our results showed that the potential N2O emission rate, N2O production rate, and denitrification rate have decreased with increasing soil vertical depth and heavy-metal pollution. More importantly, we found that the functional gene type of N2O reductase switched with the tillage state of paddy soils, which clade Ⅱ nosZ genes were the dominant gene during the tillage period, while clade Ⅰ nosZ genes were the dominant gene during the dry fallow period. The heavy-metal pollution has less effect on the niche differentiation of the nosZ gene. The N2O emission rate was significantly regulated by the genus Bradyhizobium, which contains both N2O reductase and nitrite reductase genes. Our findings suggests that the nosZ gene of N2O reductase can significantly impact the N2O emission from paddy soils.

Effects of microplastics on N2O production and reduction potential in crop soils of northern China

Microplastics (MPs) pollution are found to be increasing in vegetable soils and potentially affecting N2O production and their associated pathways; however, its specific effects remain unclear. Here, we selected two common MPs, PE and PP at four different concentration levels of 0, 0.5, 1.5 and 3%, and conducted several incubation experiments aiming to explore soil bacterial and fungal N2O production. Results showed that the bacteria were the main contributors for the production of N2O, regardless of the absence or presence of MPs; and its contribution was decreased with increasing concentrations of PE and PP. The nosZ clade I and II genes were positively correlated with N2O reduction rates, indicating a combined regulation on soil N2O reduction. PE significantly inhibited the bacterial nitrification and denitrification, but did not affect the total N2O production rates; while PP significantly reduced both the bacterial and fungal N2O production rates. The resistance of fungal N2O production to MPs pollution was stronger than that of the bacterial N2O production. It highlights that the MPs pollution could reduce the potential of N2O production and reduction, and thus disturb soil nitrogen cycling system; while the inhibition on N2O production via bacteria and fungi varies with different types of MPs. This study is conducive to an improved and more comprehensive understanding of the ecological impacts of MPs within the agroecosystem.

Effects of the three amendments on NH3 volatilization, N2O emissions, and nitrification at four salinity levels: An indoor experiment

The marked salinity and alkaline pH of coastal saline soil profoundly impact the nitrogen conversion process, leading to a significantly reduced nitrogen utilization efficiency and substantial gaseous nitrogen loss. The application of soil amendments (e.g. biochar, manure, and gypsum) was proved to be effective for the remediation of saline soils. However, the effects of the three amendments on soil nitrogen transformation in soils with various salinity levels, especially on NH3 volatilization and N2O emission, remain elusive. Here, we reported the effects of biochar, manure, and gypsum on NH3 volatilization and N2O emission under four natural salinity gradients in the Yellow River Delta. Also, high-throughput sequencing and qPCR analysis were performed to characterize the response of nitrification (amoA) and denitrification (nirS, nirK, and nosZ) functional genes to the three amendments. The results showed that the three amendments had little effect on NH3 volatilization in low- and moderate-salinity soils, while biochar stimulated NH3 volatilization in high-salinity soils and reduced NH3 volatilization in severe-salinity soils. Spearman correlation analysis demonstrated that AOA was significantly and positively correlated with the NO3--N content (r = 0.137, P < 0.05) and N2O emissions (r = 0.174, P < 0.01), which indicated that AOA dominated N2O emissions from nitrification in saline soils. Structural equation modeling indicated that biochar, manure, and gypsum affected N2O emission by influencing soil pH, conductivity, mineral nitrogen content, and functional genes (AOA-amoA and nosZ). Two-way ANOVA further showed that salinity and amendments (biochar, manure, and gypsum) had significant effects on N2O emissions. In summary, this study provides valuable insights to better understand the effects of gaseous N changes in saline soils, thereby improving the accuracy and validity of future GHG emission predictions and modeling.

Microbial, chemical, and isotopic monitoring integrated approach to assess potential leachate contamination of groundwater in a karstic aquifer (Apulia, Italy)

Landfill sites are subjected to long-term risks of accidental spill of leachate through the soil and consequential contamination of the groundwater. Wide areas surrounding the landfill can seriously be threatened with possible consequences to human health and the environment. Given the potential impact of different coexisting anthropic pollution sources (i.e., agriculture and cattle farming) on the same site, the perturbation of the groundwater quality may be due to multiple factors. Therefore, it is a challenging issue to correctly establish the pollution source of an aquifer where the landfill is not isolated from other anthropic land uses, especially in the case of a karstic coastal aquifer. The present study is aimed at setting in place an integrated environmental monitoring system that included microbiological, chemical, and isotope methods to evaluate potential groundwater pollution in a landfill district in the south of Italy located in Murgia karstic aquifer. Conventional (microbial plate count and physical-chemical analyses) and advanced methods (PCR-ARISA, isotope analysis of δ18O, δ2H, 3H, δ 13C, δ 15N-NO3-, and δ 18O-NO3-) were included in the study. Through data integration, it was possible to reconstruct a scenario in which agriculture and other human activities along with seawater intrusion in the karst aquifer were the main drivers of groundwater pollution at the monitored site. The microbiological, chemical, and isotope results confirmed the absence of leachate effects on groundwater quality, showing the decisive role of fertilizers as potential nitrate sources. The next goal will be to extend long-term integrated monitoring to other landfill districts, with different geological and hydrogeological characteristics and including different sources of pollution, to support the ecological restoration of landfills.

Unveiling the nitrogen and phosphorus removal potential: Comparative analysis of three coastal wetland plant species in lab-scale constructed wetlands

It is well accepted that tidal wetland vegetation performs a significant amount of water filtration for wetlands. However, there is currently little information on how various wetland plants remove nitrogen (N) and phosphorus (P) and how they differ in their denitrification processes. This study compared and investigated the denitrification and phosphorus removal effects of three typical wetland plants in the Yangtze River estuary wetland (Phragmites australis, Spartina alterniflora, and Scirpus mariqueter), as well as their relevant mechanisms, using an experimental laboratory-scale horizontal subsurface flow constructed wetland (CW). The results showed that all treatment groups with plants significantly reduced N pollutants as compared to the control group without plants. In comparison to S. mariqueter (77.2-83.2%), S. alterniflora and P. australis had a similar total nitrogen (TN)removal effectiveness of nearly 95%. With a removal effectiveness of over 99% for ammonium nitrogen (NH4+-N), P. australis outperformed S. alterniflora (95.6-96.8%) and S. mariqueter (94.6-96.5%). The removal of nitrite nitrogen (NO2--N)and nitrate nitrogen (NO3--N)from wastewater was significantly enhanced by S. alterniflora compared to the other treatment groups. Across all treatment groups, the removal rate of PO43--P was greater than 95%. P. australis and S. alterniflora considerably enriched more 15N than S. mariqueter, according to the results of the 15N isotope labeling experiment. While the rhizosphere and bulk sediments of S. alterniflora were enriched with more simultaneous desulfurization-denitrification bacterial genera (such as Paracoccus, Sulfurovum, and Sulfurimonas), which have denitrification functions, the rhizosphere and bulk sediments of P. australis were enriched with more ammonia-oxidizing archaea and ammonia-oxidizing bacteria. As a result, compared to the other plants, P. australis and S. alterniflora demonstrate substantially more significant ability to remove NH4+-N and NO2--N/NO3--N from simulated domestic wastewater.

Study of bacterial population dynamics in seed culture developed for ammonia reduction from synthetic wastewater

The waterbodies have been polluted by various natural and anthropogenic activities. The aquatic waste includes ammonia as one of the most toxic pollutants. Several biological treatment systems involving anoxic and semi anoxic bacteria have been proposed for reducing nitrogen loads from wastewater and increasing the efficiency and cost effectiveness. These bacteria play a vital role in the processes involved in the nitrogen cycle in nature. However, the enrichment, sustainability and identification of bacterial communities for wastewater treatment is an important aspect. Most of the chemolithotrophs are unculturable hence their identification and measurement of abundance remains a challenging task. In this study the different bacteria involved in total nitrogen removal from the wastewater are enriched for 700 days under anoxic condition. The synthetic wastewater containing 0.382 g/L of ammonium chloride was used. Molecular identification of the bacteria involved in various steps of the nitrogen cycle was carried out based on amplification of functional genes and 16S rRNA gene Polymerase chain reaction followed by DNA sequencing. Change in the abundance of chemolithotrophs was studied using qPCR. The mutual growth of various nitrifiers along with anaerobic bacteria were identified by molecular characterisation of DNA at various time intervals with the different genes involved in the nitrogen cycle. Nitrosomonas species like Nitrosomonas europaea were identified throughout the batch scale studies possessing the genes associated with ammonia oxidizing bacteria and nitrite oxidizing bacteria which act as a complete ammonia oxidizer. The uncultured species of Nitrospira and anammox bacteria were also observed which predicts the coexistence of the anammox and comammox bacteria in a batch scale study. The coexistence of the semi anoxic and anoxic bacteria helped in the growth of these bacteria for a longer duration of time. The nitrite produced by the comammox during nitrification can be utilized by anammox as an electron carrier. The other species of denitrifiers like Pseudomonas denitrificans and Aminobacter aminovorans were also observed. It is concluded that the enrichment of semi anoxic and anoxic bacteria was faster with the increase in growth of the bacteria involved in nitrification, comammox, anammox and partial denitrification process. The bacterial growth is enhanced and the efficiency is increased which can be further used in the development of small pilot scale bioreactor for total nitrogen removal.

Mitigation of soil N2O emissions by decomposed straw based on changes in dissolved organic matter and denitrifying bacteria

The return of decomposed straw represents a less explored potential option for reducing N2O emissions. However, the mechanisms underlying the effects of decomposed straw return on soil N2O mitigation are still not fully clear. Therefore, we used a helium atmosphere robotized continuous flow incubation system to compare the soil N2O and N2 emissions from four treatments: CK (control: no straw), WS (wheat straw), IWS (wheat straw decomposed with Irpex lacteus), and PWS (wheat straw decomposed with Phanerochaete chrysosporium). All the treatments have been fertilized with the same amount of KNO3. Furthermore, we also analyzed i) the chemodiversity of soil dissolved organic matter (DOM), ii) the nirS, nirK, and nosZ gene copies and relative abundances of denitrifying bacterial communities (DBCs), and iii) the specific linkages between N2O emissions and DOM and DBC. The results showed that the WS, IWS and PWS treatments increased N2O emissions compared to the CK treatment. However, applying decomposed straw to soil, especially straw treated with P. chrysosporium, effectively decreased the soil N2O and increased N2 emissions compared to WS and IWS. Moreover, the IWS and PWS treatments increased the CHO composition, but they decreased the CHON and CHOS compositions of heteroatomic compounds of DOM compared with the WS and CK treatments. Furthermore, the WS, IWS and PWS treatments all significantly increased the nirS and nosZ gene copies compared with the CK treatment. Additionally, compared with the other treatments, the PWS treatment significantly shaped the DBC and led to a higher relative abundance of Pseudomonas with nirS and nosZ genes. Meanwhile, Network analysis showed that the mitigation of N2O was closely related to particular DOM molecules, and specific DBC taxa. These results highlight the potential for decomposed straw amendments to mitigate of soil N2O emissions not only by changing soil DOM but also mediating the soil DBC.

Stimulation of primed carbon under climate change corresponds with phosphorus mineralization in the rhizosphere of soybean

Elevated CO2 and temperature likely alter photosynthetic carbon inputs to soils, which may stimulate soil microbial activity to accelerate the decomposition of soil organic carbon (SOC), liberating more phosphorus (P) into the soil solution. However, this hypothesis on the association of SOC decomposition and P transformation in the plant rhizosphere requires robust soil biochemical evidence, which is critical to nutrient management for the mitigation of soil quality against climate change. This study investigated the microbial functional genes relevant to P mineralization together with priming processes of SOC in the rhizosphere of soybean grown under climate change. Soybean plants were grown under elevated CO2 (eCO2, 700 ppm) combined with warming (+ 2 °C above ambient temperature) in open-top chambers. Photosynthetic carbon flow in the plant-soil continuum was traced with 13CO2 labeling. The eCO2 plus warming treatment increased the primed carbon (C) by 43 % but decreased the NaHCO3-extratable organic P by 33 %. Furthermore, NaHCO3-Po was negatively correlated with phosphatase activity and microbial biomass C. Elevated CO2 increased the abundances of C degradation genes, such as abfA and ManB, and P mineralization genes, such as gcd, phoC and phnK. The results suggested that increased photosynthetic carbon inputs to the rhizosphere of plants under eCO2 plus warming stimulated the microbial population and metabolic functions of both SOC and organic P mineralization. There is a positive relationship between the rhizosphere priming effect and P mineralization. The response of microorganisms to plant-C flow is decisive for coupled C and P cycles, which are likely accelerated under climate change.

Effects of nitrification and urease inhibitors on ammonia-oxidizing microorganisms, denitrifying bacteria, and greenhouse gas emissions in greenhouse vegetable fields

Soil microorganisms and N cycling are important components of biogeochemical cycling processes. In addition, the study of the effects of nitrification and urease inhibitors on N and microorganisms in greenhouse vegetable fields is essential to reducing N loss and greenhouse gas emissions. The effects of nitrification inhibitors [2-chloro-6-(trichloromethyl) pyridine (CP), dicyandiamide (DCD)], and urease inhibitor [N-(n-butyl) thiophosphoric triamide (NBPT)] on soil inorganic N (NH4+-N, NO2--N and NO3--N) concentrations and the production rates of greenhouse gases (N2O, CH4, and CO2) in greenhouse vegetable fields were investigated via indoor incubation experiments. Polymerase chain reaction amplification and high-throughput sequencing technology (Illumina Miseq) were used to explore the community structure and abundance changes of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and denitrifying bacteria (nirK and nirS). The results showed that CP and DCD obviously inhibited NH4+-N conversion, and NO2--N, and NO3--N accumulation, NBPT slowed down urea hydrolysis and NH4+-N production, and the apparent nitrification rates of soil were in the following order: NBPT > DCD > DCD + NBPT > CP + NBPT > CP. Compared with urea treatment, the peak N2O production rate of inhibitor treatment decreased by 73.30-99.30%, and the production rate of CH4 and CO2 decreased by more than 66.16%. DCD and CP reduced the abundance of AOA and AOB, respectively. Furthermore, NBPT hindered the growth of ammonia-oxidizing microorganisms and nirS-type denitrifying bacteria, and urea and nitrification inhibitors were detrimental to the growth of Ensifer and Sinorhizobium in the nirK community. Nitrification and urease inhibitors can effectively slow down nitrification and greenhouse gas emissions, reduce N loss and improve soil quality by inhibiting the growth of ammonia-oxidizing microorganisms and denitrifying bacteria.

Effect of different types of volatile fatty acids on the performance and bacterial population in a batch reactor performing biological nutrient removal

Different ratios of four volatile fatty acids (VFAs) were used as the primary feed to a laboratory scale biological nutrient reactor during four operational stages. The reactor performed efficiently over 500 days of operation with over 90% dissolved phosphorus and over 98% ammonium-nitrogen (NH4+-N) removal. Through in the first experimental phase, acetate and propionate were present in a significant proportion as carbon sources, the relative abundance of Candidatus Accumulibacter, a potential polyphosphate accumulating organism, increased from 10% to 57% and the Defluviicoccus genus, a known glycogen accumulating organism (GAO), decreased from 41% to 5%. Further tests indicated the presence of denitrifying phosphorus accumulating organisms (DPAO) belonging to Clade IIC, that could use nitrite as the electron acceptor during P-uptake. In general, VFAs favored the increase of the genus Defluviicoccus and Candidatus Accumulibacter. High relative abundance of Defluviicoccus did not affect the stability and the performance of the BNR process.

Effects of tillage patterns and stover mulching on N2O production, nitrogen cycling genes and microbial dynamics in black soil

Stover-covered no-tillage (NT) is of great significance to the rational utilization of stover resources and improvement of cultivated land quality, and also has a profound impact on ensuring groundwater, food and ecosystem security. However, the effects of tillage patterns and stover mulching on soil nitrogen turnover remain elusive. Based on the long-term conservation tillage field experiment in the mollisol area of Northeast China since 2007, the shotgun metagenomic sequencing of soils and microcosm incubation were combined with physical and chemical analyses, alkyne inhibition analysis to elucidate the regulatory mechanisms of NT and stover mulching on the farmland soil nitrogen emissions and microbial nitrogen cycling genes. Compared with conventional tillage (CT), NT stover mulching significantly reduced the emission of N2O instead of CO2, especially when 33% mulching was adopted, and correspondingly the nitrate nitrogen of NT33 was higher than that of other mulching amounts. The stover mulching was associated with higher total nitrogen, soil organic carbon and pH. The abundance of AOB (ammonia-oxidizing bacteria)-amoA (ammonia monooxygenase subunit A) was substantially increased by stover mulching, while the abundance of denitrification genes was reduced in most cases. Under alkyne inhibition, the tillage mode, treatment time, gas condition and interactions between them noticeably influenced the N2O emission and nitrogen transformation. In CT, NT0 (no mulching) and NT100 (full mulching), the relative contribution of AOB to N2O production was markedly higher than that of ammonia oxidizing archaea. Different tillage modes were associated with distinct microbial community composition, albeit NT100 was closer to CT than to NT0. Compared with CT, the co-occurrence network of microbial communities was more complex in NT0 and NT100. Our findings suggest that maintaining a low-quantity stover mulching could regulate soil nitrogen turnover toward proficiently enhancing soil health and regenerative agriculture, and coping with global climate change.

Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities

Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.

Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes

Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.

Relationships between environmental factors and N-cycling microbes reveal the indirect effect of further eutrophication on denitrification and DNRA in shallow lakes

Traditional views indicate that eutrophication and subsequent algal blooms favor denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in lake ecosystems. However, lakes tend to show an increasing propensity for inorganic nitrogen (N) limitation as they become more eutrophic. Thus, the influence of further eutrophication on denitrification and DNRA in eutrophic lakes are unclear due to the uncertainty of N availability. To fill this gap, we investigated the genes abundance (AOA, AOB, nirS, nirK and nrfA) and the composition of N-cycling microbes through quantitative PCR and 16S rRNA sequencing analysis, respectively, in 15 shallow eutrophic lakes of the Yangtze-Huaihe River basin, China. The results indicated that denitrification and DNRA rates could be modulated mainly by their functional gene abundances (nirS, nirK and nrfA), followed by the environmental factors (sediment total organic carbon and nitrogen). Denitrification rates significantly increased from slightly to highly eutrophic lakes, but DNRA rates were not. An explanation is that nitrification provided ample nitrate for denitrification, and this cooperative interaction was indicated by the positive correlation of their gene abundances. In addition, Pseudomonas and Anaeromyxobacter was the dominant genus mediated denitrification and DNRA, showing the potential to perform facultative anaerobic and strict anaerobic nitrate reduction, respectively. High level of dissolved oxygen might favor the facultatively aerobic denitrifiers over the obligately anaerobic fermentative DNRA bacteria in these shallow lakes. Chlorophyll a had a weak but positive effect on the gene abundances for nitrification (AOA and AOB). Further eutrophication had an indirect effect on denitrification and DNRA rates through modulating the genes abundances of N-cycling microbes.

Dynamics of Benthic Nitrate Reduction Pathways and Associated Microbial Communities Responding to the Development of Seasonal Deoxygenation in a Coastal Mariculture Zone

Intensive mariculture activities result in eutrophication and enhance coastal deoxygenation. Deoxygenation profoundly influences nitrate reduction processes and further the fate of nitrogen (N) in coastal systems. Herein, 15N isotope labeling, real-time PCR, and high-throughput sequencing techniques were jointly used to investigate the participation and seasonal dynamics of sediment nitrate reduction pathways and the succession of functional microbial communities during the development of seasonal deoxygenation in a coastal aquaculture zone. Denitrification dominated benthic nitrate reduction (46.26-80.91%). Both denitrification and dissimilatory nitrate reduction to ammonium were significantly enhanced by summer deoxygenation (dissolved oxygen levels fell to 2.94 ± 0.28 mg L-1), while anammox remained unchanged. The abundance of the nitrous oxide reductase gene nosZ increased during deoxygenation. The community of the nosZ gene was sensitive to deoxygenation, with Azospirillum and Ruegeria accounting for the majority. Pelobacter was overwhelming in the nrfA gene (encoding dissimilatory nitrite reductase) community, which was less affected by deoxygenation. The variations of benthic nitrate reduction processes were driven by bottom water oxygen combined with temperature, chlorophyll a, and microbial gene abundances and community compositions. Our results implicated that seasonal oxygen-deficient zones could be substantial N sinks of coastal ecosystems and important for N balance. Effective management measures need to be developed to avoid further exacerbation of coastal deoxygenation and maintain the sustainable development of mariculture.

Implemented impediment of extracellular electron transfer-dependent anammox process :Unstable nitrogen removal efficiency and decreased abundance of anammox bacteria

The present study investigates the extracellular electron transfer (EET)-dependent anammox process as a promising approach for sustainable wastewater treatment. The study examines the performance and metabolic pathway of the EET-dependent anammox process in comparison to the nitrite-dependent anammox process. The EET-dependent reactor successfully achieved nitrogen removal with a maximum removal efficiency of 93.2%, although it exhibited a lower ability to sustain high nitrogen removal load when compared to the nitrite-dependent anammox process, which poses opportunity and challenge for ammonia-wastewater treatment under applied voltage conditions. Nitrite was identified as a critical factor responsible for the changes in microbial community structure, resulting in a significant reduction in nitrogen removal load in the absence of nitrite. The study further suggests that the Candidatus Kuenenia species could dominate the EET-dependent anammox process, while nitrifying and denitrifying bacteria also contribute to the nitrogen removal in this system.

Coupling of soil methane emissions at different depths under typical coastal wetland vegetation types

As an important source of atmospheric methane, methane emissions from coastal wetlands are affected by many factors. However, the methane emission process and interrelated coupling mechanisms in coastal wetland soils of a variety of environments remain unclear owing to complex interactions between intensified anthropogenic activities and climate change in recent years. In this study, we investigated methane cycling processes and the response mechanisms of environmental and microbial factors in soils at different depths under four typical coastal wetland vegetation types of the Yellow River Delta, China, using laboratory culture and molecular biology techniques. Our results show that methane generation pathways differed among the different soil layers, and that the methane emission process has a special response to soil N compounds (NO3-, NH4+). We found that nitrogen can indirectly affect methane emission by impacting key physicochemical properties (pH, oxidation reduction potential, etc.) and some functional communities (mcrA, ANME-2d, sulfate-reducing bacteria (SRB), narG, nosZII). Methane production processes in shallow soils compete closely with sulfate reduction processes, while methane emissions facilitated in deeper soils due to denitrification processes. We believe that our results provide a reference for future research and wetland management practices that seek to mitigate the global greenhouse effect and climate change.

Promoting heterotrophic denitrification of Pseudomonas hunanensis strain PAD-1 using pyrite: A mechanistic study

Denitrification is critical for removing nitrate from wastewater, but it typically requires large amounts of organic carbon, which can lead to high operating costs and secondary environmental pollution. To address this issue, this study proposes a novel method to reduce the demand for organic carbon in denitrification. In this study, a new denitrifier, Pseudomonas hunanensis strain PAD-1, was obtained with properties for high efficiency nitrogen removal and trace N2O emission. It was also used to explore the feasibility of pyrite-enhanced denitrification to reduce organic carbon demand. The results showed that pyrite significantly improved the heterotrophic denitrification of strain PAD-1, and optimal addition amount was 0.8-1.6 g/L. The strengthening effect of pyrite was positively correlated with carbon to nitrogen ratio, and it could effectively reduce demand for organic carbon sources and enhance carbon metabolism of strain PAD-1. Meanwhile, the pyrite significantly up-regulated electron transport system activity (ETSA) of strain PAD-1 by 80%, nitrate reductase activity by 16%, Complex III activity by 28%, and napA expression by 5.21 times. Overall, the addition of pyrite presents a new avenue for reducing carbon source demand and improving the nitrate harmless rate in the nitrogen removal process.

Carbon source shaped microbial ecology, metabolism and performance in denitrification systems

The limited information on microbial interactions and metabolic patterns in denitrification systems, especially those fed with different carbon sources, has hindered the establishment of ecological linkages between microscale connections and macroscopic reactor performance. In this work, denitrification performance, metabolic patterns, and ecological structure were investigated in parallel well-controlled bioreactors with four representative carbon sources, i.e., methanol, glycerol, acetate, and glucose. After long-term acclimation, significant differences were observed among the four bioreactors in terms of denitrification rates, organic utilization, and heterotrophic bacterial yields. Different carbon sources induced the succession of denitrifying microbiota toward different ecological structures and exhibited distinct metabolic patterns. Methanol-fed reactors showed distinctive microbial carbon utilization pathways and a more intricate microbial interaction network, leading to significant variations in organic utilization and metabolite production compared to other carbon sources. Three keystone taxa belonging to the Verrucomicrobiota phylum, SJA-15 order and the Kineosphaera genus appeared as network hubs in the methanol, glycerol, and acetate-fed systems, playing essential roles in their ecological functions. Several highly connected species were also identified within the glucose-fed system. The close relationship between microbial metabolites, ecological structures, and system performances suggests that this complex network relationship may greatly contribute to the efficient operation of bioreactors.

Nitrogen removal in freshwater sediments of riparian zone: N-loss pathways and environmental controls

The riparian zone is an important location of nitrogen removal in the terrestrial and aquatic ecosystems. Many studies have focused on the nitrogen removal efficiency and one or two nitrogen removal processes in the riparian zone, and less attention has been paid to the interaction of different nitrogen transformation processes and the impact of in situ environmental conditions. The molecular biotechnology, microcosm culture experiments and 15N stable isotope tracing techniques were used in this research at the riparian zone in Weinan section of the Wei River, to reveal the nitrogen removal mechanism of riparian zone with multi-layer lithologic structure. The results showed that the nitrogen removal rate in the riparian zone was 4.14-35.19 μmol·N·kg-1·h-1. Denitrification, dissimilatory reduction to ammonium (DNRA) and anaerobic ammonium oxidation (anammox) jointly achieved the natural attenuation process of nitrogen in the riparian zone, and denitrification was the dominant process (accounting for 59.6%). High dissolved organic nitrogen and nitrate ratio (DOC:NO3-) would promote denitrification, but when the NO3- content was less than 0.06 mg/kg, DNRA would occur in preference to denitrification. Furthermore, the abundances of functional genes (norB, nirS, nrfA) and anammox bacterial 16S rRNA gene showed similar distribution patterns with the corresponding nitrogen transformation rates. Sedimentary NOX-, Fe(II), dissolved organic carbon (DOC) and the nitrogen transformation functional microbial abundance were the main factors affecting nitrogen removal in the riparian zone. Fe (II) promoted NO3- attenuation through nitrate dependent ferrous oxidation process under microbial mediation, and DOC promotes NO3- attenuation through enhancing DNRA effect. The results of this study can be used for the management of the riparian zone and the prevention and control of global nitrogen pollution.

Linking denitrification and pesticide transformation potentials with community ecology and groundwater discharge in hyporheic sediments in a lowland stream

Contamination of rivers by nitrate and pesticides poses a risk for aquatic ecosystems in lowland catchments that are often intensively used for agriculture. Here, the hyporheic zone, the streambed underneath the stream, plays a vital role due to its efficient self-purification capacity. The present study aims to evaluate the denitrification and transformation potential of 14 pesticides and three transformation products in the hyporheic sediment from a lowland stream with a high N load and by comparing an agricultural straightened section to a natural meandering part of the stream influenced by different groundwater discharges. Batch experiments were set up to evaluate the denitrification and pesticide transformation potentials in hyporheic sediment from two depths (5-15 cm (a) and 15-25 cm (b)). Our results revealed that (i) differences between the agricultural and natural sections of the river did not influence pollutant attenuation, (ii) both the nitrate and pesticide attenuation processes were more rapid in the upper "a" layer compared to the "b" layer due to higher microbial abundance, (iii) high groundwater discharge reduced the denitrification potential while pesticide transformation was unaffected, (iv) denitrification correlated with denitrifier abundance (nirK) in the "b" layer, while this correlation was not seen in the "a" layer, and (v) a microbial community with low diversity can explain limited transformation for the majority of tested pesticides. Overall, our results suggest that high groundwater discharge zones with reduced residence time in the hyporheic zone can be an important source of pesticides and nitrate to surface water.

An In Silico Analysis of Synthetic and Natural Compounds as Inhibitors of Nitrous Oxide Reductase (N2OR) and Nitrite Reductase (NIR)

Nitrification inhibitors are recognized as a key approach that decreases the denitrification process to inhibit the loss of nitrogen to the atmosphere in the form of N2O. Targeting denitrification microbes directly could be one of the mitigation approaches. However, minimal attempts have been devoted towards the development of denitrification inhibitors. In this study, we aimed to investigate the molecular docking behavior of the nitrous oxide reductase (N2OR) and nitrite reductase (NIR) involved in the microbial denitrification pathway. Specifically, in silico screening was performed to detect the inhibitors of nitrous oxide reductase (N2OR) and nitrite reductase (NIR) using the PatchDock tool. Additionally, a toxicity analysis based on insecticide-likeness, Bee-Tox screening, and a STITCH analysis were performed using the SwissADME, Bee-Tox, and pkCSM free online servers, respectively. Among the twenty-two compounds tested, nine ligands were predicted to comply well with the TICE rule. Furthermore, the Bee-Tox screening revealed that none of the selected 22 ligands exhibited toxicity on honey bees. The STITCH analysis showed that two ligands, namely procyanidin B2 and thiocyanate, have interactions with both the Paracoccus denitrificans and Hyphomicrobium denitrificans microbial proteins. The molecular docking results indicated that ammonia exhibited the second least atomic contact energy (ACE) of -15.83 kcal/mol with Paracoccus denitrificans nitrous oxide reductase (N2OR) and an ACE of -15.20 kcal/mol with Hyphomicrobium denitrificans nitrite reductase (NIR). The inhibition of both the target enzymes (N2OR and NIR) supports the view of a low denitrification property and suggests the potential future applications of natural/synthetic compounds as significant nitrification inhibitors.

Effects of grazing prohibition on nirK- and nirS-type denitrifier communities in salt marshes

Introduction

Grazing prohibition is an effective management practice to restore salt marsh functioning. However, the effects of grazing exclusion on denitrifying microbial communities and their controlling factors in salt marshes remain unclear.

Methods

In this study, we surveyed soil physicochemical properties and above- and below-ground biomass and using quantitative polymerase chain reaction and Illumina MiSeq high-throughput sequencing technology to determine the relative abundance, composition, and diversity of nitrite reductase nirS- and nirK-type denitrifying bacterial communities associated with grazing prohibition treatments and elevations.

Results

The abundance of nirS-type denitrifiers increased with grazing prohibition time, whereas the abundance of nirK-type denitrifiers remained unaltered. Moreover, nirS-type denitrifiers were more abundant and diverse than nirK-type denitrifiers in all treatments. Grazing prohibition significantly altered the operational taxonomic unit richness, abundance-based coverage estimator, and Chao1 indices of the nirS-type denitrifying bacterial communities, whereas it only minimally affected the structure of the nirK-type denitrifying bacterial community.

Discussion

The results imply that the nirS community, rather than nirK, should be the first candidate for use as an indicator in the process of salt marsh restoration after grazing prohibition. Substances of concern, total nitrogen, and salinity were the key environmental factors affecting the abundance and community composition of nirS and nirK denitrifiers. The findings of this study provide novel insights into the influence of the length of grazing prohibition and elevation on nirS- and nirK-type denitrifying bacterial community composition in salt marshes.

Mill dams impact microbiome structure and depth distribution in riparian sediments

Introduction

Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function.

Methods

Here, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States.

Results

We found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes (amoA for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes (nosZ) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification.

Discussion

Lateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects.

Denitrification contributes to N2O emission in paddy soils

Denitrification is vital to nitrogen removal and N₂O release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying mechanism of N₂O emission from denitrification in paddy soils is yet to be elucidated. In this study, the potential N₂O emission rate, enzymatic activity for N₂O production and reduction, gene abundance, and community composition during denitrification were investigated using the ¹⁵N isotope tracer technique combined with slurry incubation, enzymatic activity detection, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. Results of incubation experiments showed that the average potential N₂O emission rates were 0.51 ± 0.20 μmol⋅N⋅kg^-1⋅h^-1, which constituted 2.16 ± 0.85% of the denitrification end-products. The enzymatic activity for N₂O production was 2.77-8.94 times than that for N₂O reduction, indicating an imbalance between N₂O production and reduction. The gene abundance ratio of nir to nosZ from qPCR results further supported the imbalance. Results of metagenomic analysis showed that, although Proteobacteria was the common phylum for denitrification genes, other dominant community compositions varied for different denitrification genes. Gammaproteobacteria and other phyla containing the norB gene without nosZ genes, including Actinobacteria, Planctomycetes, Desulfobacterota, Cyanobacteria, Acidobacteria, Bacteroidetes, and Myxococcus, may contribute to N₂O emission from paddy soils. Our results suggest that denitrification is highly modular, with different microbial communities collaborating to complete the denitrification process, thus resulting in an emission estimation of 13.67 ± 5.44 g N₂O⋅m^-2⋅yr^-1 in surface paddy soils.

NosZ-II-type N2O-reducing bacteria play dominant roles in determining the release potential of N2O from sediments in the Pearl River Estuary, China

The microbial reduction of N₂O serves as a "gatekeeper" for N₂O emissions, determining the flux of N₂O release into the atmosphere. Estuaries are active regions for N₂O emissions, but the microbial functions of N₂O-reducing bacteria in estuarine ecosystems are not well understood. In this study, the ¹⁵N isotope tracer method, qPCR, and high-throughput sequencing were used to analyze N₂O production, reduction, and emission processes in surface sediments of the Pearl River Estuary. The ¹⁵N isotope tracer experiment showed that the N₂O production rates declined and the N₂O reduction potential (R_r, the ratio of N₂O reduction rates to N₂O production rates) increased from upstream to downstream of the Pearl River Estuary, leading to a corresponding decrease of the N₂O emission rates from upstream to downstream. The gene abundance ratio of nosZ/nir gradually increased from upstream to downstream and was negatively correlated with the water N₂O saturation. The gene abundance of nosZ II was significantly higher than that of nosZ I in the estuary, and the nosZ II/nosZ I abundance ratio was positively correlated with N₂O reduction potential. Furthermore, the community composition of NosZ-I- and NosZ-II-type N₂O-reducing bacteria shifted from upstream to downstream. NosZ-II-type N₂O-reducing bacteria, especially Myxococcales, Thiotrichales, and Gemmatimonadetes species, contributed to the high N₂O reduction potential in the downstream. Our results suggest that NosZ-II-type N₂O-reducing bacteria play a dominant role in determining the release potential of N₂O from sediments in the Pearl River Estuary. This study provides a new insight into the function of microbial N₂O reduction in estuarine ecosystems.

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.

Relationships between denitrification rates and functional gene abundance in a wetland: The roles of single- and multiple-species plant communities

Wetland soil denitrification removes excess inorganic nitrogen (N) and prevents eutrophication in aquatic ecosystems. Wetland plants have been considered the key factors determining the capacity of wetland soil denitrification to remove N pollutants in aquatic ecosystems. However, the influences of various plant communities on wetland soil denitrification remain unknown. In the present study, we measured variations in soil denitrification under different herbaceous plant communities including single Phragmites karka (PK), single Paspalum thunbergia (PT), single Zizania latifolia (ZL), a mixture of Paspalum thunbergia plus Phragmites karka (PTPK), a mixture of Paspalum thunbergia plus Zizania latifolia (PTZL), and bare soil (CK) in the Estuary of Nantiaoxi River, the largest tributary of Qingshan Lake in Hangzhou, China. The soil denitrification rate was significantly higher in the surface (0-10 cm) than the subsurface (10-20 cm) layer. Wetland plant growth increased the soil denitrification rate by significantly increasing the soil water content, nitrate concentration, and ln(nirS) + ln(nirK). A structural equation model (SEM) showed that wetland plants indirectly regulated soil denitrification by altering the aboveground and belowground plant biomass, nitrate concentration, abundances of denitrifying functional genes, and denitrification potential. There was no significant difference in soil denitrification rates among PT, PK and ZL. The soil denitrification rate was significantly lower in PTZL than PTPK. Two-plant communities did not necessarily enhance the denitrification rate compared to single planting, the former had a greater competitiveness on N uptake and consequently reduced the amount of nitrate available for denitrification. As PTPK had the highest denitrification rate, co-planting P. thunbergia and P. karka could effectively improve N removal efficiency and help mitigate eutrophication in adjacent aquatic ecosystems. The results of this investigation provide useful information guiding the selection of appropriate wetland herbaceous plant species for wetland construction and the removal of N pollutants in aquatic ecosystems.

Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures

Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (C_u) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing C_u. However, oxygen diffusion into the system was controlled by SD rather than C_u. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.

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.

Responses of Nitrous Oxide Emissions and Bacterial Communities to Experimental Freeze–Thaw Cycles in Contrasting Soil Types

Nitrous oxide (N2O) pulse emissions are detected in soils subjected to freeze–thaw cycles in both laboratory and field experiments. However, the mechanisms underlying this phenomenon are poorly understood. In this study, a laboratory incubation experiment that included freeze–thaw cycles (FTC), freezing (F) and control (CK) treatments was performed on three typical Chinese upland soils, namely, fluvo-aquic soil (FS), black soil (BS) and loess soil (LS). A higher similarity in soil properties and bacterial community structure was discovered between FS and LS than between FS and BS or LS and BS, and the bacterial diversity of FS and LS was higher than that of BS. FTC significantly increased the denitrification potential and the proportion of N2O in the denitrification gas products in FS and LS but decreased the denitrification potential in BS. Accordingly, with the increasing number of freeze–thaw cycles, the bacterial community composition in the FTC treatments in FS and LS diverged from that in CK but changed little in BS. Taxa that responded to FTC or correlated with denitrification potential were identified. Taken together, our results demonstrated that the effects of FTC on N2O emissions are soil-type-dependent and that the shift in the microbial community structure may contribute to the elevated N2O emissions.

Elevated atmospheric CO2 concentrations caused a shift of the metabolically active microbiome in vineyard soil

BACKGROUND

Elevated carbon dioxide concentrations (eCO₂), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO₂ enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO₂ or ambient CO₂ (aCO₂).

RESULTS

Diversity indices and redundancy analysis (RDA) demonstrated that eCO₂ changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO₂. Moreover, under eCO₂ conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N₂ fixation and NO₂^- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO₂ conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions.

CONCLUSIONS

The results of this study demonstrate that eCO₂ concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.