Denitrification Genes Research Articles

Selective enrichment of high-affinity clade II N2O-reducers in a mixed culture

Abstract Microorganisms encoding for the N2O reductase (NosZ) are the only known biological sink of the potent greenhouse gas N2O, and are central to global N2O mitigation efforts. Clade II NosZ populations are of particular biotechnological interest as they usually feature high N2O affinities and often lack other denitrification genes. We focus on the yet-unresolved ecological constraints selecting for different N2O-reducers strains, and controlling the assembly of N2O-respiring communities. Two planktonic N2O-respiring mixed cultures were enriched at low dilution rates under limiting and excess dissolved N2O availability to assess the impact of substrate affinity and N2O cytotoxicity, respectively. Genome-resolved metaproteomics was used to infer the metabolism of the enriched populations. Under N2O limitation, clade II N2O-reducers fully outcompeted clade I affiliates, a scenario previously only theorized based on pure-cultures. All enriched N2O-reducers encoded and expressed the sole clade II NosZ, while also possessing other denitrification genes. Two Azonexus and Thauera genera affiliates dominated the culture, and we hypothesize their coexistence to be explained by the genome-inferred metabolic exchange of cobalamin intermediates. Under excess N2O, clade I and II populations coexisted, yet proteomic evidence suggests that clade II affiliates respired most of the N2O, de facto outcompeting clade I affiliates. The single dominant N2O-reducer (genus Azonexus) notably expressed most cobalamin biosynthesis marker genes, likely to contrast the continuous cobalamin inactivation by dissolved cytotoxic N2O concentrations (400 μM). Ultimately, our results strongly suggest the solids dilution rate to play a pivotal role in controlling the selection among NosZ clades, albeit the conditions selecting for genomes possessing the sole nosZ remain elusive. We furthermore highlight the potential significance of N2O-cobalamin interactions in shaping the composition of N2O-respiring microbiomes.

Mechanism of nitrous oxide emission reduction in constructed wetlands based on plant harvesting management.

The impact of plant harvesting on nitrous oxide (N2O) emission reduction in constructed wetlands (CWs) remains uncertain. This study focused on the Myriophyllum aquaticum wetland treating swine wastewater, with three different plant harvesting frequencies implemented: high harvesting (HF), low harvesting (LF), and no harvesting (CK). Results showed that compared to CK, cumulative N2O emissions decreased by 7.4 % (HF) and 18.5 % (LF), with only LF showing a significant reduction. The primary reductions in N2O emissions occurred during winter and summer, accounting for 26.2 %∼39.7 % and 14.0 %∼49.2 % of the total reductions, respectively. Crucial contributors to mitigating N2O emissions included water redox potential, sediment dissolved organic carbon, and ammonia nitrogen levels. Additionally, increased denitrification gene abundance in harvesting treatments reduced N2O emissions. These findings suggest that low-frequency plant harvesting, particularly in winter and summer, can significantly reduce N2O emissions from CWs.

Enhancing compost quality: Biochar and zeolite's role in nitrogen transformation and retention.

This research evaluated how addition of biochar and zeolite affected nitrogen transformation and retention during the composting of kitchen waste. Four treatments, control (CK), 10% biochar (B), 10% zeolite (Z), and 5% biochar +5% zeolite (BZ) were used to study nitrogen transformation and retention. The results showed that biochar and zeolite can significantly reduce the loss of NH4+-N during the thermophilic phase (CK: 42.6%, B: 35.1%, Z: 35.7%, and BZ: 31.3%). Network analysis showed that biochar and zeolite increased the number of microorganisms associated with nitrification genes while decreasing the number of microorganisms associated with denitrification genes, preventing nitrogen volatilization in N2O. Mantel tests further demonstrated that biochar and zeolite enhanced the correlation between bacterial communities and the relationship between NH4+-N, NO3--N, and organic nitrogen was weakened, thus inhibiting the mineralization of organic nitrogen. Therefore, biochar and zeolite played an active role in promoting the transformation and retention of nitrogen components. Biochar and zeolite for kitchen waste also provided a new perspective on the treatment of kitchen waste.

Diversified crop rotations exert a profound influence on the nosZI denitrifier community.

Agricultural soils are a significant contributor to global nitrous oxide (N2O) emissions, which is primarily driven by microbial nitrification and denitrification processes. Diversifying crop rotations can enhance soil nitrogen (N) utilization and influence N-cycling microbes, particularly the denitrifiers. Here, we evaluated the abundance, diversity, and community structure of soil denitrifiers by analyzing the denitrification genes (nirS, nirK, and nosZI) with a 14-year experiment of continuous and rotated crop systems. Compared to continuous cotton (C), crop rotations altered abundance of the nirS, nirK, and nosZI genes, but the responses varied among different rotation patterns (p<0.05). Diversified crop rotations decreased Shannon index of the nirS and nirK gene communities, while increased that of the nosZI gene communities. Diversified crop rotations greatly changed community structure of the nirS, nirK and nosZI gene communities (p<0.05). Among the responsive operational taxonomic units (OTUs), 2.62%, 2.52%, and 4.31% of the nirS, nirK, and nosZI genes were involved in the responses, respectively. Notably, a significant increase in OTUs belonged to N-fixing groups (i.e., Herbaspirillum and Rhodanobacter), while a decrease in OTUs affiliated to Achromobacter and Bosea was observed in diversified crop rotations. Furthermore, soil pH and C/N ratio correlated significantly with the nirS gene community structure (p<0.05), SOC and C/N ratio correlated with the nirK gene community (p<0.05), and soil pH, TN, NO3--N, and C/N ratio correlated with the nosZI gene community (p<0.05), respectively. In conclusion, our study demonstrates that long-term diversified crop rotations significantly altered the microbial communities related to denitrification, especially the nosZI gene community. These findings highlight the importance of diversified crop rotations in fostering soil denitrifiers communities that contribute to N₂O reduction, potentially supporting sustainable agricultural practices by reducing greenhouse gas emissions. However, future studies should be focus on both the nosZI and nosZII clades communities to offer a more complete picture of microbial contributions to soil N-cycling and N2O emission reduction.

Tire Wear Particles Exposure Enhances Denitrification in Soil by Enriching Labile DOM and Shaping the Microbial Community.

Tire wear particles (TWP) are emerging contaminants in the soil environment due to their widespread occurrence and potential threat to soil health. However, their impacts on soil biogeochemical processes remain unclear. Here, we investigated the effects of TWP at various doses and their leachate on soil respiration and denitrification using a robotized continuous-flow incubation system in upland soil. Fourier transform ion cyclotron resonance mass spectrometry and high-throughput sequencing were employed to elucidate the mechanisms underpinning the TWP effects. We show that TWP increased soil CO2, N2, and N2O emissions, which were attributed to the changes in content and composition of soil dissolved organic matter (DOM) induced by TWP and their leachate. Specifically, the labile DOM components (H/C ≥ 1.5 and transformation >10), which were crucial in shaping the denitrifying community, were significantly enriched by TWP exposure. Furthermore, the abundances of denitrification genes (nirK/S and nosZ-I) and the specific denitrifying genera Pseudomonas were increased following TWP exposure. Our findings provide new insights into impacts of TWP on carbon and nitrogen cycling in soil, highlighting that TWP exposure may exacerbate greenhouse gas emissions and fertilizer N loss, posing adverse effects on soil fertility in peri-urban areas and climate change mitigation.

Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation.

Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH4), and nitrous oxide (N2O) fluxes. Soil CO2 emission increased (doubling from approximately 200 mg C m-2 h-1), while CH4 emissions decreased (from 200 µg C m-2 h-1 to slightly negative) following land use changes. The N2O emissions in the oil palm plantation reached approximately 1,510 µg N m-2 h-1, significantly higher than previous land uses. The CH4 fluxes were driven by groundwater table, humification levels, and C:N ratio, with Methanomicrobia populations dominating methanogenesis and Methylocystis as the main CH4 oxidizer. The N2O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant nirK-type denitrifiers (13-fold nir to nosZ) and a minor role by nitrification (a threefold increase in amoA) in the plantation. Proteobacteria and Acidobacteria encoding incomplete denitrification genes potentially impact N2O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.IMPORTANCETropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation efforts and proper land management practices.

Lanthanum and cerium added to soil influence microbial carbon and nitrogen cycling genes

The soil microbiome plays an important role in carbon (C) and nitrogen (N) processing and storage and is influenced by rare earth elements (REEs), which can have both direct and indirect effects on plant metabolic processes. Using conventional physicochemical methods and metagenomic-based analyses, we investigated REEs effects on soil respiration, soil mineral N, soil microbial community structure and functional genes related to C and N metabolism. High doses of cerium (0.16 and 0.32 mmol kg−1 soil) increased CO2 net production rate by 59 and 42%, and N2O net production rate by 255 and 609%, respectively, compared to no REEs. Similarly, high doses of lanthanum (0.16 and 0.32 mmol kg−1 soil) increased CO2 net production rate by 47 and 39%, and N2O net production rate by 105 and 187%, respectively. Increased soil respiration from altered relative abundances of key soil microorganisms associated with soil N cycling and organic matter degradation and functional genes encoding enzymes involved in C and N metabolism, accelerated N mineralization. Elevated REEs levels substantially increased the relative abundances of functional genes related to cellulose, chitin, glucans, hemicellulose, lignin, and peptidoglycan degradation. REEs also influenced multiple functional genes associated with the N cycle. The abundance of genes responsible for organic N degradation and synthesis, such as asnB, gdh_K15371, glsA, and gs, increased with elevated cerium and lanthanum concentrations. Similarly, the abundances of denitrification genes, including narl, narJ, narZ, and nosZ, also rose with increasing amounts of cerium and lanthanum. However, the decrease in narB and nirB gene abundance with increasing REE concentrations was attributed to the reduction of nitrate to amino groups. Our findings highlight the influence of REEs on key soil microorganisms associated with soil N cycling and organic matter degradation and key functional genes in soil C and N metabolism, with implications for agriculture, environmental protection, and human health.

Metagenomic Insights into the Enhancement of Bioavailable Nitrogen in Continuous Cropping Soil Through the Application of Traditional Chinese Medicine Residue Following Fumigation.

Background/Objectives: Chemical fumigation can effectively inhibit the occurrence of soil-borne diseases; however, this approach can negatively affect the structure of the soil microbial community. The combination of soil fumigant and organic fertilizer application thus represents a widely adopted strategy in agricultural practice. Traditional Chinese medicine residue (TCMR) is a high-quality organic fertilizer; however, the impact of post-fumigation TCMR application on keystone taxa and their functional traits remains uncertain. Methods: This study examined the effects of five fertilization treatments on the diversity, key species, and related functional genes of microbial communities in rhizosphere soil of continuous cropping pepper. Results: Chemical fumigation followed by TCMR application markedly enhanced soil nutrient content in the rhizosphere and significantly influenced microbial community composition as well as functional gene patterns associated with microbial nitrogen cycling. It was also strongly correlated with soil bioavailable nitrogen content. The abundance of keystone bacterial species (Pseudomonadota, Actinomycetota, and Bacillota) substantially increased following TCMR application, alongside a notable rise in Ascomycota abundance within the fungal community. This shift contributed to an increase in beneficial bacterial abundance while reducing that of harmful bacteria. Additionally, TCMR addition affected the abundance of denitrification and DNRA genes involved in nitrogen cycling; specifically, nirB and nirK were strongly associated with soil organic nitrogen content. Conclusions: The combined application of chemical fumigants and TCMR modified the composition of keystone microbial community species by influencing rhizosphere soil TN and other nutrients, and these alterations were linked to multiple nitrogen-cycling functional genes.

Bio-augmentation driven sulfur autotrophic denitrification process: Focusing on denitrification performance, microbial community and gene characteristics

The long time and poor efficiency of transforming activated sludge directly into autotrophic denitrifiers pose considerable challenges to sulfur autotrophic denitrification (SAD) technology. To address these issues, bio-augmentation was used to rapidly enrich numerous sulfur autotrophic denitrifiers and maintain high nitrate removal efficiency. The results showed that bio-augmentation with 10 % mixed autotrophic denitrifiers reduced the construction time of the SAD system and significantly improved the total nitrogen (TN) removal efficiency. Even at influent NO3--N concentrations of 150 mg/L and 200 mg/L, the TN removal efficiency in the bio-augmented system improved to 97.1 % and 66.0 %, respectively, whereas it was, only 1.4 % and 1.5 % in a black system. The bio-augmented system operated stably, showing a greater TN removal efficiency (57.6 %) even at an influent composition of 222.3 mg/L NO2--N and 152.7 mg/L NO3--N. This study revealed that bio-augmentation accelerated the alteration of microbial community structures, enriched autotrophic denitrifier species, and increased the abundance of autotrophic denitrifiers. Additionally, network analysis between microorganisms revealed well-connected associations and cooperation among the microbes induced by bio-augmentation. Furthermore, according to predicted function profiles, bio-augmentation enhanced the activity of nitrate reduction enzymes, especially the napAB, nirK, norBC, and nosZ genes, thereby improving nitrogen removal efficiency. Genes involved in sulfur oxidation included fccAB, dsrAB, sorA, and SUOX, whereas sat, aprAB, cysJI and sir were involved in sulfate reduction. These results enable the rapid construction of SAD systems.

Soil properties drive nitrous oxide accumulation patterns by shaping denitrifying bacteriomes

In agroecosystems, nitrous oxide (N₂O) emissions are influenced by both microbiome composition and soil properties, yet the relative importance of these factors in determining differential N₂O emissions remains unclear. This study investigates the impacts of these factors on N₂O emissions using two primary agricultural soils from northern China: fluvo-aquic soil (FS) from the North China Plain and black soil (BS) from Northeast China, which exhibit significant differences in physicochemical properties. In non-sterilized controls (NSC), we observed distinct denitrifying bacterial phenotypes between FS and BS, with BS exhibiting significantly higher N₂O emissions. Cross-inoculation experiments were conducted by introducing extracted microbiomes into sterile recipient soils of both types to disentangle the relative contributions of soil properties and microbiomes on N₂O emission potential. The results showed recipient-soil-dependent gas kinetics, with significantly higher N₂O/(N₂O + N₂) ratios in BS compared to FS, regardless of the inoculum type. Metagenomic analysis further revealed significant shifts in denitrification genes and microbial diversity of the inoculated bacteriomes influenced by the recipient soil. The higher ratios of nirS/nosZ in FS and nirK/nosZ in BS indicated that the recipient soil dictates the formation of different denitrifying guilds. Specifically, the BS environment fosters nirK-based denitrifiers like Rhodanobacter, contributing to higher N₂O accumulation, while FS supports a diverse array of denitrifiers, including Pseudomonas and Stutzerimonas, associated with complete denitrification and lower N₂O emissions. This study underscores the critical role of soil properties in shaping microbial community dynamics and greenhouse gas emissions. These findings highlight the importance of considering soil physicochemical properties in managing agricultural practices to mitigate N₂O emissions.

Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils

BackgroundArsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.ResultsFive ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.ConclusionsOur results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils.5-kbCdqq-d7KqfyvRVSSUfVideo

Response of ammonium transformation in bioanodes to potential regulation: Performance, electromicrobiome and implications

Understanding how potential regulation affects ammonium transformation in bioanodes is crucial for promoting their application. This study explored the performance, electrochemical properties, electromicrobiome of bioanodes across potentials from 0.0 V to 0.4 V vs. standard hydrogen electrode (SHE). Higher anode potentials enhanced the performance of electroactive biofilms and ammonium removal but suppressed nitrite oxidation while favoring dissimilatory nitrate reduction (DNRA), leading to increased nitrite accumulation. A reduction in nitrite-oxidizing bacteria (NOB) and an increase in DNRA-related genes resulted in an optimal nitrite-to-ammonium ratio of 1.32 for the Anammox process. Higher anodic potentials (0.3 and 0.4 V) were less effective for TN removal than lower potentials (0, 0.1, and 0.2 V), likely due to increased NOB and denitrification genes at lower potentials enhancing nitrite oxidation and denitrification. These findings indicate that regulating anodic potential effectively directs ammonium transformation in bioanodes, optimizing its conversion to N2 or nitrite.

The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures.

Strain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate ( ) reduction. Strain JAM1T can reduce to nitrite ( ) but not to nitric oxide (NO) as it lacks a NO-forming reductase. Strain GP59 on the other hand can carry the complete reduction of to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before reduction occurs. In strain JAM1T cultures, reduction begins immediately with accumulation of . Furthermore, is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth. Both strains were cultured under oxic conditions either with or without , or under anoxic conditions with . Transcript levels of selected denitrification genes (nar1 and nar2 encoding reductases, nirK encoding reductase, narK12f encoding / transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles. The transcript levels of nar1 were very low in strain GP59 cultured under oxic conditions without . These levels were 37 times higher in strain JAM1T cultured under the same conditions, suggesting that Nar1 was expressed at sufficient levels in strain JAM1T before the inoculation of the oxic and anoxic cultures to carry reduction with no lag phase. Transcriptomic analysis revealed that each strain had distinct relative gene expression profiles, and oxygen had high impact on these profiles. Among denitrification genes and regulatory genes, the nnrS3 gene encoding factor involved in NO-response function had its relative gene transcript levels 5 to 10 times higher in strain GP59 cultured under oxic conditions with than those in both strains cultured under oxic conditions without . Since NnrS senses NO, these results suggest that strain GP59 reduced to NO under oxic conditions, but because of the oxic environment, NO is oxidized back to by flavohemoproteins (NO dioxygenase; Hmp), explaining why reduction is not observed in strain GP59 cultured under oxic conditions. Understanding how these two strains manage the regulation of the denitrification pathway provided some clues on how they response to environmental changes in the original biofilm community, and, by extension, how this community adapts in providing efficient denitrifying activities.

Assessing the effects of NapA gene overexpression on denitrification and denitrogenation in magnetospirillum gryphiswaldense MSR-1.

Previous research on Magnetospirillum gryphiswaldense MSR-1 found that MSR-1 has a good denitrification nitrogen removal ability and specific application prospects in the sewage biological nitrogen removal field. Therefore, this study selected the essential denitrification gene NapA in MSR-1-wt for overexpression, and the overexpressed MSR-1-NapA was successfully constructed. Q-PCR amplification experiment and AGAR gel electrophoresis experiment proved that the relative transcription level of the NapA gene was increased by more than four times, and the denitrification ability of MSR-1-wt and MSR-1-NapA was further determined by enzyme activity experiment, denitrification experiment, and flow cytometry. The results showed that overexpression of the NapA gene increased nitrate reductase activity in MSR-1-NapA by more than four times. In the solution with a nitrate concentration of 118.33 ± 3.23mgN/L, the denitrification efficiency of MSR-1-NapA was superior to that of MSR-1-wt, significantly enhancing both the denitrification and nitrogen removal capacities of MSR-1. This indicates its greater potential for biological nitrogen removal in wastewater treatment.

The combined nitrogen and phosphorus fertilizer application reduced soil multifunctionality in Qinghai-Tibet plateau grasslands, China

The impact of nitrogen (N) and phosphorus (P) fertilizer inputs on soil nutrient cycling and ecological function processes has garnered significant attention. Soil multifunctionality primarily refers to the soil's ability to perform multiple functions simultaneously, particularly the functions related to the genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycles, which are critical for ecosystem sustainability. Despite this, the effects of N and P fertilizers on the expression of genes involved in soil carbon (C), nitrogen (N), and phosphorus (P) cycles, and their consequent influence on soil multifunctionality, remain unclear. To investigate this, we conducted a long-term nine-year experiment. The experimental site was fenced to prevent grazing and included four treatments: Control (no fertilizer), N (10 g N m−2 y−1, urea), P (5 g P m−2 y−1, Ca(H2PO4)2), and NP (10 g N and 5 g P m−2 y−1, urea and Ca(H2PO4)2). We examined the effects of these treatments on soil microbial functional gene abundance and multifunctionality. Our findings revealed that N addition altered the composition of soil microbial functional genes but did not affect functional diversity. Both N and P inputs, as well as their combination, negatively impacted soil carbon fixation and the genes encoding enzymes for the degradation of starch, hemicellulose, cellulose, and chitin. N input also disrupted soil nitrogen and phosphorus cycling by inhibiting the expression of soil denitrification genes (nirS and nosZ), phytate hydrolase gene (cphy), and a phosphatase gene (phoD). Additionally, P input significantly inhibited functional genes involved in soil nitrification, denitrification, ammonification, nitrogen fixation, and ammonia oxidation processes. It also adversely affected phytate synthesis and degradation. The combined N and P inputs had a substantial negative impact on soil nitrification (hao), denitrification (narG, nirK, nirS, and norZ), ammonification (gdh), nitrogen fixation, annamox, and nitrogen reduction, and inhibited the expression of soil phosphorus cycle genes. Long-term phosphorus application was found to have a more detrimental effect on soil multifunctionality compared to nitrogen application. Furthermore, our study showed that vegetation diversity and abundance are crucial drivers of soil carbon, nitrogen, and phosphorus cycling functional genes and multifunctionality. We concluded that N and P inputs alter soil multifunctionality by influencing vegetation diversity; therefore, maintaining vegetation diversity is essential for sustaining soil multifunctionality.

SiO2 nanoparticles can enhance nitrogen retention and reduce copper resistance genes during aerobic composting of swine manure

SiO2 nanoparticles (SiO2 NPs) are low-cost, environmentally friendly materials with significant potential to remove pollutants from complex environments. In this study, SiO2 NPs were used for the first time as an additive in aerobic composting to enhance nitrogen retention and reduce the expression of copper resistance genes. The addition of 0.5 g kg−1 SiO2 NPs effectively reduced nitrogen loss by 72.33 % by decreasing denitrification genes (nosZ, nirK, and napA) and increasing nitrogen fixation gene (nifH). The dominant factors affecting nitrification and denitrification genes were Firmicutes and C/N ratio. Additionally, SiO2 NPs decreased copper resistance genes by 28.96 % − 37.52 % in compost products. Copper resistance genes decreased most in the treatment with 0.5 g kg−1 SiO2 NPs. In summary, 0.5 g kg−1 SiO2 NPs have the potential to reduce copper resistance genes and enhance nitrogen retention during aerobic composting, which may be used to improve compost quality.

Hysteresis response of carbon release and nitrate reduction in polymer denitrification systems

Polymer denitrification has received much attention in the field of advanced wastewater treatment. It can release carbon source stably during long-term operation, which can be used as electron donor for denitrification. However, the response of the polymer denitrification system to the transient changes of nitrate is not sufficiently disclosed yet. In this study, the response of a polymer denitrification system to nitrate was comprehensively investigated through a series of experiments. Therefore, real-time response and hysteresis response phenomena were identified. The time dependence of microorganisms in the system and the recovery of the hysteresis response were elucidated. The experimental results revealed distinct response patterns before and after the hysteresis tipping point. The denitrifying microorganisms, which showed a high adaptive capacity, exhibited a real-time response over a range of low nitrate concentration variations (∼20–30 mg/L). In contrast, microbial recovery is poor over a range of high nitrate concentration variation (∼35–40 mg/L), which is referred to as a hysteresis response. Finally, the hysteresis response mechanism was revealed by monitoring the recovery of denitrification enzymes, gene and microbial communities. The results showed that transient shocks of high nitrate loads affect microbial community structure stability, denitrifying enzyme activity and gene expression. Meanwhile, the abundance of Microbacterium associated with carbon release was reduced. The combination of these factors leads to a hysteresis response in denitrification and carbon release. This work contributes to a deeper understanding of the hysteresis behavior in polymer denitrification systems, offering critical insights for optimizing system performance and improving nitrogen removal efficiency.

Fulvic acid mediated highly efficient heterotrophic nitrification-aerobic denitrification by Paracoccus denitrificans XW11 with reduced C/N ratio

Reducing the C/N ratio requirements for heterotrophic nitrification-aerobic denitrification (HNAD) is crucial for its practical application; however, it remains underexplored. In this study, a highly efficient HNAD bacterium, Paracoccus denitrificans XW11, was isolated. The HNAD characteristics of XW11 were studied, and the redox mediator fulvic acid (FA) was used to reduce the C/N requirements. Whole-genome sequencing revealed multiple denitrification genes in XW11; however, nitrification genes were not identified, because heterotrophic nitrification-related gene sequences were not included in the database. However, the nitrogen removal related enzyme activity test revealed complete nitrification and denitrification pathways. Reverse transcription PCR showed that the membrane-bound nitrate reductase (NarG), rather than the periplasmic nitrate reductase, was responsible for aerobic denitrification. The conventional nitrite reductase (NirS) also does not mediate nitrite denitrification. When the C/N ratio was 10, the ammonia removal efficiency of the Control was 71.71 % and the addition of FA increased it to 86.12 %. Transcriptomic analysis indicated electron flow from the carbon source to FA without proton transmembrane transport, and the presence of FA constructs another electron transfer system. The redox potential of oxidized FA/reduced FA is 0.3679 V, avoiding competition for electrons from Complex III. Thus, ammonia monooxygenase obtains electrons more easily, thereby promoting nitrification. The enzyme activity test of the nitrification process confirmed this view. In addition, NarG expression increased, and the denitrification process was enhanced. Overall, FA improved HNAD efficiency by facilitating electron transfer to the nitrogen dissimilation process, offering a novel approach to reduce the C/N requirement of HNAD.

Nitrate removal by a novel aerobic denitrifying Pelomonas puraquae WJ1 in oligotrophic condition: Performance and carbon source metabolism

Reducing nitrate contamination in drinking water has become a critical issue in urban water resource management. Here a novel oligotrophic aerobic denitrifying bacterium, Pelomonas puraquae WJ1, was isolated and purified from artificial lake sediments. For the first time, excellent aerobic denitrification capabilities were demonstrated. At a carbon-to‑nitrogen ratio of 5.0, strain WJ1 achieved 100.0 % nitrate removal and 84.92 % total nitrogen removal within 24 h, with no nitrite accumulation. PCR amplification and sequencing confirmed the presence of the denitrification genes napA, nirS, and nosZ in the strain. The nitrogen balance demonstrated that approximately 74.95 % of the initial nitrogen was eliminated as gaseous products under aerobic conditions. Furthermore, carbon balance analysis showed that most electron donors from strain WJ1 were directed towards oxygen, with limited availability for nitrate reduction. A combination of bio-ECO analysis and network modeling indicated that strain WJ1 has robust metabolic capabilities for diverse carbon sources and exhibits high adaptability to complex carbon environments. Overall, Pelomonas puraquae WJ1 removed approximately 45.89 % of the nitrates in raw water, demonstrating significant potential for practical applications in oligotrophic denitrification.

Interactions between arsenic and nitrogen regulate nitrogen availability and arsenic mobility in flooded paddy soils

In paddy soils, arsenic (As) stress influences nitrogen (N) transformation while application of N fertilizers during rice cropping affects As transformation. However, specific interactive effects between As and N in flooded paddy soils on As mobility and N availability were unclear. Here, we examined N and As dynamics in flooded paddy soils treated with four As levels (0, 30, 80 and 150 mg kg−1) and three urea additions (0, 4 and 8 mmol N kg−1). Arsenic contamination inhibited diazotrophs (nifH) and fungi but promoted AOA and denitrification genes (narG, nirK, nirS), decreasing dissolved organic N, NH4+-N and NO3–-N. Besides, urea application stimulated As- and Fe-reducing bacteria (arrA and Geo) coupled with anammox. On Day 28, the addition of 8 mmol N kg–1 increased total As concentrations in solutions of soils treated with 30 and 80 mg As kg−1 by 2.4 and 1.8 times compared with the nil-N control. In contrast, at 150 mg As kg−1, it decreased the total As concentration in soil solution by 63 % through facilitating As(III) oxidation coupled with NO3–-N reduction. These results indicate that As contamination decreases N availability, but urea application affects As mobility, depending on As contamination level.