Search Results (97)

Ammonia−oxidizing archaea (AOA), ammonia−oxidizing bacteria (AOB), and Comammox are key drivers of soil nitrification and play crucial roles in soil nitrogen cycling, with distinct functional contributions. AOA and AOB primarily drive the first step of nitrification by oxidizing ammonia to nitrite, while comammox bacteria can directly oxidize ammonia to nitrate. In this study, quantitative real−time polymerase chain reaction (qPCR) and Illumina MiSeq high−throughput sequencing were employed to determine the absolute abundance, diversity, and community structure of AOA, AOB, and Comammox in alkaline soybean farmland soil under single biochar application. Combined with soil chemical properties, the driving factors shaping ammonia−oxidizing microbial community structure were analyzed to clarify the impact of biochar on ammonia−oxidizing microorganisms from the perspective of soil microbial ecology. The results showed that biochar application effectively modified soil physicochemical properties, increased the absolute abundance of AOA, AOB, and Comammox, influenced their α–diversity, and reshaped community structure. Redundancy analysis revealed that after biochar application, AOA, AOB, and Comammox exhibited positive correlations with soil total phosphorus (TP), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), total organic carbon (TOC), and available potassium (AK). In conclusion, biochar application regulates soil nutrient cycling, particularly by modulating the ammonia oxidation and nitrite oxidation processes, thereby regulating soil nitrogen cycling and ammonia−oxidizing microbial communities, with potential benefits for sustaining soil quality in agricultural systems. Full article

Nitrogen cycling during the biological treatment of organic waste is governed by a consortium of microorganisms whose activity determines whether nitrogen is conserved as a fertiliser resource or lost as ammonia, nitrous oxide, or dinitrogen. Composting and anaerobic digestion are the dominant biological platforms for organic waste valorisation, yet they impose contrasting selective pressures on nitrogen-cycling guilds. In composting, thermophilic conditions and fluctuating oxygen availability shape sequential communities of ammonifiers, ammonia oxidisers, and denitrifiers, with volatilisation and incomplete denitrification as principal loss pathways. In anaerobic digestion, nitrification is effectively absent and high organic nitrogen loading generates free ammonia that inhibits methanogenic archaea, constraining process stability and reshaping community structure toward ammonia-tolerant taxa. This review synthesises understanding of the functional guilds, enzymes, and regulatory genes involved in nitrogen mineralisation, nitrification, denitrification, and ammonia assimilation across both systems. It sets out the feedstock categories and regulatory frameworks that constrain treatment and product use, the operating parameters governing nitrogen retention, and the strategies used to mitigate loss, including additives, bioaugmentation, ammonia stripping, and struvite precipitation. We propose a comparative framework that positions the two systems along a shared continuum of microbial nitrogen regulation, in which redox regime determines which transformation pathways are available while pH, temperature, carbon-to-nitrogen ratio, moisture, and retention time govern the magnitude of loss. Attention is given to how upstream process outcomes determine nitrogen use efficiency and environmental risk after land application. We conclude by identifying research gaps, including paired cross-system studies, standardised molecular monitoring, field-scale validation, and harmonised quality standards. Full article

Summer hypoxia in the bottom water of the Bohai Sea is accompanied by marked changes in water-column structure and nutrient conditions, which may affect ammonia-oxidizing microorganisms and thus alter nitrification-related nitrogen cycling. To examine these responses, seawater samples were collected along an inshore–offshore transect from the coastal waters off Qinhuangdao City to the central Bohai Sea in June, July, and August 2018. Surface, middle, and bottom waters were sampled, and physicochemical variables, including temperature, salinity, dissolved oxygen (DO), and inorganic nitrogen concentrations, were measured. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were then analyzed using amoA amplicon sequencing to compare their diversity, community structure, genus-level composition, and dominant OTU patterns. From June to August, along with temperature increase, the water column showed stronger stratification and oxygen depletion in the bottom water, together with shifts in salinity and inorganic nitrogen distributions. AOA and AOB showed different temporal responses. AOA diversity surpassed that of AOB in July, but AOB became more diverse in August. Principal coordinates analysis showed clear separation of AOA communities between July and August, and sampling month had a significant effect on AOA community structure (PERMANOVA, p = 0.009). In contrast, AOB communities did not show significant month-related separation (p = 0.157). According to environmental fitting analysis, AOA community structure was predominantly associated with temperature and salinity, with only a marginal link to NH₄⁺, while pH and salinity were the key factors shaping AOB communities. At the genus level, AOA was dominated by Nitrosopumilus and AOB was dominated by Nitrosospira. Overall, the results indicate that AOA showed stronger temporal variation than AOB during the development of summer hypoxia in seawater of Bohai Sea. Full article

Constructed wetlands (CWs) are widely used for wastewater treatment but can also serve as significant sources of nitrous oxide (N₂O), a potent greenhouse gas. Balancing efficient nitrogen removal with N₂O mitigation remains a critical challenge for sustainable wastewater management. This review systematically elucidates the key microbial mechanisms underlying N₂O emissions in CWs and summarizes corresponding mitigation strategies. Mechanistically, N₂O production is primarily driven by hydroxylamine oxidation and nitrifier denitrification mediated by ammonia-oxidizing microorganisms, as well as incomplete heterotrophic denitrification resulting from electron-donor limitation. These pathways are tightly regulated by spatiotemporal redox gradients, carbon-to-nitrogen ratios, and influent strength conditions. To address these emissions, this review synthesizes mitigation strategies from an engineering perspective. Optimization of operational parameters, such as intermittent aeration and water-level regulation, together with the application of novel functional substrates, such as biochar and iron-carbon micro-electrolysis, can effectively facilitate electron transfer and improve micro-redox conditions. Furthermore, optimized plant species selection and community design, along with emerging low-carbon biological nitrogen removal processes, such as autotrophic denitrification and partial denitrification coupled with anammox, offer promising approaches for substantial emission reduction. Overall, this review provides practical guidance for designing efficient, low-carbon CWs toward carbon neutrality. Full article

Tobacco cultivation leads to nicotine accumulation in soil, but how nicotine affects soil nitrification and ammonia-oxidizing microorganisms remains poorly understood. This study conducted a microcosm incubation using soil collected from a 10-year tobacco monoculture field. The soil was spiked with nicotine at 0, 10, or 100 mg kg⁻¹ (the two concentrations representing realistic root-zone levels and a worst-case residue hotspot, respectively) and incubated for 42 days under controlled conditions. Gross nitrification rates were measured by ¹⁵N isotope dilution, and the abundance (qPCR) and community composition (amplicon sequencing) of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were determined at multiple time points. Results showed nicotine at 10 mg kg⁻¹ slightly stimulated nitrification, whereas 100 mg kg⁻¹ caused a transient inhibition (day 1) followed by a sustained stimulation, with gross nitrification rates increased by up to 2-fold compared to the control. Nicotine explained 22% of the variation in bacterial community composition and significantly enriched Intrasporangiaceae and Bryobacter while suppressing Bradyrhizobium. AOB-amoA copy numbers increased within 3 days of nicotine addition and correlated strongly with nitrification rates, whereas AOA-amoA responded only after 6 weeks. Phylogenetic analysis showed that Nitrosospira (cluster Np 39-19) dominated the AOB community. We conclude that nicotine exerts concentration-dependent, biphasic effects on soil nitrification and that AOB, not AOA, drive the nitrification response to nicotine in this agricultural soil. Our findings highlight the potential of nicotine to shape nitrogen cycling in tobacco-cultivated ecosystems and call for field validation under long-term residue conditions. Full article

In situ coagulation is regarded as the most effective measure in response to the frequent metal spills in China. Excessive coagulant is often used in pursuit of extremely high removal rates of contaminants. Yet the secondary ecological impact of the iron-containing coagulation flocs left on the river sediments after emergency response is still unclear. In the current study, we investigated the impact of flocs derived from three different iron-based coagulants, polymeric ferric sulfate (PFS), polymeric ferric chloride (PFC), and ferric chloride (FeCl₃), on microbial communities in sediment based on microcosm experiments. Metagenomics, quantitative PCR, and determination of ammonia oxidation potential were adopted to elucidate community shifts. The results indicate that the community structure and function of microorganisms in sediments have been affected, especially processes and species related to nitrogen cycling, and the effect was coagulant-specific. Flocs retrieved from FeCl₃ caused a more pronounced decline in diversity, shifts in community composition, and decreased potential ammonia oxidation. Ammonia-oxidizing archaea (AOA) was more sensitive to iron-containing flocs than ammonia-oxidizing bacteria (AOB), while PFS-flocs tended to reduce multiple genes involved in nitrate reduction. This indicates that the pre-polymerization of inorganic coagulants may be the primary factor leading to different microbial ecological effects. Sulfate, on the other hand, may affect specific biogeochemical processes due to its competition for electron donors. Our results confirmed that even without heavy metals as contaminants, coagulant flocs alone could present an effect on nitrogen cycling in sediments. The results will provide a scientific basis for environmental emergency decision-making: in emergency response to metal pollution incidents, the use of coagulants should be limited to only the necessary level. Full article

The study of microorganisms inhabiting extreme environments offers a valuable opportunity to explore their potential ecological roles. This study aimed to reveal and compare the microbial taxonomic diversity of largely unexplored permafrost regions located in different climatic zones (dry and wet) in the Chilean Andes, separated by thousands of kilometers. Permafrost active layer samples were collected from the Ojos del Salado (Atacama Desert) and the Torres del Paine (Patagonia) from different sampling depths. Illumina 16S rRNA gene-based amplicon sequencing revealed that the Andean permafrost active layer provides diverse habitats for distinct microbial communities, with higher taxonomic diversity of Bacteria than Archaea. The wet Patagonian Andes samples showed higher diversity, with a greater abundance of Chloroflexota and Bacteroidota, while the dry Ojos del Salado samples were dominated by Actinomycetota, indicating desiccation stress. Archaea were classified as ammonia-oxidizing members of the Thermoproteota phylum. Beta-diversity analyses suggested that differences in environmental conditions (mainly available moisture) contributed more to community structure differentiation than geographical distances. Nevertheless, the effect of sampling depth on microbial diversity was insignificant. Full article

Composting chicken manure is a source of significant ammonia (NH₃) emissions, which, because of propagation, contributes to the eutrophication of the environment and decreases in air quality. Therefore, it is reasonable to use methods to limit its emission into the atmosphere. Biofiltration, using the metabolic activity of nitrifying and heterotrophic microorganisms capable of oxidizing ammonia, is an effective method to reduce ammonia emissions. In addition, the performance of the biofiltration process depends on operational parameters such as the humidity of the medium, the temperature, the contact time of the gas with the biofiltering medium, and the chemical composition and structure of the filter material. The aim of the study was to evaluate the effectiveness of biofilter fillings in reducing ammonia emissions from composting chicken manure along with the identification of factors allowing us to determine the proposed design solution as the most advantageous in terms of efficiency. Experiments on reducing odour emissions with biofiltration were carried out in two compact composting reactors, in which a compost mixture with a C:N ratio of 10:1 was used. The mixture was prepared in a ratio of 5:1 of chicken manure to the structuring material, with wheat straw used as the structuring material. Based on the results of the research on the course of the composting process, high values of ammonia concentration were recorded. Ammonia concentrations of 886 ppm (composter 1) and 811 ppm (composter 2) were recorded, which confirms the intensive nature of this gas emissions during the process of stabilizing the chicken manure. As part of the conducted research, the effectiveness of biofiltration in reducing ammonia emissions was evaluated by analysing the influence of the aeration intensity of the biofilter (20 dm³/h and 50 dm³/h), directly determining the time of contact of the gas with the bed (EBCT—Empty Bed Contact Time). Coconut-activated carbon was used as a filter bed, which was an effective carrier for the development of microorganisms responsible for the biological removal of ammonia from waste gases generated during composting. In addition, this material showed the ability to physically adsorb ammonia, thus supporting the process of its elimination. Each of the test stations has been equipped with a biofiltration installation. To determine the effectiveness of biological removal of ammonia and to assess the legitimacy of the use of selected strains of microorganisms in the process of biological removal of ammonia, the bed of one of the biofilters (biofilter 2) was inoculated with a strain of nitrifying bacteria. During the study, the high efficiency of ammonia removal because of biofiltration was noted in each of the configurations. In the case of an aeration intensity of 20 dm³/h, a reduction in emissions of 99% was achieved; with a higher aeration value, i.e., 50 dm³/h, the efficiency was 89%. These results indicate that the intensity of aeration has a significant impact on the efficiency of the biofiltration process. The analysis of a biofilter enriched with a strain of nitrifying bacteria requires long-term testing. This is important to reliably determine the effect of inoculation on the efficiency of the biological removal of ammonia in biofilters. It has been shown that optimizing these factors allows us to achieve a reduction in ammonia emissions of up to 90%, while minimizing the formation of unpleasant odours. The use of biofiltration in composting systems for organic waste of animal origin is an effective, sustainable solution that fits into the idea of sustainable development, combining the efficiency of air purification technology with environmental protection and the responsible management of resources. This study demonstrates that biofiltration using coconut-shell-activated carbon is an effective and economical method for reducing ammonia and odour emissions from composting chicken manure. The results provide valuable theoretical and practical information on emissions management in organic waste composting processes. Data from this study could be useful in developing strategies to minimize odour emissions, including from the agricultural sector. Full article

Nitrous oxide (N₂O) emissions in cereal-based rotations often show short-lived peaks after fertilization, but their contribution to annual budgets and their responsiveness to straw management remain poorly quantified. We combined a 13-year legacy fertilization experiment with two years of high-frequency N₂O monitoring in a rice–wheat rotation in central China to quantify post-fertilization peak windows and test how straw-return rate modulates these windows and annual emissions. Five long-term treatments were compared: an unfertilized control (CK), straw only (2M, 12 t ha⁻¹ yr⁻¹), mineral fertilizer (NPK), and NPK with 6 or 12 t ha⁻¹ yr⁻¹ straw (MNPK and 2MNPK). Under N input, wheat-season emissions dominated annual totals, with the ratio of wheat-season to annual N₂O emissions (WN/TN, where WN denotes wheat-season N₂O emissions and TN denotes annual cumulative N₂O emissions) of ~73–75% for NPK and MNPK, significantly higher than in CK and the straw-only control. Decomposition of annual fluxes showed that 56.6–65.4% of N₂O in N-applied treatments occurred within short windows after the two wheat-season fertilizations, whereas rice-season peaks were small and largely insensitive to treatment. Planned contrasts expressed as geometric mean ratios (GMRs) with 95% confidence intervals (CIs) highlighted a strong management leverage point: increasing straw from 6 to 12 t ha⁻¹ yr⁻¹ with NPK reduced annual and wheat-season N₂O by ~47% and 58%, respectively, primarily by lowering peak magnitude and shortening peak duration. Microbial analyses suggested that treatment effects on N₂O were better reflected by community compositional shifts (β-diversity) than by α-diversity, while amoA abundance showed guild-specific responses. Collectively, this study provides an event-window quantification framework that links high-frequency field measurements to a specific, actionable mitigation lever (straw-return rate) in rice–wheat systems. Together, these results identify wheat-season post-fertilization windows as the main control points for annual N₂O in rice–wheat rotations and show that pairing NPK fertilization with higher straw return can temper short-lived peaks. By explicitly pinpointing when (which windows) and how (attenuating peak magnitude and duration) mitigation is achieved, our findings offer a management-ready and transferable basis for targeted N₂O abatement in double-cropping systems. Full article

Over the past few decades, the discovery of novel microbial processes, biochemical reactions, and previously uncharacterized microorganisms has significantly enhanced our understanding of nitrogen (N) cycling across terrestrial and aquatic ecosystems, including engineered environments such as wastewater treatment systems. These scientific advancements are catalyzing a paradigm shift toward treatment strategies that are not only energy-efficient and cost-effective, but also environmentally sustainable, with the added benefit of mitigating greenhouse gas emissions. The current review highlights recent breakthroughs in microbial N cycling, with particular emphasis on their practical applications in wastewater treatment. Emerging processes, such as nitrous oxide (N₂O) mitigation, electro-anammox, ferric iron-dependent ammonium oxidation (Feammox), and complete ammonia oxidation (comammox), offer promising strategies for sustainable and low-energy N removal. Nevertheless, a significant challenge persists in translating these laboratory-scale innovations into full-scale, real-world applications, especially within decentralized treatment infrastructures. Bridging this gap is essential for realizing robust, low-carbon, and sustainable wastewater management systems in the decades to come. Full article

Denitrification and nitrification are two pivotal microbial processes relating to N₂O emissions. However, the difference in N₂O emission fluxes and N₂O-producing bacteria between a karst (KA) and non-karst area (NKA) remains unclear. The objective of this study is to compare the differences in soil N₂O emissions, nitrifying bacteria, and denitrifying bacteria during the growth period of rice in KA and NKA, and to explore the mechanisms by which microorganisms and environmental factors drive N₂O emissions. Here, N₂O emission fluxes of paddy fields were collected using the static dark chamber and measured using gas chromatography at KA and NKA in the Maocun Karst Experimental Site in Guilin, China. The nitrifying bacteria (ammonia-oxidizing bacteria, AOB) and denitrifying bacteria (nirK-denitrifier) were determined using real-time PCR and high-throughput sequencing, respectively. Results showed that during the rice growth period, the N₂O emission fluxes in KA was generally lower than that in NKA, with cumulative N₂O emissions of −0.054 and 0.229 kg·hm⁻² in KA and NKA, respectively. The absolute abundance of AOB in KA (8.91 × 10⁶–2.68 × 10⁷ copies·g⁻¹) was significantly higher than that in NKA (1.57 × 10⁶–6.48 × 10⁶ copies·g⁻¹), while the absolute abundance of nirK-denitrifier had no significant difference between the two areas. The composition and diversity of AOB and nirK-denitrifier differed significantly between KA and NKA. Results from partial least squares structural equation modeling (PLS-SEM) indicated that soil properties, carbon sources, and nitrogen sources had positive effects on AOB and nirK-denitrifier, while nirK-denitrifier had a negative effect on N₂O emissions. Partial least squares regression (PLSR) predictions revealed that NO₃⁻-N, SOC, TN, Mg²⁺, Ca²⁺, and pH were the most important factors influencing N₂O emission fluxes. This study highlights the critical role of the typical characteristics of KA soils in reducing N₂O emissions from paddy fields by driving the evolution of AOB and nirK-denitrifier. Full article

Pyrochar has been identified as a favorable soil conditioner that can effectively ameliorate soil acidification. Hydrochar is considered a more affordable carbon material than pyrochar, but its effect on the process of soil acidification has yet to be investigated. An indoor incubation and a soil column experiment were conducted to study the effect of rice straw hydrochar application on nitrification and NO₃⁻-N leaching in acidic red soil. Compared to the control and pyrochar treatments, respectively, hydrochar addition mitigated the net nitrification rate by 3.75–48.75% and 57.92–78.19%, in the early stage of urea fertilization. This occurred mainly because a greater amount of dissolved organic carbon (DOC) was released from hydrochar than the other treatments, which stimulated microbial nitrogen immobilization. The abundances of ammonia-oxidizing archaea and ammonia-oxidizing bacteria were dramatically elevated by 25.62–153.19% and 12.38–22.39%, respectively, in the hydrochar treatments because of DOC-driven stimulation. The cumulative leaching loss of NO₃⁻-N in soils amended with hydrochar was markedly reduced by 43.78–59.91% and 61.70–72.82% compared with that in the control and pyrochar treatments, respectively, because hydrochar promoted the soil water holding capacity by 2.70–9.04% and reduced the residual NO₃⁻-N content. Hydrochar application can dramatically diminish total H⁺ production from soil nitrification and NO₃⁻-N leaching. Thus, it could be considered an economical soil amendment for ameliorating soil acidification. Full article

To analyze the microbiological mechanisms of biological denitrification during low-temperature operations, continuous sampling of influent and activated sludge samples was conducted at the Changchun Municipal Wastewater Treatment Plant. The relative abundance and absolute gene abundance of ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and denitrifying bacteria were determined using high-throughput sequencing technology and reverse transcription–polymerase chain reaction (RT–PCR) technology, respectively. Nitrosomonas and Nitrosospira were the dominant bacteria in ammonia-oxidizing bacteria; the detection rate was 100%; and the abundance distribution fluctuated greatly. The percentages of net proliferation rate greater than −0.05 were 75% and 62.5%, respectively, but the temperature effect was not obvious. The detection rate of Nitrosomonadaceae (norank) was 76.67%, and the percentage of net proliferation rate greater than −0.05 was 50%. The growth of ammonia-oxidizing archaea was limited at low temperature, and the abundance of most bacteria fluctuated greatly. The frequencies of net proliferation rate of Crenarchaeota (norank), Thaumarchaeota (norank), and Nitrososphaera greater than −0.05 were more than 50%. Of the 20 OUTs of denitrifying bacteria, 16 had a net increment rate greater than −0.2/d with a frequency greater than 50 per cent, of which Sinorhizobium and Alphaproteobacteria were detected with a frequency of 100% in activated sludge. The frequency of AOB and denitrifying bacteria net proliferation rate greater than zero during the low-temperature period was relatively high, which ensured the smooth progress of the denitrification process and reasonably explains the microbiological mechanism. In addition, it can be inferred that the migration of influent microorganisms can shape the population structure of denitrifying bacteria, as the net proliferation rate of most bacterial populations was less than 0. Full article

The denitrification process is the main process of the soil nitrogen (N) cycle in paddy fields, which leads to the production of large amounts of nitrous oxide (N₂O) and increases N loss in paddy soil. Plant-derived bio denitrification inhibitor procyanidins are thought to inhibit soil denitrification, thereby reducing N₂O emissions and soil N loss. However, the denitrification inhibition effect of procyanidins in paddy soils with high organic matter content remains unclear, and their high price is not conducive to practical application. Therefore, this study conducted a 21-day incubation experiment using low-cost proanthocyanidins (containing procyanidins) and paddy soil with high organic matter content in Northeast China to explore the effects of proanthocyanidins on N₂O emissions and related microorganisms in paddy soil. The results of the incubation experiment showed that the application of proanthocyanidins in paddy soil in Northeast China could promote the production of N₂O in the first three days but inhibited the production of N₂O thereafter. Throughout the incubation period, proanthocyanidins inhibited the enzyme nitrate reductase (NaR) activity and the abundance of nirS and nirk denitrifying bacteria, with a significant dose-response relationship. Although the application of proanthocyanidins also reduced the soil nitrate nitrogen (NO₃⁻-N) content, the soil NO₃⁻-N content increased significantly with increasing incubation time. In addition, the application of proanthocyanidins increased soil microbial respiration, ammonia-oxidizing archaea (AOA) amoA gene abundance, and soil ammonium nitrogen (NH₄⁺-N) content. Therefore, the application of proanthocyanidins to paddy soil in Northeast China can effectively regulate denitrification. However, in future studies, it is necessary to explore the impact of proanthocyanidins on the nitrification process and use them in combination with urease inhibitors and/or nitrification inhibitors to better regulate soil N transformation and reduce N₂O emissions in paddy soil. Full article

The Anaerobic–Swing Aerobic–Anoxic–Oxic (ASAO) process was developed to tackle problems such as temperature sensitivity during the Anaerobic–Oxic–Anoxic (AOA) process. By introducing a swing zone (S zone) with adjustable dissolved oxygen (DO), during the 112-day experimentation period, the ASAO system achieved removal rates of 88.18% for total inorganic nitrogen (TIN), 78.23% for total phosphorus (TP), and 99.78% for ammonia nitrogen. Intermittent aeration effectively suppressed nitrite-oxidizing bacteria (NOB), and the chemical oxygen demand (COD) removal rate exceeded 90%, with 60% being transformed into internal carbon sources like polyhydroxyalkanoates (PHAs) and glycogen (Gly). The key functional microorganisms encompassed Dechloromonas (denitrifying phosphorus-accumulating bacteria), Candidatus Competibacter, and Thauera, which facilitated simultaneous nitrification–denitrification (SND) and anaerobic ammonium oxidation (ANAMMOX). The enrichment of Candidatus Brocadia further enhanced the ANAMMOX activity. The flexibility of DO control in the swing zone optimized microbial activity and mitigated temperature dependence, thereby verifying the efficacy of the ASAO process in enhancing the removal rates of nutrients and COD in low-C/N wastewater. The intermittent aeration strategy and the continuous low-dissolved-oxygen (DO) operating conditions inhibited the activity of nitrite-oxidizing bacteria (NOB) and accomplished the elimination of NOB. Full article