A critical review of aerobic denitrification: Insights into the intracellular electron transfer

Overlooked potential of overlying water disturbances on nitrification and denitrification in urban secondary wetlands

Urban secondary wetlands, open urban landscape systems, provide both aesthetic and water purification functions. However, the effects of frequent human disturbances on the nitrification-denitrification potential of these wetlands system remains unclear. This study simulated horizontal, vertical and hybrid flow disturbances, along with scenarios of external NH4+-N input leading to the gradual deterioration of water quality, to investigate the effects of human interference on the nitrification-denitrification potential of urban secondary wetlands. The findings revealed that all modes of flow disturbances significantly enhanced the nitrification and denitrification potential of wetland sediments. Hybrid flow disturbance most significantly improved the nitrification potential, with improvements of 6.01 %-8.84 % compared to the undisturbed reactor (CK), especially as water quality deteriorated from Class Ⅰ to poor Class V. Horizontal flow disturbance most significantly boosted denitrification potential, ranging from 5.21 % to 19.9 % over the CK. As water quality gradually deteriorated, hybrid and horizontal flow disturbances improved the microbial alpha-diversity within the wetland sediments. Hybrid flow disturbance also elevated the abundance of nitrification functional genes such as hao and nxrAB, as well as Hao activity in the sediments, favoring the growth of nitrifiers such as unclassified__c__Deltaproteobacteria. Horizontal flow disturbance, on the other hand, significantly increased the abundance of denitrifiers such as unclassified__d__Bacteria and unclassified__c__Gammaproteobacteri, along with the abundance of denitrification functional genes like nirK, nirS, and nosZ. This study important insights for optimizing the management and improving the ecological functions of urban secondary wetlands.

Inorganic bioelectric system for nitrate removal with low N2O production at cold temperatures of 4 and 10 °C

Groundwater, essential for ecological stability and freshwater supply, faces escalating nitrate contamination. Traditional biological methods struggle with organic carbon scarcity and low temperatures, leading to an urgent need to explore efficient approaches for groundwater remediation. In this work, we proposed an inorganic bioelectric system designed to confront these challenges. At 10 and 4 °C, the system achieved total nitrogen (TN) removal efficiencies of 95.4 ± 2.7% and 90.9 ± 1.9% at 2 h hydraulic retention time (HRT), while maximum TN removal rates were recorded as 206.0 ± 6.3 and 178.3 ± 9.4 g N·m-3·d-1 at 1 h HRT. The microbial analysis uncovered shifts in dominant genera across temperatures, with Dechloromonas prevalent at 10 °C and Chryseobacterium at 4 °C, highlighting adaptability to cold-tolerant species. Gene analysis on narG, napA, nirS, nirK, norB, nosZI, nosZII, and nifA examined the nitrate reduction processes, and analysis on mtrC and omcA hinted at electrotrophic processes. Additionally, we demonstrated system resilience to disruptions of power outage and short periods without flow through. These findings establish a foundational understanding of electricity-driven nitrate bioreduction in cold environments, crucial in groundwater remediation strategies and paving the way for future optimization and upscaling efforts.

The nitrogen removal characterization and ecological risk assessment of Bacillus sp. isolated from mariculture systems in China with spatiotemporal difference

The accumulation of nitrogen compounds may worsen the aquatic environment and cause serious economic losses in the aquaculture industry. In this study, the denitrification performance and ecological safety of 120 Bacillus sp. isolates with spatial and temporal differences were evaluated based on the aspects of hemolysis, drug resistance, denitrification performance, and purification effect for mariculture wastewater. Firstly, 55/120 safe strains with no hemolytic activity were detected through hemolysis testing. Then, based on selective denitrification medium and colorimetric reagent method, 34/55 Bacillus sp. with denitrification effect were screened. For these 34 Bacillus sp. isolates, the drug resistance phenotype and genotype, denitrification genes, and enzyme activities related to the nitrogen metabolizing (AMO, HAO, NAR, NIR) were examined. And the MARI was 0.00-0.25, with a multi-drug resistance rate of 17.6%. The drug resistance genes tetB, blaTEM, and cfr and the denitrification genes nap, nor, and narG were detected. Ultimately, 27/34 strains with denitrification function and ecological safety were obtained. In addition, eight Bacillus sp. showed certain denitrification effects on nitrogen-containing wastewater treatment. Among them, B. subtilis B24 has outstanding denitrification ability, with removal rates of 92%, 62%, 68%, and 30% for NH4 + -N, NO2--N, NO3--N, and TN in simulated wastewater, respectively. It also has a good denitrification effect in practical applications. This study provides candidate bacterial strains for the treatment of mariculture wastewater.

Recent advances in the nitrogen cycle involving actinomycetes: Current situation, prospect and challenge

Actinomycetes are essential for sustaining the ecosystem's nitrogen balance and stimulating plant development. In contrast, existing detection and culture techniques for actinomycetes are still limited, making it difficult to fully assess their role in the nitrogen cycle. This review emphasized the advantages of actinomycetes in ecological restoration, outlined the current status and challenges of research on nitrogen cycling by actinomycetes. Special attention was paid to the metabolic pathways and related gene regulatory mechanisms of nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction to ammonium, and ammonium assimilation processes. The limitations and strategies of actinomycetes nitrogen metabolic pathways were revealed. In addition, the involvement of carbon, sulphur and phosphorus in the nitrogen cycle of actinomycetes was pointed out. The aim of the review is to improve our understanding of the function of actinomycetes in the nitrogen cycle, which is crucial for enhancing wastewater treatment, ecological preservation, and agricultural output.

Enhancement of aerobic denitrification process on antibiotics removal: Mechanism and efficiency: A review

Traditionally, the removal of nitrogenous pollutants from wastewater relied on conventional anaerobic denitrification as well as aerobic nitrification and anoxic denitrification. However, anaerobic denitrification is complicated since it requires stringent environmental conditions as well as a large land, therefore, denitrification and nitrification were performed in two separate reactors. Although high pollutant removal efficiency has been achieved via aerobic nitrification and anoxic denitrification, the demerits of this approach include high operational costs. Other traditional nitrogen removal methods include air stripping, reverse osmosis, adsorption, ion exchange, chemical precipitation, advanced oxidation process, and breakpoint chlorination. Traditional nitrogen removal methods are not only complicated but they are also uneconomical due to the high operational costs. Researchers have discovered that denitrification can be carried out by heterotrophic nitrification-aerobic denitrification (HNAD) microorganisms which remove nitrogen in a single aerobic reactor that does not require stringent operating conditions. Despite the significant effort that researchers have put in, there is still little information known about the mechanisms of antibiotic removal during HNAD. This review begins with an update on the current state of knowledge on the removal of nitrogenous pollutants and antibiotics from wastewater by HNAD. The mechanisms of antibiotic removal via HNAD were examined in detail. Followed by, the enhancement of antibiotics removal via co-metabolism and oxidation of sulfamethoxazole (SMX) as well as the response of microbial communities to antibiotic toxicity. Lastly, the conditions favorable for antibiotic biodegradation and mechanisms for nitrogen removal via HNAD were examined. The findings in this review show that co-metabolism and oxidation of SMX were the main antibiotic biodegradation mechanisms, pathways for antibiotic removal by co-metabolism and oxidation of SMX were also proposed in the discussion. This research indicated the potential of aerobic denitrification in the removal of antibiotics from wastewater. Understanding the mechanisms and pathways of antibiotic removal by HNAD helps wastewater engineers and researchers apply the technology more efficiently. PRACTITIONER POINTS: The mechanisms of antibiotic removal via HNAD were examined in detail. Co-metabolism and oxidation of SMX were the main antibiotic biodegradation mechanisms. Pathways for antibiotic removal by co-metabolism and oxidation of SMX were also proposed. Conditions favorable for antibiotic biodegradation were examined. This research indicated the potential of aerobic denitrification in the removal of antibiotics from wastewater.

Effects of decabromodiphenyl ethane (DBDPE) exposure on soil microbial community: Nitrogen cycle, microbial defense and repair and antibiotic resistance genes transfer

DBDPE, a widely used brominated flame retardant, is frequently detected in soil. However, the toxic effects of DBDPE on soil microbial communities remain unclear. This study investigated the effects of DBDPE on the microbial community shifts, the nitrogen cycle, microbial defense and repair, and antibiotic resistance genes (ARGs) transfer. After 28 days of DBDPE exposure, the soil microbial community was altered. Denitrifier were enriched by 4.07-78.22% under DBDPE exposure concentrations of 100-1000 ng/g. Additionally, the abundances of genes encoding enzymes involved in nitrification and denitrification processes were up-regulated at 100 ng/g DBDPE exposure, and further promoted at 1000 ng/g DBDPE exposure. Meanwhile, DBDPE exposure at concentrations of 100-1000 ng/g stimulated the production of extracellular polymers substances (EPS) (2155-2347 mg/kg), increased the accumulation of reactive oxygen species (ROS) (by 97.95-108.38%), and activated the antioxidant defense system of soil microorganisms, which correspondingly down-regulated catalase (CAT) genes (by 4.65-4.91%), while up-regulated superoxide dismutase (SOD) (by 0.52-2.63%) and glutathione (GSH) genes (by 19.03%-44.61%). Genes related to the tricarboxylic acid (TCA) cycle, glycerophospholipid metabolism, and peptidoglycan biosynthesis were up-regulated, enhancing cell membrane repair in response to DBDPE exposure. Moreover, the increase in DBDPE concentration selectively enriched and promoted the transmission of ARGs. The co-occurrence network of ARGs and mobile genetic elements (MGEs) revealed that DBDPE facilitated the horizontal gene transfer (HGT)-mediated transmission of transposase, ist, and insertion sequence-associated ARGs.

Deciphering the internal mechanism of nitrogen removal from sludge and biofilm under low temperature from the perspective of microbial function metabolism

Nitrogen emissions up to the standard are a major challenge for wastewater treatment plants in alpine and high-altitude areas. The dosing of carriers can improve the nitrogen removal efficiency of the system at low temperatures; however, the mechanism of action of sludge and biofilm in nitrogen removal remains unclear. This study elucidated the internal mechanism of nitrogen removal via the function of microbial metabolism in sludge and biofilm at low temperatures. At low temperatures, the biofilm facilitated the enrichment of nitrifying bacteria (5.21%-6.62%) and nitrifying functional genes (amoABC); the average removal efficiency of NH4+-N peaked at 94.14%. The denitrification performance of biofilm (14.34-20.67 mg N/(gMLVSS·h) was weaker than that of sludge (27-30.95 mg N/(gMLVSS·h) at low temperatures. The relative abundance of chemical oxygen demand-degrading, denitrifying bacteria, and denitrification functional genes (napAB, nirS, norB, and nosZ) in the sludge was higher than in the biofilm. With a decrease in temperature, the upregulation of carbon metabolism and quorum-sensing functional genes improved the adaptability of sludge to low temperatures. The enhancement of c-type cytochromes and cyclic dimeric guanosine monophosphate functional genes promoted nitrogen removal by endorsing extracellular electron transfer between microorganisms and releasing extracellular polymeric substances at low temperatures. This study offers new insights into improving the mechanism of nitrogen removal from sludge and biofilm at low temperatures.

Optimal nitrite degradation by isolated Bacillus subtilis sp. N4 and applied for intensive aquaculture water quality management with immobilized strains

The toxicity of nitrite is an issue that cannot be overlooked in nitrogen pollution within aquaculture. A highly efficient bacterium capable of simultaneous nitrification and denitrification was screened from natto, and its 16S rRNA gene sequence was compared to existing records, confirming its identification as Bacillus subtilis sp. N4. The optimal conditions for nitrite degradation by B. subtilis sp. N4 were identified using response surface methodology as 167 rpm, pH 6.4, 1 g/8 mL feed, 0.6 OD600, and 30 °C, with a predicted 99 % nitrite removal efficiency. The B. subtilis sp. N4 demonstrated a maximum nitrite concentration tolerance of 60 mg/L, with μmax and Ks values calculated using a Monod model analysis of 1.67 mg/L/h and 0.29 mg/L, respectively. Immobilized B. subtilis sp. N4 could be reused for ten cycles while maintaining a nitrite degradation efficiency of >99 %, and retained a high nitrite-degrading ability after being refrigerated at 4 °C for three months. Immobilized B. subtilis sp. N4 effectively reduced ammonia nitrogen, nitrite, and nitrate concentrations in Nile tilapia aquaculture, maintaining them at consistently low levels. Therefore, free or immobilized B. subtilis sp. N4, with both nitrification and denitrification capabilities, has considerable potential for application in the aquaculture industry in the future.

Coupling Thiosulfate-Driven denitrification and anammox to remove nitrogen from actual wastewater

A coupled thiosulfate-driven denitrification and anammox (TDDA) process was established to remove nitrogen from wastewater. It was optimized in an up-flow anaerobic sludge blanket reactor using synthetic wastewater, and its reliability was then verified with actual wastewater. The results demonstrated that nitrate, nitrite, and ammonium could be synergistically removed, and the highest total nitrogen removal efficiency reached 97.8% at a loading of 1.39 kgN/(m3·d). Anammox bacteria, primarily Candidatus_Brocadia, were the main contributors to nitrogen removal, while sulfur-oxidizing bacteria such as Thiobacillus and Rhodanobacter played a supportive role. By optimizing substrate conditions to enhance the anammox process, the coupled system attained higher abundances of functional genes such as napA, nirS, hzs, soxXA, and soxYZ, along with the corresponding microbial species. The data suggested that microbial cross-feeding and self-adaptation strategies were key to efficient nitrogen removal by TDDA.

Natural bioink of interpenetrating network hydrogels mimicking extracellular polymeric substances for microbial immobilization in water pollution control

Artificial biomanufacturing has been developed as a promising biotechnology for water pollution control. Effective bioimmobilization techniques are limited in application because of low productivity and the difficulty in achieving both mechanical strength and biocompatibility. Bioprinting technology, using biomaterials as bioink to enable the rapid on-demand production of bioactive structures, opens a new path for bioimmobilization. In this study, mimicking extracellular polysaccharide and protein of aerobic granular sludge (AGS), sodium alginate (SA) and silk fibroin methacryloyl (SilMA) were developed as the dual-component bioink with a suitable viscosity for bioprinting hydrogel. Interpenetrating network (IPN) hydrogel beads were manufactured using 1.5% (w/v) SA combined with 20% (w/v) SilMA through physical and covalent crosslinking, which exhibited excellent structural stability and bioactivity. The addition of SilMA provided a solution to the poor mechanical stability of SA-Ca hydrogels limited by Ca2+-Na+ ionic exchange. The unique structure of SilMA contributed to the reduction of hydrogel swelling as well as the prevention of SA loss. IPN hydrogels showed a swelling rate of less than 20% compared to the high swelling rate of more than 60% for SA hydrogels. On the other hand, SA controlled the hardening induced by excessive self-assembly of SilMA and improved mass transport in SilMA hydrogels. Compared to IPN hydrogels, SilMA hydrogels experienced a 15% volumetric shrinkage and exhibited a low water content of 92%. Sonication pretreatment of the dual-component bioink not only increased the intermolecular chain entanglement to form IPN, but also led to β-sheet content in SiMA reaching 46%-48%, which resulted in the formation of stable IPN hydrogels dominated entirely by physical crosslinking. Satisfactory proliferation and viability were achieved for the encapsulated bacteria in IPN hydrogels (μmax 1.49-2.18 d-1). Further, the IPN biohydrogels could maintain structural stability as well as achieve pollutant removal for treating synthetic wastewater with high Na+ concentration of 300 mg/L. The novel SA/SilMA hydrogel bioprinting strategy established in this study offers a new direction for bioimmobilization in water pollution control and other environmental applications.

Microbial nitrogen cycling in Microcystis colonies and its contribution to nitrogen removal in eutrophic Lake Taihu, China

Cyanobacterial blooms induced by excessive loadings of nitrogen (N) and other nutrients are a severe ecological problem in aquatic ecosystems. Previous studies of N removal have primarily focused on sediment-water interface, yet the role of cyanobacterial colonies has recently been attracting more research attention. In this study, N cycling processes were quantified for cyanobacterial colonies (primarily Microcystis colonies) and their contribution to N removal was estimated for a large, shallow eutrophic lake in China, Lake Taihu. Various N cycling processes were determined via stable 15N isotope, together with 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) chip. Denitrification was found to be the most prominent process, estimated to be 36.63, 9.85, 3.35, and 3.15 times higher than dissimilatory nitrate reduction to ammonium (DNRA), nitrification, ammonium (NH4+) uptake and nitrate (NO3-) uptake rates, respectively. Denitrifiers accounted for a large part of the bacterial taxa (35.50 ± 24.65%), and the nirS gene was the most abundant among N cycling-related genes, with (2.54 ± 0.51) × 109 copies g-1Microcystis colonies. A field investigation revealed a positive correlation between the potential denitrification rate and the Chl-a concentration (mostly derived from Microcystis colonies). Based on a multiple stepwise regression model and historical data from 2007 to 2015 for Lake Taihu, the total amount of N removed via denitrification by Microcystis colonies was estimated at 171.72 ± 49.74 t yr-1; this suggests that Microcystis colonies have played an important role in N removal in Lake Taihu since the drinking water crisis in 2007. Overall, this study revealed the importance of denitrification within Microcystis colonies for N removal in eutrophic lakes, like Lake Taihu.

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.

Enhancing bioremediation of petroleum-contaminated soil by sophorolipids-modified biochar: Combined metagenomic and metabolomic analyses

In this study, sophorolipids (SLs)-modified biochar (BC-SLs) was used to enhance the bioremediation of petroleum hydrocarbons (PHs) contaminated soil. The biodegradation rate of petroleum hydrocarbons (PHs) by BC-SLs and BC treatments were 62.86 % and 52.64 % after 60 days of remediation experiments, respectively, higher than non-biochar treatment group (24.09 %). The metagenomic analysis showed that the abundance of petroleum-degrading bacteria Actinobacteria and Proteobacteria were increased by 3.8 % and 5.3 %, respectively in BC-SLs treatment, and the abundance of functional genes for PHs degradation, such as alkB, nidA and pcaG, were significantly increased by 12.85 %, 30.08 % and 21.01 %, respectively. The metabolomic analysis showed that BC-SLs facilitated the metabolic process of PHs, the microbial metabolism of petroleum hydrocarbons (PHs) became more active. Fatty acid degradation and polycyclic aromatic hydrocarbons (PAHs) degradation were up-regulated, indicating the promoting effect of the BC-SLs for PHs metabolism. The combined metagenomic and metabolomic analysis demonstrated the strong positive correlations between PHs metabolites and PHs-degrading bacteria, such as lauric acid vs. Actinobacteria, benzoic vs. Proteobacteria. The strong positive correlations between PHs metabolites and PHs-degrading genes were also observed, such as o-ehyltoluene vs. nahD, 4-isopropylbenzoic acid vs. etbAa. The modification of biochar with SLs increased the oxygen-containing functional groups on the surface of biochar. Meanwhile, the emulsification and solubilization of SLs promoted the bioavailability of PHs. The effects of BC-SLs on the nitrogen cycle during PHs remediation showed that it facilitated the accumulation of nitrogen-fixing genes, promoted nitrification but inhibited denitrification process. This study confirms that the application of BC-SLs is an effective remediation of PHs contamination and a sustainable method for controlling agricultural waste resources.

Aerobic denitrifying bacterial community with low C/N ratio remove nitrate from micro-polluted water: Metagenomics unravels denitrification pathways

The efficient nitrogen removal from micro-polluted source water is an international challenge to be solved urgently. However, the inner denitrification mechanism of native aerobic denitrifying bacterial communities in response to carbon scarcity remains relatively unclear. Here, the bacterial community XT6, screened from an oligotrophic reservoir, exhibited aerobic denitrifying capacity under low-carbon environments. Up to 76.79-81.64 % of total organic carbon (TOC) and 51.48-67.60 % of NO3--N were removed by XT6 within 48 h at C/N ratios of 2.0-3.0. Additionally, the nitrogen balance experiments further manifested that 26.27-38.13 % of NO3--N was lost in gaseous form. As the C/N ratio decreased, XT6 tended to generate more extracellular polymeric substances (EPS), with the tightly bound EPS showing the largest increase. Pseudomonas and Variovorax were quite abundant in XT6, constituting 59.69 % and 28.65 % of the total sequences, respectively. Furthermore, metagenomics analysis evidenced that XT6 removed TOC and nitrate mainly through the tricarboxylic acid cycle and aerobic denitrification. Overall, the abovementioned results provide a deeper understanding of the nitrogen metabolic pathways of indigenous aerobic denitrifying bacterial communities with low C/N ratios and offer useful guidance for controlling nitrogen pollution in oligotrophic ecosystems.

Regulation mechanism of nitrite degradation in Lactobacillus plantarum WU14 mediated by Fnr

Fumarate and nitrate reduction regulatory protein (Fnr)-a global transcriptional regulator-can directly or indirectly regulate many genes in different metabolic pathways at the top of the bacterial transcription regulation network. The present study explored the regulatory mechanism of Fnr-mediated nitrite degradation in Lactobacillus plantarum WU14 through gene transcription and expression analysis of oxygen sensing and nir operon expression regulation by Fnr. The interaction and the mechanism of transcriptional regulation between Fnr and GlnR were also examined under nitrite stress. After Fnr and GlnR purification by glutathione S-transferase tags, they were successfully expressed in Escherichia coli by constructing an expression vector. The results of electrophoresis mobility shift assay and qRT-PCR indicated that Fnr specifically bound to the PglnR and Pnir promoters and regulated the expression of nitrite reductase (Nir) and GlnR. After 6-12 h of culture, the expressions of fnr and nir under anaerobic conditions were higher than under aerobic conditions; the expression of these two genes increased with sodium nitrite (NaNO2) addition during aerobic culture. Overall, the present study indicated that Fnr not only directly participated in the expression of Nir and GlnR but also indirectly regulated the expression of Nir through GlnR regulation.

Enterobacter sp. HIT-SHJ4 isolated from wetland with carbon, nitrogen and sulfur co-metabolism and its implication for bioremediation

Both autotrophic and heterotrophic denitrification are known as important bioprocesses of microbe-mediated nitrogen cycle in natural ecosystems. Actually, mixotrophic denitrification co-driven by organic matter and reduced sulfur substances are also common, especially in hypoxic environments such as estuarine sediments. However, carbon, nitrogen and sulfur co-metabolism during mixotrophic denitrification in natural water ecosystems has rarely been reported in detail. Therefore, this study investigated the co-metabolism of carbon, nitrogen and sulfur using samples collected from four distinct natural water ecosystems. Results demonstrated that samples from various sources all exhibited the ability for co-metabolism of carbon, nitrogen and sulfur. Microbial community analysis showed that Pseudomonas and Paracoccus were dominant bacteria ranging from 65.6% to 75.5% in mixotrophic environment. Enterobacter sp. HIT-SHJ4, a mixotrophic denitrifying strain which owned the capacity for co-metabolism of carbon, nitrogen and sulfur, was isolated and reported here for the first time. The strain preferred methanol as its carbon source and demonstrated remarkable efficiency for removing sulfide and nitrate with below 100 mg/L sulfide. Under weak acid conditions (pH 6.5-7.0), it exhibited enhanced capability in converting sulfide to elemental sulfur. Its bioactivity was evident within a temperature from 25 °C to 40 °C and C/N ratios from 0.75 to 3. This study confirmed the widespread presence of microbial-mediated synergistic carbon, nitrogen and sulfur metabolism in natural aquatic ecosystems. HIT-SHJ4 emerges as a novel strain, shedding light on carbon, nitrogen and sulfur co-metabolism in natural water bodies. Furthermore, it also serves as a promising candidate microorganism for in-situ ecological remediation, particularly in dealing with contamination posed by nitrate, sulfide, and organic matter.

Deciphering the roles of nitrogen source in sharping synchronous metabolic pathways of linear alkylbenzene sulfonate and nitrogen in a membrane biofilm for treating greywater

Nitrogen (N) source is an important factor affecting biological wastewater treatment. Although the oxygen-based membrane biofilm showed excellent greywater treatment performance, how N source impacts the synchronous removal of organics and N is still unclear. In this work, how N species (urea, nitrate and ammonia) affect synchronous metabolic pathways of organics and N were evaluated during greywater treatment in the membrane biofilm. Urea and ammonia achieved efficient chemical oxygen demand (>97.5%) and linear alkylbenzene sulfonate (LAS, >98.5%) removal, but nitrate enabled the maximum total N removal (80.8 ± 2.6%). The nitrate-added system had poor LAS removal ratio and high residual LAS, promoting the accumulation of effluent protein-like organics and fulvic acid matter. N source significantly induced bacterial community succession, and the increasing of corresponded functional flora can promote the transformation and utilization of microbial-mediated N. The nitrate system was more conducive to the accumulation of denitrification related microorganisms and enzymes, enabling the efficient N removal. Combining with high amount of ammonia monooxygenase that contributing to LAS and N co-metabolism, LAS mineralization related microbes and functional enzymes were generously accumulated in the urea and ammonia systems, which achieved the high efficiency of organics and LAS removal.

Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture

Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality in biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT in aquaculture industries, our comprehension of the community composition and functional potential of the floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate the FAB community in shrimp aquaculture systems, resulting in the reconstruction of 520 metagenome-assembled genomes (MAGs) spanning both bacterial and archaeal domains. Taxonomic analysis identified Pseudomonadota and Bacteroidota as core community members, with approximately 93% of recovered MAGs unclassified at the species level, indicating a large uncharacterized phylogenetic diversity hidden in the FAB community. Functional annotation of these MAGs unveiled their complex carbohydrate-degrading potential and involvement in carbon, nitrogen, and sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction to ammonia, thiosulfate oxidation, and sulfide oxidation pathways, suggesting the FAB community's versatility for both aerobic and anaerobic metabolisms. Conversely, genes associated with heterotrophic nitrification, anaerobic ammonium oxidation, assimilatory nitrate reduction, and sulfate reduction were undetected. Members of Rhodobacteraceae emerged as the most abundant and metabolically versatile taxa in this intriguing community. Our MAGs compendium is expected to expand the available genome collection from such underexplored aquaculture environments. By elucidating the microbial community structure and metabolic capabilities, this study provides valuable insights into the key biogeochemical processes occurring in biofloc aquacultures and the major microbial contributors driving these processes.

IMPORTANCE

Biofloc technology has emerged as a sustainable aquaculture approach, utilizing microbial aggregates (bioflocs) to improve water quality and animal health. However, the specific microbial taxa within this intriguing community responsible for these benefits are largely unknown. Compounding this challenge, many bacterial taxa resist laboratory cultivation, hindering taxonomic and genomic analyses. To address these gaps, we employed metagenomic binning approach to recover over 500 microbial genomes from floc-associated microbiota of biofloc aquaculture systems operating in South Korea and China. Through taxonomic and genomic analyses, we deciphered the functional gene content of diverse microbial taxa, shedding light on their potential roles in key biogeochemical processes like nitrogen and sulfur metabolisms. Notably, our findings underscore the taxa-specific contributions of microbes in aquaculture environments, particularly in complex carbon degradation and the removal of toxic substances like ammonia, nitrate, and sulfide.

Responses of endogenous partial denitrification process to acetate and propionate as carbon sources: Nitrite accumulation performance, microbial community dynamic changes, and metagenomic insights

Endogenous partial denitrification (EPD) offered a promising pathway for supplying nitrite to anammox, and it also enabled energy-efficient and cost-effective nitrogen removal. However, information about the impact of different carbon sources on the EPD system was limited, and the metabolic mechanisms remained unclear. This study operated the EPD system for 180 days with various acetate and propionate ratios over eight phases. The nitrate-to-nitrite transformation ratio (NTR) decreased from 81.7 % to 0.4 % as the acetate/propionate (Ac/Pr) ratio shifted from 3:0 to 0:3, but the NTR returned to 86.1 % after propionate was replaced with acetate. Typical cycles indicated that PHB (126.8 and 133.9 mg COD/g VSS, respectively) was mainly stored, facilitating a higher NTR (87.8 % and 67.7 %, respectively) on days 58 and 180 in the presence of acetate. In contrast, on day 158 in the presence of propionate, PHV (84.8 mg COD/g VSS) was predominantly stored, resulting in negligible nitrite accumulation (0.2 mg N/L). Metagenomic analysis revealed that the microbial community structure did not significantly change, and the (narGHI+napAB)/nirKS ratio consistently exceeded 7:2, despite variations in the carbon source. Compared with acetate, propionate as carbon source reduced the abundance of genes encoding NADH-producing enzymes (e.g., mdh), likely owing to a shift in PHAs synthesis and degradation pathways. Consequently, limited NADH affected electron distribution and transfer rates, thereby decreasing the nitrate reduction rate and causing nitrite produced by narGHI and napAB to be immediately reduced by nirKS. This study provided new insights and guidance for EPD systems to manage the conditions of carbon deficiency or complex carbon sources.

Forage conservation is a neglected nitrous oxide source

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

Genomic analysis and metabolic characteristics provide insights into inorganic nitrogen metabolism of novel bacterium Acinetobacter pittii J08

A novel A. pittii J08 with heterotrophic nitrification and aerobic denitrification (HN-AD) isolated from pond sediments could rapidly degrade inorganic nitrogen (N) and total nitrogen (TN-N) with ammonium (NH4+-N) preference. N degradation rate of NH4+-N, nitrite (NO2--N) and nitrate (NO3--N) were 3.9 mgL-1h-1, 3.0 mgL-1h-1 and 2.7 mgL-1h-1, respectively. In addition, strain J08 could effectively utilize most of detected low-molecular-weight carbon (LMWC) sources to degrade inorganic N with a wide adaptability to various culture conditions. Whole genome sequencing (WGS) analysis revealed that assembled genome of stain J08 possessed the crucial genes involved in dissimilatory/assimilatory NO3--N reduction and NH4+-N assimilation. These results indicated that strain J08 could be applied to wastewater treatment in aquaculture.

Effects of nitrate reduction on the biotransformation of 1H-1,2,4-triazole: Mechanism and community evolution

Due to the refractory of 1 H-1,2,4-triazole (TZ), conventional anaerobic biological treatment technology is usually restricted by low removal efficiency and poor system stability. In this study, TZ biodegradation and nitrate reduction was coupled to improve the removal efficiency of TZ from polluted wastewater. Batch assay was performed with pure culture strain Raoultella sp. NJUST42, which was reported to have the capability to degrade TZ in our previous study. Based on batch assay result, complete removal of TZ could be achieved in the presence of nitrate, whereas only 50% of TZ could be removed in the control system. Long-term stability experiment indicated that the relative abundance of microorganisms (Bacteroidetes_vadinHA17, Georgenia, Anaerolinea, etc) was obviously enhanced under nitrate reduction condition. During long-term period, major intermediates for TZ biodegradation such as [1,2,4]Triazolidine-3,5-diol, hydrazine dibasic carboxylic acid and carbamic acid were detected. A novel TZ biotransformation approach via hydration, TZ-ring cleavage, deamination and oxidation was speculated. PICRUSt1 and KEGG pathway analyses indicated that hydration (dch), oxidation (adhD, oah, pucG, fdhA) of TZ and nitrate reduction (Nar, napA, nrfA, nirBK, norB, nosZ) were significantly enhanced in the presence of nitrate. Moreover, the significant enrichment of TCA cycle (gab, sdh, fum, etc.) indicated that carbon and energy metabolism were facilitated with the addition of nitrate, thus improved TZ catabolism. The proposed mechanism demonstrated that TZ biodegradation coupled with nitrate reduction would be a promising approach for efficient treatment of wastewater contaminated by TZ.

Effects of antibiotics on microbial nitrogen cycling and N2O emissions: A review

Sulfonamides, quinolones, tetracyclines, and macrolides are the most prevalent classes of antibiotics used in both medical treatment and agriculture. The misuse of antibiotics leads to their extensive dissemination in the environment. These antibiotics can modify the structure and functionality of microbial communities, consequently impacting microbial-mediated nitrogen cycling processes including nitrification, denitrification, and anammox. They can change the relative abundance of nirK/norB contributing to the emission of nitrous oxide, a potent greenhouse gas. This review provides a comprehensive examination of the presence of these four antibiotic classes across different environmental matrices and synthesizes current knowledge of their effects on the nitrogen cycle, including the underlying mechanisms. Such an overview is crucial for understanding the ecological impacts of antibiotics and for guiding future research directions. The presence of antibiotics in the environment varies widely, with significant differences in concentration and type across various settings. We conducted a comprehensive review of over 70 research articles that compare various aspects including processes, antibiotics, concentration ranges, microbial sources, experimental methods, and mechanisms of influence. Antibiotics can either inhibit, have no effect, or even stimulate nitrification, denitrification, and anammox, depending on the experimental conditions. The influence of antibiotics on the nitrogen cycle is characterized by dose-dependent responses, primarily inhibiting nitrification, denitrification, and anammox. This is achieved through alterations in microbial community composition and diversity, carbon source utilization, enzyme activities, electron transfer chain function, and the abundance of specific functional enzymes and antibiotic resistance genes. These alterations can lead to diminished removal of reactive nitrogen and heightened nitrous oxide emissions, potentially exacerbating the greenhouse effect and related environmental issues. Future research should consider diverse reaction mechanisms and expand the scope to investigate the combined effects of multiple antibiotics, as well as their interactions with heavy metals and other chemicals or organisms.

Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss

Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d-1 and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d-1, respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.

A novel derivative synchronous fluorescence method for the rapid, non-destructive and intuitive differentiation of denitrifying bacteria

It is challenging to differentiate bacteria residing in the same habitat by direct observation. This difficulty impedes the harvest, application and manipulation of functional bacteria in environmental engineering. In this study, we developed a novel method for rapid differentiation of living denitrifying bacteria based on derivative synchronous fluorescence spectroscopy, as exemplified by three heterotrophic nitrification-aerobic denitrification bacteria having the maximum nitrogen removal efficiencies greater than 90%. The intact bacteria and their living surroundings can be analyzed as an integrated target, which eliminates the need for the complex pre-processing of samples. Under the optimal synchronous scanning parameter (Δλ = 40 nm), each bacterium possesses a unique fluorescence spectral structure and the derivative synchronous fluorescence technique can significantly improve the spectral resolution compared to other conventional fluorescence methods, which enables the rapid differentiation of different bacteria through derivative synchronous fluorescence spectra as fast as 2 min per spectrum. Additionally, the derivative synchronous fluorescence technique can extract the spectral signals contributed by bacterial extracellular substances produced in the biological nitrogen removal process. Moreover, the results obtained from our method can reflect the real-time denitrification properties of bacteria in the biological nitrogen removal process of wastewater. All these merits highlight derivative synchronous fluorescence spectroscopy as a promising analytic method in the environmental field.

Recovery mechanism of bio-promoters on Cr(VI) suppressed denitrification: Toxicity remediation and enhanced electron transmission

Although the biotoxicity of heavy metals has been widely studied, there are few reports on the recovery strategy of the inhibited bio-system. This study proposed a combined promoter-I (Primary promoter: l-cysteine, biotin, and cytokinin + Electron-shuttle: PMo12) to recover the denitrification suppressed by Cr(VI). Compared with self-recovery, combined promoter-I shortened the recovery time of 28 cycles, and the recovered reactor possessed more stable long-term operation performance with >95 % nitrogen removal. The biomass increased by 7.07 mg VSS/(cm3 carrier) than self-recovery due to the promoted bacterial reproduction, thereby reducing the toxicity load of chromium per unit biomass. The combined promoter-I strengthened the toxicity remediation by promoting 92.84 % of the intracellular chromium release and rapidly activating anti-oxidative stress response. During toxicity remediation, ROS content quickly decreased, and the PN/PS value was 2.27 times that of self-recovery. PMo12 relieved Cr(VI) inhibition on NO3--N reduction by increasing NAR activity. The enhanced intracellular and intercellular electron transmission benefited from the stimulated NADH, FMN, and Cyt.c secretion by the primary promoter and the improved transmembrane electron transmission by Mo. PMo12 and the primary promoter synergized in regulating community structure and improving microbial richness. This study provided practical approaches for microbial toxicity remediation and maintaining high-efficiency denitrification.

Review of the mechanisms involved in dissimilatory nitrate reduction to ammonium and the efficacies of these mechanisms in the environment

Dissimilatory nitrate reduction to ammonium (DNRA) is currently of great interest because it is an important method for recovering nitrogen from wastewater and offers many advantages, over other methods. A full understanding of DNRA requires the mechanisms, pathways, and functional microorganisms involved to be identified. The roles these pathways play and the effectiveness of DNRA in the environment are not well understood. The objectives of this review are to describe our current understanding of the molecular mechanisms and pathways involved in DNRA from the substrate transfer perspective and to summarize the effects of DNRA in the environment. First, the mechanisms and pathways involved in DNRA are described in detail. Second, our understanding of DNRA by actinomycetes is reviewed and gaps in our understanding are identified. Finally, the effects of DNRA in the environment are assessed. This review will help in the development of future research into DNRA to promote the use of DNRA to treat wastewater and recover nitrogen.

Lumen air pressure regulated multifunctional microbiotas in membrane-aerated biofilm reactors for simultaneous nitrogen removal and antibiotic elimination from aquaculture wastewater

In this study, two membrane-aerated biofilm reactors (MABRs) were constructed: one solely utilizing biofilm and another hybrid MABR (HMABR) incorporating both suspended-sludge and biofilm to treat low C/N aquaculture wastewater under varying lumen air pressure (LAP). Both HMABR and MABR demonstrated superior nitrogen removal than conventional aeration reactors. Reducing LAP from 10 kPa to 2 kPa could enhance denitrification processes without severely compromising nitrification, resulting in an increase in total inorganic nitrogen (TIN) removal from 50.2±3.1 % to 71.6±1.0 %. The HMABR exhibited better denitrification efficacy than MABR, underscoring its potential for advanced nitrogen removal applications. A decline in LAP led to decreased extracellular polymeric substance (EPS) production, which could potentially augment reactor performance by minimizing mass transfer resistance while maintaining microbial matrix stability and function. Gene-centric metagenomics analysis revealed decreasing LAP impacted nitrogen metabolic potentials and electron flow pathways. The enrichment of napAB at higher LAP and the presence of complete ammonia oxidation (Comammox) Nitrospira at lower LAP indicated aerobic denitrification and Comammox processes in nitrogen removal. Multifunctional microbial communities developed under LAP regulation, diversifying the mechanisms for simultaneous nitrification-denitrification. Increased denitrifying gene pool (narGHI, nirK, norB) and enzymatic activity at a low LAP can amplify denitrification by promoting denitrifying genes and electron flow towards denitrifying enzymes. Sulfamethoxazole (SMX) was simultaneously removed with efficiency up to 80.2 ± 3.7 %, mainly via biodegradation, while antibiotic resistome and mobilome were propagated. Collectively, these findings could improve our understanding of nitrogen and antibiotic removal mechanisms under LAP regulation, offering valuable insights for the effective design and operation of MABR systems in aquaculture wastewater treatment.

Native microalgal-bacterial consortia from the Ecuadorian Amazon region: an alternative to domestic wastewater treatment

In low-middle income countries (LMIC), wastewater treatment using native microalgal-bacterial consortia has emerged as a cost-effective and technologically-accessible remediation strategy. This study evaluated the effectiveness of six microalgal-bacterial consortia (MBC) from the Ecuadorian Amazon in removing organic matter and nutrients from non-sterilized domestic wastewater (NSWW) and sterilized domestic wastewater (SWW) samples. Microalgal-bacterial consortia growth, in NSWW was, on average, six times higher than in SWW. Removal rates (RR) for NH4 +- N and PO4 3--P were also higher in NSWW, averaging 8.04 ± 1.07 and 6.27 ± 0.66 mg L-1 d-1, respectively. However, the RR for NO3 - -N did not significantly differ between SWW and NSWW, and the RR for soluble COD slightly decreased under non-sterilized conditions (NSWW). Our results also show that NSWW and SWW samples were statistically different with respect to their nutrient concentration (NH4 +-N and PO4 3--P), organic matter content (total and soluble COD and BOD5), and physical-chemical parameters (pH, T, and EC). The enhanced growth performance of MBC in NSWW can be plausibly attributed to differences in nutrient and organic matter composition between NSWW and SWW. Additionally, a potential synergy between the autochthonous consortia present in NSWW and the native microalgal-bacterial consortia may contribute to this efficiency, contrasting with SWW where no active autochthonous consortia were observed. Finally, we also show that MBC from different localities exhibit clear differences in their ability to remove organic matter and nutrients from NSWW and SWW. Future research should focus on elucidating the taxonomic and functional profiles of microbial communities within the consortia, paving the way for a more comprehensive understanding of their potential applications in sustainable wastewater management.

Feast/famine ratio regulates the succession of heterotrophic nitrification-aerobic denitrification and autotrophic ammonia oxidizing bacteria in halophilic aerobic granular sludge treating saline wastewater

Heterotrophic nitrification-aerobic denitrification (HN-AD) shows innovation potential of wastewater treatment process in a single tank. However, how to enrich HN-AD bacteria in activated sludge to enhance their contribution remained unknown. This study explored the impact of the feast/famine (F/F) ratio on the succession of autotrophic ammonia oxidizing bacteria (AOB) and HN-AD bacteria in a halophilic aerobic granular sludge (HAGS) system. As the F/F ratio decreased from 1/9 to 1/15, the total inorganic nitrogen (TIN) removal performance significantly decreased. The proportion of heterotrophic bacteria was dropped from 79.0 % to 33 %. Accordingly, the relative abundance of Paracoccus decreased from 70.8 % to 25.4 %, and the copy number of the napA gene was reduced from 2.2 × 1010 copies/g HAGS to 8.1 × 109 copies/g HAGS. It found the F/F ratio regulated the population succession of autotrophic AOB and HN-AD bacteria, thereby providing a solution to achieve the enrichment of HN-AD bacteria in HAGS.

Enhanced denitrification of biodegradable polymers using Bacillus pumilus in aerobic denitrification bioreactors: Performance and mechanism

Nitrate accumulation is an important issue that affects animal health and causes eutrophication. This study combined biodegradable polymers with degrading bacteria to lead to high denitrification efficiency. The results showed polycaprolactone had the highest degradation and carbon release rate (0.214 mg/g∙d) and nitrogen removal was greatest when the Bacillus pumilus and Halomonas venusta ratio was 1:2. When the hydraulic retention time was extended to 12 h, the nitrate removal rate for H. venusta with B. pumilus and polycaprolactone increased by 48 %. Furthermore, the group with B. pumilus contained more Proteobacteria (77.34 %) and denitrifying functional enzymes than the group without B. pumilus. These findings indicated B.pumilus can enhance the degradation of biodegradable polymers especially polycaprolactone to improve the denitrification of the aerobic denitrification bacteria H.venusta when treating maricultural wastewater.

Denitrification in low oxic environments increases the accumulation of nitrogen oxide intermediates and modulates the evolutionary potential of microbial populations

Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this phenomenon is well-established, its consequences on ecological and evolutionary processes remain poorly understood. We hypothesize here that denitrification in oxic environments can modify the accumulation profiles of nitrogen oxide intermediates with cascading effects on the evolutionary potentials of denitrifying microorganisms. To test this, we performed laboratory experiments with Paracoccus denitrificans and complemented them with individual-based computational modelling. We found that denitrification in low oxic environments significantly increases the accumulation of nitrite and nitric oxide. We further found that the increased accumulation of these intermediates has a negative effect on growth at low pH. Finally, we found that the increased negative effect at low pH increases the number of individuals that contribute to surface-associated growth. This increases the amount of genetic diversity that is preserved from the initial population, thus increasing the number of genetic targets for natural selection to act upon and resulting in higher evolutionary potentials. Together, our data highlight that denitrification in low oxic environments can affect the ecological processes and evolutionary potentials of denitrifying microorganisms by modifying the accumulation of nitrogen oxide intermediates.

Optimization of nitrogen removal conditions based on response surface methodology and nitrogen removal pathway of Paracoccus sp. QD-19

The strain Paracoccus sp. QD-19 was isolated from the sludge-water mixture of aerobic tanks at the southern wastewater treatment plant in Shenyang, China. The optimal nitrogen removal conditions for strain QD-19 were determined using the Plackett-Burman design, path of steepest ascent method, and response surface methodology (RSM). The optimum nitrogen removal conditions were C/N 12.93, temperature 37 °C, and shaking speed 175.50 r/min. Strain QD-19 achieved 83.82 ± 0.80 % nitrogen removal efficiency at 10 h under optimum conditions. Functional enzyme-encodinge genes amplified via 16S rRNA sequence analysis included amoA, hao, napA, nirS, nirK, norB, and nosZ. The results revealed that NH4+-N → NH2OH → NO2--N → NO3--N → NO2--N → NO → N2O → N2 was the pathway for heterotrophic nitrification - aerobic denitrification. The strain was used to treat wastewater from a sewage treatment plant under optimal response surface methodology conditions. As a result, the TN removal efficiency was 77.11 %. The findings demonstrated that strain QD-19 exhibits favorable potential for heterotrophic nitrification and aerobic denitrification (HN-AD) of actual wastewater, presenting a promising application for biological wastewater treatment.

Aerobic denitrification as an N2O source from microbial communities

Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.

Iron-based multi-carbon composite and Pseudomonas furukawaii ZS1 co-affect nitrogen removal, microbial community dynamics and metabolism pathways in low-temperature aquaculture wastewater

Aerobic denitrification is the key process in the elimination of nitrogen from aquaculture wastewater, especially for wastewater with high dissolved oxygen and low carbon/nitrogen (C/N) ratio. However, a low C/N ratio, especially in low-temperature environments, restricts the activity of aerobic denitrifiers and decreases the nitrogen elimination efficiency. In this study, an iron-based multi-solid carbon source composite that immobilized aerobic denitrifying bacteria ZS1 (IMCSCP) was synthesized to treat aerobic (DO > 5 mg/L), low temperature (<15 °C) and low C/N ratio (C/N = 4) aquaculture wastewater. The results showed that the sequencing batch biofilm reactor (SBBR) packed with IMCSCP exhibited the highest nitrogen removal performance, with removal rates of 95.63% and 85.44% for nitrate nitrogen and total nitrogen, respectively, which were 33.03% and 30.75% higher than those in the reactor filled with multi-solid carbon source composite (MCSC). Microbial community and network analysis showed that Pseudomonas furukawaii ZS1 successfully colonized the SBBR filled with IMCSCP, and Exiguobacterium, Cellulomonas and Pseudomonas were essential for the nitrogen elimination. Metagenomic analysis showed that an increase in gene abundance related to carbon metabolism, nitrogen metabolism, extracellular polymer substance synthesis and electron transfer in the IMCSCP, enabling denitrification in the SBBR to be achieved via multiple pathways. The results of this study provided new insights into the microbial removal mechanism of nitrogen in SBBR packed with IMCSCP at low temperatures.

Indigenous mixotrophic aerobic denitrifiers stimulated by oxygen micro/nanobubble-loaded microporous biochar

The prevalence of hypoxia in surface sediment inhibits the growth of aerobic denitrifiers in natural waters. A novel oxygen micro/nanobubble-loaded microporous biochar (OMB) was developed to activate indigenous aerobic denitrifiers in this study. The results indicate a thin-layer OMB capping mitigates hypoxia effectively. Following a 30-day microcosm-based incubation, a 60 % decrease in total nitrogen concentration was observed, and the oxygen penetration depth in the sediment was increased from <4.0 mm to 38.4 mm. High-throughput sequencing revealed the stimulation of indigenous mixotrophic aerobic denitrifiers, including autotrophic denitrifiers such as Hydrogenophaga and Thiobacillus, heterotrophic denitrifiers like Limnobacter and unclassified_f_Methylophilaceae, and heterotrophic nitrification aerobic denitrification bacteria, including Shinella and Acidovorax, with total relative abundance reaching up to 38.1 %. Further analysis showed OMB enhanced the overall collaborative relationships among microorganisms and promoted the expression of nitrification- and denitrification-related genes. This study introduces an innovative strategy for stimulating indigenous aerobic denitrifiers in aquatic ecosystems.

Insights into the nitrogen transformation mechanism of Pseudomonas sp. Y15 capable of heterotrophic nitrification and aerobic denitrification

Excessive nitrogen (N) discharged in water is a major cause of eutrophication and other severe environmental issues. Biological N removal via heterotrophic nitrification and aerobic denitrification (HN-AD) has drawn particular attention, owing to the merit of concurrent nitrification and denitrification inside one cell. However, the mechanisms underlying N transformation during HN-AD remain unclear. In the present study, the HN-AD strain Pseudomonas sp. Y15 (Y15) was isolated to explore the N distribution and flow, based on stoichiometry and energetics. The total N removal efficiency by Y15 increased linearly with C/N ratio (in the range of 5-15) to ∼96.8%. Of this, ∼32.2% and ∼64.6% were transformed into gas-N and biomass-N, respectively. A new intracellular N metabolic bypass (NO → NO2) was found, to address the substantial gaseous N production during HN-AD. Concering energetics, the large portion of the biomass-N is ascribed to the synthesis of the amino acids that consume low energy. Finally, two novel stoichiometric equations for different N sources were proposed, to describe the overall HN-AD process. This study deepens the fundamental knowledge on HN-AD bacteria and enlightens their use in treating N-contaminated wastewater.

Quorum-sensing gene regulates hormetic effects induced by sulfonamides in Comamonadaceae

IMPORTANCE

Antibiotics can induce dose-dependent hormetic effects on bacterial cell proliferation, i.e., low-dose stimulation and high-dose inhibition. However, the underlying molecular basis has yet to be clarified. Here, we showed that sulfonamides play dual roles as a weapon and signal against Comamonas testosteroni that can modulate cell physiology and phenotype. Subsequently, through investigating the hormesis mechanism, we proposed a comprehensive regulatory pathway for the hormetic effects of Comamonas testosteroni low-level sulfonamides and determined the generality of the observed regulatory model in the Comamonadaceae family. Considering the prevalence of Comamonadaceae in human guts and environmental ecosystems, we provide critical insights into the health and ecological effects of antibiotics.

Extracellular electron transfer for aerobic denitrification mediated by the bioelectric catalytic system with zero-carbon source

The slow rate of electron transfer and the large consumption of carbon sources are technical bottlenecks in the biological treatment of wastewater. Here, we first proposed to domesticate aerobic denitrifying bacteria (ADB) from heterotrophic to autotrophic by electricity (0.6 V) under zero organic carbon source conditions, to accelerate electron transfer and shorten hydraulic retention time (HRT) while increasing the biodegradation rate. Then we investigated the extracellular electron transfer (EET) mechanism mediated by this process, and additionally examined the integrated nitrogen removal efficiency of this system with composite pollution. It was demonstrated that compared with the traditional membrane bioreactor (MBR), the BEC displayed higher nitrogen removal efficiency. Especially at C/N = 0, the BEC exhibited a NO3--N removal rate of 95.42 ± 2.71 % for 4 h, which was about 6.5 times higher than that of the MBR. Under the compound pollution condition, the BEC still maintained high NO3--N and tetracycline removal (94.52 ± 2.01 % and 91.50 ± 0.001 %), greatly superior to the MBR (10.64 ± 2.01 % and 12.00 ± 0.019 %). In addition, in-situ electrochemical tests showed that the nitrate in the BEC could be directly converted to N2 by reduction using electrons from the cathode, which was successfully demonstrated as a terminal electron acceptor.

Microalgae-assisted heterotrophic nitrification-aerobic denitrification process for cost-effective nitrogen and phosphorus removal from high-salinity wastewater: Performance, mechanism, and bacterial community

A microalgae-assisted heterotrophic nitrification-aerobic denitrification (HNAD) system for efficient nutrient removal from high-salinity wastewater was constructed for the first time as a cost-effective process in the present study. Excellent nutrient removal (∼100.0 %) was achieved through the symbiotic system. The biological removal process, biologically induced phosphate precipitation (BIPP), microalgae uptake, and ammonia stripping worked together for nutrient removal. Furthermore, the biological removal process achieved by biofilm contributed to approximately 55.3-71.8 % of nitrogen removal. BIPP undertook approximately 45.6-51.8 % of phosphorus removal. Batch activity tests confirmed that HNAD fulfilled an extremely critical role in nitrogen removal. Microalgal metabolism drove BIPP to achieve efficient phosphorus removal. Moreover, as the main HNAD bacteria, OLB13 and Thauera were enriched. The preliminary energy flow analysis demonstrated that the symbiotic system could achieve energy neutrality, theoretically. The findings provide novel insights into strategies of low-carbon and efficient nutrient removal from high-salinity wastewater.

Homogeneous environmental selection mainly determines the denitrifying bacterial community in intensive aquaculture water

Nitrate reduction by napA (encodes periplasmic nitrate reductase) bacteria and nitrous oxide reduction by nosZ (encodes nitrous oxide reductase) bacteria play important roles in nitrogen cycling and removal in intensive aquaculture systems. This study investigated the diversity, dynamics, drivers, and assembly mechanisms of total bacteria as well as napA and nosZ denitrifiers in intensive shrimp aquaculture ponds over a 100-day period. Alpha diversity of the total bacterial community increased significantly over time. In contrast, the alpha diversity of napA and nosZ bacteria remained relatively stable throughout the aquaculture process. The community structure changed markedly across all groups over the culture period. Total nitrogen, phosphate, total phosphorus, and silicate were identified as significant drivers of the denitrifying bacterial communities. Network analysis revealed complex co-occurrence patterns between total, napA, and nosZ bacteria which fluctuated over time. A null model approach showed that, unlike the total community dominated by stochastic factors, napA and nosZ bacteria were primarily governed by deterministic processes. The level of determinism increased with nutrient loading, suggesting the denitrifying community can be manipulated by bioaugmentation. The dominant genus Ruegeria may be a promising candidate for introducing targeted denitrifiers into aquaculture systems to improve nitrogen removal. Overall, this study provides important ecological insights into aerobic and nitrous oxide-reducing denitrifiers in intensive aquaculture, supporting strategies to optimize microbial community structure and function.

Performance evaluation, enzymatic activity change and metagenomic analysis of sequencing batch reactor under divalent zinc stress

Divalent zinc (Zn2+) are widely detected in domestic and industrial wastewater, and it is essential to evaluate the effect of Zn2+ on wastewater biological treatment process due to its bio-toxicity. In this study, the nitrogen removal rates and their corresponding enzymatic activities of sequencing batch reactor decreased with the increase of Zn2+ concentration. The Zn2+ accumulation in activated sludge caused significant antioxidant response, and the reactive oxygen species (ROS) production and antioxidant enzymatic activities were positively correlated with Zn2+ concentration. The presence of Zn2+ inhibited the metabolic pathways related to energy production and electron transport. The abundance decreases of nitrification and denitrification functional genes led to the deterioration of nitrogen removal performance under Zn2+ stress. The correlation analysis between functional gene modules and microbial genera revealed that Zoogloea had obvious Zn2+ resistance. This study can provide the insights into the influencing mechanism of Zn2+ on the biological nitrogen removal process.

Enhanced bioelectricity generation in thermophilic microbial fuel cell with lignocellulose as an electron donor by resazurin-mediated electron transfer

Microbial fuel cell (MFC) with lignocellulose as an electron donor is considered a sustainable biorefinery. However, low lignocellulose degradation and energy output restrict the scale of application. Herein, the extracellular electron transfer (EET) capacity of Acetivibrio thermocellus DSM 1313 with lignocellulose as substrate was shown to be mediated by the self-produced flavin, and its intracellular electron transfer went through the whole respiratory chain. Thermophilic MFC with resazurin exhibited an increase in the open circuit voltage by 37.78%, and a 2.60 folds increase in power density of 77.85 mW/m2, respectively. Differential pulse voltammetry and electrochemical impedance spectroscopy analysis indicated that resazurin decreased the solution and anode charge transfer resistance, and enhanced the extracellular electrochemical activity. Furthermore, resazurin resulted in a lower redox potential, allowing preferential electron transfer to resazurin rather than flavin. This research establishes a resazurin-mediated thermophilic MFC with lignocellulose as substrate, which provides novel idea on the biomass refinery.

Exploring influence mechanism of small-molecule carbon source on heterotrophic nitrification-aerobic denitrification process from carbon metabolism, nitrogen metabolism and electron transport process

The heterotrophic nitrification-aerobic denitrification (HNAD) process can remove nitrogen and organic carbon under aerobic conditions. To get the in-depth mechanism of the HAND process, a strain named Acinetobacter johnsonii ZHL01 was isolated, and enzyme activity, electron transport, energy production, and gene expression of the strain were studied with small-molecule carbon sources, including sodium citrate, sodium acetate, sodium fumarate, and sodium succinate. The HNAD pathway of ZHL01 was NH4+→NH2OH → NO, and nitrogen balance analysis shows that ZHL01 could assimilate and denitrify 58.29 ± 1.05 % and 16.58 ± 1.07 % of nitrogen, respectively. The assimilation, the nitrification/denitrification, and the respiration processes were regulated by the concentration of reduced nicotinamide adenine dinucleotide (NADH) produced from the different metabolic pathways of small-molecule carbon sources. The HNAD process occurs to reduce intracellular redox levels related to NADH concentrations. This discovery provides a theoretical basis for the practical application of HAND bacteria.

Combination of sequencing batch reactor activated sludge process with sludge lysis using thermophilic bacterial community for minimizing excess sludge

Sludge reduction is a major challenge in biological wastewater treatment. Hydrolytic enzymes secreted by thermophilic bacteria can lyse sludge and thus achieve sludge reduction, and the indigenous thermophilic community in sludge can lyse sludge more effectively. In this study, the feasibility of combining a sludge lysis reactor based on thermophilic bacteria community (LTBC reactor, 75 °C) with a conventional sequencing batch activated sludge reactor (SBR) for sludge reduction (i.e., LTBC-SBR process) was systematically investigated first time. The effect of lysed sludge returning to the biochemical tank on pollutant removal efficiency, sludge flocculation, sludge settling, and microbial community and function of the LTBC-SBR process was studied. In the LTBC1-SBR process, a sludge growth rate of 0.71 g TSS/day was observed when the lysed sludge reflux ratio (LRR) was 1, and the sludge generation was reduced by 81.5% compared to the conventional SBR reactor. In the LTBC1-SBR process, the removal efficiencies of chemical oxygen demand and total nitrogen were 94.0% and 80.5%, respectively. There was no significant difference in the sludge volume index from the SBR to the LTBC1-SBR stage, however, the effluent suspended solids concentration increased from 35.2 ± 2.1 mg/L to 80.1 ± 5.3 mg/L. This was attributed to the reflux of sludge lysate. In addition, the changes in extracellular polymers content and composition resulted in poor sludge flocculation performance. Heterotrophic bacteria associated with Actinobacteria and Patescibacteria enriched in LTBC1-SBR with relative abundance of 28.51 ± 1.25% and 20.01 ± 1.21%, respectively, which decomposed the macromolecules in the refluxed lysed sludge and contributed to the sludge reduction. Furthermore, due to the inhibition of nitrite-oxidizing bacteria, the nitrite concentration in the effluent of the LTBC1-SBR system reached 4.7 ± 1.1 mg/L, and part of the denitrification process was achieved by short-cut nitrification and simultaneous denitrification. These results indicate that in-situ sludge reduction technology based on lyse sludge lysing by thermophilic community has considerable potential to be widely used in wastewater treatment.

Regulating mechanism of denitrifier Comamonas sp. YSF15 in response to carbon deficiency: Based on carbon/nitrogen functions and bioaggregation

There is an urgent demand to investigate mechanisms for the improvement of denitrification in carbon-deficient environment, which will effectively reduce the eutrophication in water bodies polluted by nitrate. In this study, denitrifying bacterium Comamonas sp. YSF15 was used to explore the differences in different carbon source concentrations, with the complete genome, metabolomics, and other detecting methods. Results showed that strain YSF15 was able to achieve efficient denitrification, with complete pathways for denitrification and central carbon metabolism. The carbon deficiency prompted the bacteria to use extracellular amino acid-like metabolites initially, to alleviate inhibition and maintain bioactivity, which also facilitated glycogen storage. The biogenic inhibitors (tautomycin, navitoclax, and glufosinate) at extremely low level potentially favored the competitiveness and intraspecific utilization of extracellular polysaccharides (PS). Optimal solutions for bioaggregation in carbon-deficient condition are achieved by regulating the hydrophobicity, and hydrogen bond in extracellular metabolites. The strategy contributes to the maintenance of bioactivity and adaptation to carbon deficiency. Overall, this study provides a new perspective on understanding the denitrification strategies in carbon-deficient environment, and helps to improve the nitrate removal in low-carbon wastewater treatment.

Transcriptomics uncover the response of an aerobic denitrifying bacteria to zinc oxide nanoparticles exposure

Zinc oxide nanoparticles (ZnO NPs) show adverse impacts on aerobic denitrifying bacteria, little is known about the response of these bacteria to ZnO NPs exposure at cellular level. This study assessed the multiple responses of Pseudomonas aeruginosa PCN-2 under ZnO NPs exposure. We demonstrated that ZnO NPs exposure could inhibit the intracellular metabolism and stimulate the antioxidant defence capability of PCN-2. At lower exposure concentration (5 mg/L), exogenous ROS generated and resulted in the inhibition of pyruvate metabolism and citrate cycle, which caused deficient energy for aerobic denitrification. At higher concentrations (50 mg/L), endogenous ROS additionally generated and triggered to stronger down-regulation of oxidative phosphorylation, which caused suppressed electron transfers for aerobic denitrification. Meanwhile, ZnO NPs exposure promoted EPS production and biofilm formation, and antioxidases was especially particularly stimulated at higher concentration. Our findings are significant for understanding of microbial bacterial susceptibility, tolerance and resistance under the exposure of ZnO NPs.

Nitrogen removal performance of aerobic denitrifying bacteria enhanced by an iron-anode pulsed electric field

Pulsed electric field (PEF) technology has attracted considerable attention because it can efficiently treat pollutants that are difficult to degrade. In this study, a PEF system using iron as the electrode was constructed to investigate the effect of PEF-Fe on the growth and metabolism of aerobic denitrifying bacteria and the effectiveness of wastewater nitrogen removal. The chemical oxygen demand, NO3--N and nitrate removal rates were 98.93%, 97.60% and 24.40 mg·L-1·h-1, respectively, under optimal conditions. As confirmed in this study, PEF-Fe could improve the key enzyme activities of W207-14. Scanning electron microscopy revealed that the surface of PEF-Fe-treated W207-14 was intact and smooth without any irreversible deformation. Flow cytometry combined with fluorescence staining analysis also confirmed reversible electroporation on the cell membrane surface of PEF-Fe-treated W207-14. Differentially expressed gene enrichment analysis showed that PEF-Fe activated the transmembrane transport function of ATP-binding cassette transporte (ABC) transport proteins and enhanced the cell membrane permeability of aerobic denitrifying bacteria. The significant differential expression of iron-sulphur cluster proteins facilitated the regulation of electron transport and maintenance of the dynamic balance of iron ions within the PEF-Fe system.

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.

Enhanced nitrogen removal in low-carbon saline wastewater by adding functional bacteria into Sesuvium portulacastrum constructed wetlands

Functional bacterial communities (FBC) have members of different taxonomic biochemical groups, such as N2-fixation, nitrification and denitrification. This study explored the mechanism of the FBC from an upflow three-dimensional biofilm electrode reactor on enhancing the nitrogen removal efficiencies in a Sesuvium potulacastum (S. potulacastum) constructed wetland. There were high abundances of denitrifying bacteria detected in the FBC, and they had potential metabolic processes for nitrogen reduction. In the constructed wetland, cellular nitrogen compounds of S. potulacastum were enriched by overexpressed differentially expressed genes (DEGs), and the napA, narG, nirK, nirS, qnorB, and NosZ genes related to the denitrification process had more copies under FBC treatment. Nitrogen metabolism in root bacterial communities (RBCs) was activated in the FBC group compared with the control group without FBC. Finally, these FBCs improved the removal efficiencies of DTN (dissolved total nitrogen), NO3¯-N, NO2¯-N, and NH4+-N by 84.37 %, 87.42 %, 67.51 %, and 92.57 %, respectively, and their final concentrations met the emission standards of China. These findings indicate that adding FBC into S. potulacastum-constructed wetlands would result in high nitrogen removal efficiencies from wastewater and have large potential applications in further water treatment technology.