The nitrogen removal characterization of a cold-adapted bacterium: Bacillus simplex H-b

Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were thought to be carried-out by anaerobic bacteria constrained to anoxic conditions as they use nitrate (NO3-) as a terminal electron acceptor instead of molecular O2. Three soil bacilli, Neobacillus spp. strains PS2-9 and PS3-12 and Bacillus salipaludis PS3-36, were isolated from rice paddy field soil in Korea. The bacterial strains were selected as possible candidates performing aerobic denitrification and DNRA as they observed to reduce NO3- and produce extracellular NH4+ regardless of oxygen presence at the initial screening. Whole genome sequencing revealed that these strains possessed all the denitrification and DNRA functional genes in their genomes, including the nirK, nosZ, nirB, and nrfA genes, which were simultaneously cotranscribed under aerobic condition. The ratio between the assimilatory and dissimilatory NO3- reduction pathways depended on the availability of a nitrogen source for cell growth, other than NO3-. Based on the phenotypic and transcriptional analyses of the NO3- reductions, all three of the facultative anaerobic strains reduced NO3- likely in both assimilatory and dissimilatory pathways under both aerobic and anoxic conditions. To our knowledge, this is the first report that describes coexistence of NO3- assimilation, denitrification, and DNRA in a Bacillus or Neobacillus strain under aerobic condition. These strains may play a pivotal role in the soil nitrogen cycle.

Characteristics of a heavy metal resistant heterotrophic nitrification-aerobic denitrification bacterium isolated from municipal activated sludge

The heterotrophic nitrification-aerobic denitrification (HNAD) is a new biological denitrification technology, the present study isolated a new HNAD strain named Cupriavidus metallidurans TX6 with heavy metal resistance. The gene expression, electron transport, enzyme activity and nitrogen removal property of strain TX6 were studied with different influencing factors. Strain TX6 has five nitrogen metabolism pathways (NH4+ → NH2OH → NO → NO2- → NH4+ → GOGAT/GDH; NH4+-N → NH2OH → NO → N2O → N2; NH4+ → NH2OH → NO → NO2- → NO3-; NO3- → NO2- → NH4+ → GOGAT/GDH; NO3-→ NO2- → NH4+ → GOGAT/GDH). Nitrogen balance analysis shows that 29 ± 4 mg/L of N was converted to intracellular nitrogen by assimilation and 50 ± 3 mg/L N loss may be attributed to aerobic denitrification. The results provide a theoretical basis for the HAND bacteria application in nitrogen removal from wastewaters containing heavy metals.

Transcriptome analysis expands underlying mechanisms of quorum sensing mediating heterotrophic nitrification-aerobic denitrification process at low temperature

Quorum sensing (QS) could regulate the behavior of microbial communities and help them resist adverse low-temperature environments. A newly isolated heterotrophic nitrification-aerobic denitrification (HN-AD) bacterium, strain YB1107, exhibited strong tolerance to harsh cold environments, removing 93.5 % of ammonia within 36 h and achieving a maximum specific growth rate of 0.28 h-1 at 10 °C. Strain YB1107 secreted large amounts of N-butanoyl-L-homoserine or N-octanoyl-L-homoserine lactones in response to cold stimuli. The add-back experiments indicated that these two signaling molecules jointly manipulated microbial physiological behavior by improving ammonia oxidation and biofilm formation, while inhibiting aerobic denitrification. The transcriptome analysis revealed that QS systems enhanced the cold resistance of HN-AD bacteria by promoting nitrogen assimilation and reducing dissimilation through regulating related genes. This study provided new molecular insights into how QS mediated HN-AD at low temperatures and laid the foundation for the potential applications of psychrophilic HN-AD bacteria in wastewater treatment.

Enhancing nitrogen transformation and humification in cow manure composting through psychrophilic and thermophilic nitrifying bacterial consortium inoculation

Excessive nitrogen release during composting poses significant challenges to both the environment and compost quality. Biological enhancement of humification and nitrogen conservation is an environmentally friendly and cost-effective approach to composting. The aim of this study was to develop a psychrophilic and thermophilic nitrifying bacterial consortium (CNB) and investigate its role in nitrogen transformation and humification during cow manure composting. Analysis revealed that CNB inoculation promoted microbial proliferation and metabolism, significantly increased the number of nitrifying bacteria (p < 0.05), and elevated the activity of nitrite oxidoreductase and nxrA gene abundance. Compared to the control, CNB inoculation promoted the formation of NO3--N (77.87-82.35 %), while reducing NH3 (48.89 %) and N2O (20.05 %) emissions, and increased humus content (16.22 %). Mantel analysis showed that the higher abundance of nitrifying bacteria and nxrA facilitated the nitrification of NH4+-N. The improvement in nitrite oxidoreductase activity promoted NO3--N formation, leading to increased humus content and enhanced compost safety.

Enhanced degradation of phenolic pollutants by a novel cold-adapted laccase from Peribacillus simplex

Laccase (EC 1.10.3.2), as eco-friendly biocatalysts, holds immense potential for sustainable applications across various environmental and industrial sectors. Despite the growing interest, the exploration of cold-adapted laccases, especially their unique properties and applicability, remains limited. In this study, we have isolated, cloned, expressed, and purified a novel laccase from Peribacillus simplex (GenBank: PP430751), which was derived from permafrost layer. The recombinant laccase (PsLac) exhibited optimal activity at 30 °C and a pH optimum of 3.5. Remarkably, PsLac exhibited remarkable stability in the presence of organic solvents, with its enzyme activity increasing by 20 % after being incubated in a 30 % trichloromethane solution for 12 h, compared to its initial activity. Furthermore, the enzyme preserved 100 % of its activity after undergoing eight freeze-thaw cycles. Notably, the catalytic center of PsLac contains Zn2+ instead of the typically observed Cu2+ found in other laccases, and metal-ion substitution experiments raised the catalytic efficiency to 3-fold when Zn2+ was replaced with Fe2+. Additionally, PsLac has demonstrated a proficient ability to degrade phenolic pollutants, such as hydroquinone, even at a low temperature of 16 °C, positioning it as a promising candidate for environmental bioremediation and contributing to cleaner production processes.

Effect of carbon source on carbon and nitrogen metabolism of common heterotrophic nitrification-aerobic denitrification pathway

Pseudomonas sp. ZHL02, removing nitrogen via ammonia nitrogen (NH4+) → hydroxylamine (HN2OH) → nitrite (NO2-) → nitrate (NO3-) → NO2- → nitric oxide (NO) → nitrous oxide (N2O) pathway was employed for getting in-depth information on the heterotrophic nitrification-aerobic denitrification (HNAD) pathway from carbon oxidation, nitrogen conversion, electron transport process, enzyme activity, as well as gene expression while sodium succinate, sodium citrate, and sodium acetate were utilized as the carbon sources. The nitrogen balance analysis results demonstrated that ZHL02 mainly removed NH4+-N through assimilation. The carbon source metabolism resulted in the discrepancies in electron transport chain and nitrogen removal between different HNAD bacteria. Moreover, the prokaryotic strand-specific transcriptome method showed that, amo and hao were absent in ZHL02, and unknown genes may be involved in ZHL02 during the HNAD process. As a fascinating process for removing nitrogen, the HNAD process is still puzzling, and the relationship between carbon metabolism and nitrogen metabolism among different HNAD pathways should be studied further.

Isolation and characterization of a cold-tolerant heterotrophic nitrification-aerobic denitrification bacterium and evaluation of its nitrogen-removal efficiency

With a view toward addressing the poor efficiency with which nitrogen is removed from wastewater below 10 °C, in this study, we isolated a novel cold-tolerant heterotrophic nitrification-aerobic denitrification (HN-AD) bacterium from a wetland and characterized its nitrogen removal performance and nitrogen metabolic pathway. On the basis of 16S rRNA gene sequencing, this strain was identified as a species of Janthinobacterium, designated J1-1. At 8 °C, strain J1-1 showed excellent removal efficiencies of 89.18% and 68.18% for single-source NH4+-N and NO3--N, respectively, and removal efficiencies of 96.23% and 79.64% for NH4+-N and NO3--N, respectively, when supplied with mixed-source nitrogen. Whole-genome sequence analysis and successful amplification of the amoA, napA, and nirK functional genes related to nitrogen metabolism provided further evidence in support of the HN-AD capacity of strain J1-1. The deduced HN-AD metabolic pathway of the strain was NH4+-N→NH2OH→NO2--N→NO3--N→NO2--N→NO→N2O. In addition, assessments of NH4+-N removal under different conditions revealed the following conditions to be optimal for efficient removal: a temperature of 20 °C, pH of 7, shaking speed of 150 rpm, sodium succinate as a carbon source, and a C/N mass ratio of 16. Given its efficient nitrogen removal capacity at 8 °C, the J1-1 strain characterized in this study has considerable application potential in the treatment of low-temperature wastewater.

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.

Multi-omics analysis to reveal key pathways involved in low C/N ratio stress response in Pseudomonas sp. LW60 with superior nitrogen removal efficiency

In practical engineering, nitrogen removal at low temperatures or low C/N ratios is difficult. Although strains can remove nitrogen well at low temperatures, there is no research on the performance and deep mechanism of strains under low C/N ratio stress. In this study, Pseudomonas sp. LW60 with superior nitrogen removal efficiency under low C/N ratio stress was isolated at 4 °C. With a C/N ratio of 2-10, the NH4+-N removal efficiency was 40.02 %-100 % at 4 °C. Furthermore, the resistance mechanism of Pseudomonas sp. LW60 to low C/N ratio stress was deeply investigated by multi-omics. The results of transcriptome, proteome, and metabolome revealed that the resistance of strain LW60 to low C/N ratio stress was attributed to enhanced central carbon metabolism, amino acid metabolism, and ABC transporters, rather than nitrogen removal pathways. This study isolated a strain with low C/N ratio tolerance and deeply explored its tolerance mechanism by multi-omics.

Performance evaluation of H2S and NH3 removal by biological trickling filter reactors with various fillers under heterotrophic conditions

A pilot-scale biological trickling filter (BTF) reactor (13.5 L) packed with different fillers (Pine bark, Cinder, Straw, and MBBR (mobile bed biofilm reactor) filler was employed to evaluate their removal performance of H2S and NH3 after heterotrophic bacterium addition, and some parameters, including different packing heights, empty bed residence time (EBRT), inlet titers, loading ratios, and restart trial, were investigated in this study. According to the experimental results, BTF filled with pine bark exhibited better removal efficiency than other reactors under a variety of conditions. The removal efficiency of H2S and NH3 reached to as high as 81.31 % and 91.72 %, respectively, with the loading range of 3.29-67.70 g/m3·h. Moreover, due to the addition of heterotrophic bacterium, the removal efficiency was enhanced and capable to eliminate majority of H2S and NH3 even though the packing height was reduced to 400 mm. After 15 days of idle, the BTF reactor was able to resume rapidly and execute deodorization with high efficiency. The degradation mechanism was further explored by a thorough examination of microbial species which degraded contaminants, as well as by functional prediction and correlation analyses. In a word, these results laid a foundation for the application of heterotrophic microorganisms in BTF, which could improve the removal efficiency of biological deodorization.

Simply Versatile: The Use of Peribacillus simplex in Sustainable Agriculture

Peribacillus simplex is a Gram-positive, spore-forming bacterium derived from a vast range of different origins. Notably, it is part of the plant-growth-promoting rhizobacterial community of many crops. Although members of the Bacillaceae family have been widely used in agriculture, P. simplex has, so far, remained in the shadow of its more famous relatives, e.g., Bacillus subtilis or Bacillus thuringiensis. Recent studies have, however, started to uncover the bacterium's highly promising and versatile properties, in particular in agricultural and environmental applications. Hence, here, we review the plant-growth-promoting features of P. simplex, as well as its biocontrol activity against a variety of detrimental plant pests in different crops. We further highlight the bacterium's potential as a bioremediation agent for environmental contaminants, such as metals, pesticide residues, or (crude) oil. Finally, we examine the recent developments in the European regulatory landscape to facilitate the use of microorganisms in plant protection products. Undoubtedly, further studies on P. simplex will reveal additional benefits for agricultural and environmentally friendly applications.

A novel hypothermic strain, Pseudomonas reactans WL20-3 with high nitrate removal from actual sewage, and its synergistic resistance mechanism for efficient nitrate removal at 4 °C

Nitrate can be well removed by bacteria at 25-30 °C. However, nitrate removal almost ceases at temperatures lower than 5 °C. In this study, a novel hypothermic strain, Pseudomonas reactans WL20-3 exhibited an excellent aerobic nitrate removal ability at 4 °C. It had high capability for the removal of nitrate, total dissolved nitrogen (TDN), and dissolved organic carbon (DOC) at 4 °C, achieving removal efficiencies of 100%, 87.91%, and 97.48%, respectively. The transcriptome analysis revealed all genes involved in the nitrate removal pathway were significantly up-regulated. Additionally, the up-regulation of ABC transporter genes and down-regulation of respiratory chain genes cooperated with the nitrate metabolism pathway to resist low-temperature stress. In actual sewage, inoculated with WL20-3, the nitrate removal efficiency was found to be 70.70%. Overall, these findings demonstrated the impressive capacity of the novel strain WL20-3 to remove nitrate and provided novel insights into the synergistic resistance mechanism of WL20-3 at low temperature.

Efficient nitrogen removal by a novel extreme strain, Pseudomonas reactans WL20-3 under dual stresses of low temperature and high alkalinity: Characterization, mechanism, and application

Although many studies report the resistance of heterotrophic nitrification-aerobic denitrification (HN-AD) strains to single environmental stress, there is no research on its resistance to dual stresses of low temperature and high alkalinity. A novel bacterium Pseudomonas reactants WL20-3 isolated in this study showed removal efficiencies of 100%, 100%, and 97.76% for ammonium, nitrate, and nitrite, respectively, at 4 °C and pH 11.0. Transcriptome analysis revealed that the resistance of strain WL20-3 to dual stresses was attributed not only to the regulation of genes in the nitrogen metabolic pathway, but also to genes in other pathways such as the ribosome, oxidative phosphorylation, amino acid metabolism, and ABC transporters. Additionally, WL20-3 removed 83.98% of ammonium from actual wastewater at 4 °C and pH 11.0. This study isolated a novel strain WL20-3 with superior nitrogen removal under dual stresses and provided a molecular understanding of its tolerance mechanism to low temperature and high alkalinity.

Genomics and nitrogen metabolic characteristics of a novel heterotrophic nitrifying-aerobic denitrifying bacterium Acinetobacter oleivorans AHP123

A novel aerobic strain of Acinetobacter oleivorans AHP123 was isolated from activated sludge, which could conduct heterotrophic nitrification and denitrification simultaneously. This strain has excellent NH₄⁺-N removal ability, with 97.93% removal rate at 24-hour. To identify the metabolic pathways of this novel strain, genes of gam, glnA, gdhA, gltB, nirB, nasA, nar, nor, glnK and amt were detected by genome analysis. Through RT-qPCR, it was found that the expression of key genes confirmed two possible ways of nitrogen removal in strain AHP123: nitrogen assimilation and heterotrophic nitrification aerobic denitrification (HNAD). However, the absence of some common HNAD genes (amo, nap and nos) suggested that strain AHP123 might have a different HNAD pathway from other HNAD bacteria. Nitrogen balance analysis revealed that strain AHP123 assimilated most of the external nitrogen sources into intracellular nitrogen.

Biotechnological and food synthetic biology potential of platform strain: Bacillus licheniformis

Bacillus licheniformis is one of the most characteristic Gram-positive bacteria. Its unique genetic background and safety characteristics make it have important biologic applications in the food industry, including, the biosynthesis of high value-added bioproducts, probiotic functions, biological treatment of wastes derived from food production, etc. In this review, these recent advances are summarized and presented systematically for the first time. In addition, we highlight synthetic biology strategies as a potential driver of developing this strain for wider and more efficient application in the food industry. Finally, we present the current challenges faced and provide our unique perspective on relevant future research directions. In summary, this review will provide an illuminating and comprehensive perspective that will allow an in-depth understanding of B. licheniformis and promote its more effective development in the food industry.

Insight into the Cold Adaptation Mechanism of an Aerobic Denitrifying Bacterium: Bacillus simplex H-b

Psychrophilic bacteria with aerobic denitrification ability have promising potential for application in nitrogen-contaminated wastewater treatment, especially under cold conditions. A better understanding of the cold adaptation mechanism during aerobic denitrification would be beneficial for the practical application of this type of functional bacterium. In this study, Bacillus simplex H-b with good denitrification performance at 5°C was used to investigate the corresponding cold tolerance mechanism. Transcriptomics and nitrogen removal characterization experiments were conducted at different temperatures (5°C, 20°C, and 30°C). At low temperatures, more nitrogen was utilized for assimilation, accompanied by the accumulation of ATP and extracellular polymeric substances (EPS), rather than transforming inorganic nitrogen in the dissimilation pathway. In addition, the proportion of unsaturated fatty acids was higher in strains cultured at low temperatures. At the molecular level, the adjustment of membrane transport, synthesis of cofactors and vitamins, and transcriptional regulators might contribute to the survival of the strain under cold conditions. Moreover, nucleotide precursor synthesis, translation, and oxidative and temperature stress response mechanisms also enhanced the resistance of strain H-b to low temperatures. The results suggest that combining multiple regulatory mechanisms and synergistic adaptation to cold stress enabled the growth and relatively high nitrogen removal rate (27.22%) of strain H-b at 5°C. By clarifying the mechanism of regulation and cold resistance of strain H-b, a theoretical foundation for enhancing the application potential of this functional bacterium for nitrogen-contaminated wastewater treatment was provided. IMPORTANCE The newly isolated aerobic denitrifying bacterium Bacillus simplex H-b removed various forms of inorganic nitrogen (nitrate, nitrite, and ammonium) from wastewater, even when the temperature was as low as 5°C. Although this environmentally functional bacterium has been suggested as a promising candidate for nitrogen-contaminated water treatment at low temperatures, understanding its cold adaptation mechanism during aerobic denitrification is limited. In this study, the cold tolerance mechanism of this strain was comprehensively explained. Furthermore, a theoretical basis for the practical application of this type of functional bacterium for nitrogen removal in cold regions is provided. The study expands our understanding of the survival strategy of psychrophilic bacteria and hence supports their further utilization in wastewater treatment applications.

Heterotrophic nitrification and aerobic denitrification characteristics of the psychrotolerant Pseudomonas peli NR-5 at low temperatures

The nitrogen removal efficiency of heterotrophic nitrification and aerobic denitrification (HN-AD) bacteria can be seriously inhibited at low temperatures (< 15 °C). A novel psychrotolerant bacterium, Pseudomonas peli NR-5 (P. peli NR-5), with efficient HN-AD capability was isolated and screened from river sediments in cold areas. When P. peli NR-5 was aerobically cultivated for 60 h at 10 °C with NH₄⁺-N, NO₃^--N, and NO₂^--N as the sole nitrogen sources (N 105 mg/L), the nitrogen removal efficiencies were 97.3, 95.3, and 87.8%, respectively, without nitrite accumulation, and the corresponding average nitrogen removal rates were 1.71, 1.67, and 1.55 mg/L/h, respectively. Meanwhile, P. peli NR-5 exhibited excellent simultaneous nitrification and denitrification capabilities at 10 °C. Sodium succinate was the most favorable carbon substrate for bacterial growth and ammonia removal by strain NR-5. The optimal culture conditions determined by the response surface methodology model were a carbon to nitrogen ratio of 5.9, temperature of 11.5 °C, pH of 7.0, and shaking speed of 144 rpm. Under these conditions, 99.1% of the total nitrogen was removed in the verification experiments, which was not significantly different from the predicted maximum removal in the model (99.6%). Six functional genes participating in the HN-AD process were successfully obtained by polymerase chain reaction amplification, which further confirmed the HN-AD capability of P. peli NR-5 and proposed the metabolic pathway of HN-AD. The above results provide a theoretical background of psychrotolerant HN-AD bacteria in wastewater purification under low-temperature conditions.

Nitrogen removal characterization and functional enzymes identification of a hypothermia bacterium Pseudomonas fragi EH-H1

A novel hypothermic strain, Pseudomonas fragi EH-H1, was found to effectively perform heterotrophic nitrification and aerobic denitrification at 15 °C. This strain could consume 100 %, 100 % and 99.95 % of ammonium (54.90 mg∙L^-1), nitrate (56.12 mg∙L^-1) and nitrite (54.15 mg∙L^-1), accompanied by peak removal rates of 5.51, 3.63 and 3.14 mg/L/h, respectively. The ammonium was removed preferentially during simultaneous nitrification and denitrification. Notably, the elimination rate of the toxic nitrite nitrogen remained approximately 3.14 mg/L/h, whether supplemented with ammonium or not. Stepwise inhibition experiments revealed that the key enzymes of ammonia monooxygenase (AMO) and nitrite oxidoreductase (NiR) for nitrification and denitrification coexisted in strain EH-H1. AMO, nitrate reductase and NiR were successfully expressed and detected at 0.637, 0.239 and 0.018 U/mg proteins, respectively. Overall, strain EH-H1 had an outstanding ability to remove nitrogen at low temperatures and could provide guidance for cryogenic wastewater treatment.

Nitrogen removal characteristics of efficient heterotrophic nitrification-aerobic denitrification bacterium and application in biological deodorization

A heterotrophic nitrifying aerobic denitrifying (HN-AD) strain HY-1 with excellent capacity, identified as Paracoccus denitrificans, was isolated from activated sludge. HY-1 was capable of removing NH₄⁺, NO₂^-, and NO₃^- with the corresponding rate of 17.33 mg-N L^-1 h^-1, 21.83 mg-N L^-1 h^-1, and 32.37 mg-N L^-1 h^-1, as well as the mixture of multiple nitrogen sources. Meanwhile, HY-1 could execute denitrification function under anaerobic conditions with a rate of 14.56 mg-N L^-1 h^-1. HY-1 required less energy investment, which exhibited average denitrification rate of 5.19 mg-N L^-1 h^-1 at carbon-nitrogen ratio was 1. After nitrification-denitrification metabolic pathway analysis, HY-1 was applied in a biological trickling filter reactor for compost deodorization. The results showed that adding of HY-1 greatly reduced the ionic concentration of NH₄⁺ and NO₃^- in the circulating liquid without impairing the deodorization effect (NH₃ removal rate＞98.07%). These findings extend the field of application of HN-AD and provide new insights for biological deodorization.

Potential and mechanism for bioremediation of papermaking black liquor by a psychrotrophic lignin-degrading bacterium, Arthrobacter sp. C2

To meet the challenge of bioremediation of black liquor in pulp and paper mills at low temperatures, a psychrotrophic lignin-degrading bacterium was employed in black liquor treatment for the first time. In this study, Arthrobacter sp. C2 exhibited excellent cold adaptability and lignin degradation ability, with a lignin degradation rate of 65.5% and a mineralization rate of 43.9% for 3 g/L lignin at 15 °C. Bioinformatics analysis and multiple experiments confirmed that cold shock protein 1 (Csp1) was the dominant cold regulator of strain C2, and dye-decolorizing peroxidase (DyP) played a crucial role in lignin degradation. Moreover, structural equation modeling (SEM), mRNA monitoring, and phenotypic variation analysis demonstrated that Csp1 not only mediated cold adaptation but also modulated DyP activity by controlling dyp gene expression, thus driving lignin depolymerization for strain C2 at low temperatures. Furthermore, 96.4% of color, 64.2% of chemical oxygen demand (COD), and 100% of nitrate nitrogen (NO₃--N) were removed from papermaking black liquor by strain C2 within 15 days at 15 °C. This study provides insights into the association between the cold regulator and catalytic enzyme of psychrotrophic bacteria and offers a feasible alternative strategy for the bioremediation of papermaking black liquor in cold regions.

Biological nitrogen removal and metabolic characteristics of a novel cold-resistant heterotrophic nitrification and aerobic denitrification Rhizobium sp. WS7

For improving the poor de-nitrogen efficiency and effluent quality faced by wastewater treatment plants in winter, a novel cold-resistant strain, Rhizobium sp. WS7 was isolated. Strain WS7 presented dramatic de-nitrogen efficiencies including 98.73 % of NH₄⁺-N, 99.98 % of NO₃^--N, 100 % of NO₂^--N and approximately 100 % of mixed nitrogen (NH₄⁺-N and NO₃^--N) at 15 °C. Optimum parameters of WS7 for aerobic denitrification were determined. Additionally, functional genes (amoA, napA, nirK, norB, and nosZ) and key enzymes (nitrate reductase and nitrite reductase) activities were determined. Nitrogen balance analysis suggested that assimilation played a dominant role in de-nitrogen by WS7, the NH₄⁺-N metabolic pathway was deduced as NH₄⁺-N → NH₂OH → NO → N₂O → N₂, and the NO₃^--N/NO₂^--N metabolic pathway was deduced as NO₃^--N → NO₂^--N → NO → N₂O → N₂. The cold-resistant Rhizobium sp. WS7 has great application feasibility in cold sewage treatment.

Understanding and application of Bacillus nitrogen regulation: A synthetic biology perspective

BACKGROUND

Nitrogen sources play an essential role in maintaining the physiological and biochemical activity of bacteria. Nitrogen metabolism, which is the core of microorganism metabolism, makes bacteria able to autonomously respond to different external nitrogen environments by exercising complex internal regulatory networks to help them stay in an ideal state. Although various studies have been put forth to better understand this regulation in Bacillus, and many valuable viewpoints have been obtained, these views need to be presented systematically and their possible applications need to be specified.

AIM OF REVIEW

The intention is to provide a deep and comprehensive understanding of nitrogen metabolism in Bacillus, an important industrial microorganism, and thereby apply this regulatory logic to synthetic biology to improve biosynthesis competitiveness. In addition, the potential researches in the future are also discussed.

KEY SCIENTIFIC CONCEPT OF REVIEW

Understanding the meticulous regulation process of nitrogen metabolism in Bacillus not only could facilitate research on metabolic engineering but also could provide constructive insights and inspiration for studies of other microorganisms.

Metagenomics analysis unraveled the influence of sulfate radical-mediated compost nitrogen transformation process

The mechanism of nitrogen transformation of sulfate radical (SO- 4⋅) in the process of composting is unclear. The objectives of this study were to investigate the influence of SO- 4⋅ on nitrogen biotransformation during composting and to compare the differences in physicochemical parameters and metagenomics analysis between CK (fresh dairy manure and bagasse pith) and PS (the composting raw materials added with potassium persulfate). The results indicated that SO^-₄⋅ guides electron transfer in the conversion of NH⁺₄-N to NO- 3-N and breaches the extracellular polysaccharide (EPS) structure to promote nitrogen removal. Aminomonooxygenase (AMO) and nitrate reductase (NR) levels displayed an interactive relationship between microorganisms and substrates. Metagenomics analysis revealed distinct microbial community compositions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways between nitrification and denitrification. Correlation analysis indicated that Methanobrevibacter, Bacillus and Pseudomonas were closely related to these processes. This work demonstrates the effect of SO- 4⋅ on nitrogen cycling and retention, and possible mechanisms of nitrification and denitrification during composting.

Performance of Paracoccus pantotrophus MA3 in heterotrophic nitrification-anaerobic denitrification using formic acid as a carbon source

Excess amount of nitrogen in wastewater has caused serious concerns, such as water eutrophication. Paracoccus pantotrophus MA3, a novel isolated strain of heterotrophic nitrification-anaerobic denitrification bacteria, was evaluated for nitrogen removal using formic acid as the sole carbon source. The results showed that the maximum ammonium removal efficiency was observed under the optimum conditions of 26.25 carbon to nitrogen ratio, 3.39% (v/v) inoculation amount, 34.64 °C temperature, and at 180 rpm shaking speed, respectively. In addition, quantitative real-time PCR technique analysis assured that the gene expression level of formate dehydrogenase, formate tetrahydrofolate ligase, 5,10-methylenetetrahydrofolate dehydrogenase, serine hydroxymethyltransferase, respiratory nitrate reductase beta subunit, L-glutamine synthetase, glutamate dehydrogenase, and glutamate synthase were up-regulated compared to the control group, and combined with nitrogen mass balance analysis to conclude that most of the ammonium was removed by assimilation. A small amount of nitrate and nearly no nitrite were accumulated during heterotrophic nitrification. MA3 exhibited significant denitrification potential under anaerobic conditions with a maximum nitrate removal rate of 4.39 mg/L/h, and the only gas produced was N₂. Additionally, 11.50 ± 0.06 mg/L/h of NH₄⁺-N removal rate from biogas slurry was achieved.

Nitrogen removal by a novel heterotrophic nitrification and aerobic denitrification bacterium Acinetobacter calcoaceticus TY1 under low temperatures

A new bacterial strain, Acinetobacter calcoaceticus TY1, was identified in activated sludge. This strain efficiently metabolized nitrogen from ammonium at low temperatures, utilizing NH₄⁺-N, NO₃^--N, and NO₂^--N as nitrogen sources. Of these, NH₄⁺-N was superior in terms of both assimilation and heterotrophic nitrification at 8 °C. The nitrogen metabolism-associated genes amoA, nirK, and nosZ were identified in TY1. Optimal requirements for growth and nitrogen removal were pH 7, shaking speed of 90 rpm, a C/N ratio of 10, and sodium citrate for the carbon supply. The ability to denitrify at low temperature suggests TY1's potential for wastewater management.

Response of the aerobic denitrifying phosphorus accumulating bacteria Pseudomonas psychrophila HA-2 to low temperature and zinc oxide nanoparticles stress

Performance and molecular changes of an aerobic denitrifying phosphorus accumulating bacteria Pseudomonas psychrophila HA-2 have been investigated under different temperatures and ZnO nanoparticles (NPs) exposures. Strain HA-2 removed 95.7% of total nitrogen (TN) and 24.6% of phosphorus at 10 °C, which was attributed to the joint up-regulation of intracellular energy metabolism and ribosome. Moreover, with the increase of ZnO NPs from 0 to 100 mg/L, TN and phosphurs removal efficiencies decreased from 95.7% to 44.5% and 24.6% to 6.8% at 10 °C, respectively, whereas phosphorus removal rate increased from 10.5% to 24.5% at 20 °C. Further transcriptomics and proteomics revealed that significant down-regulation of purine and amino acid metabolisms was the main reason for the inhibitory effect at 10 °C, while the up-regulation of antioxidant pathways and functional genes expressions was responsible for the promoted phosphorus accumulation at 20 °C. This study provides a potential solution for improving biological nutrients removal processes in winter months.

Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification

Aerobic denitrification has been proved to be profoundly affected by temperature and antibiotics, but little is known about how aerobic denitrifiers respond to temperature and antibiotic stress. In this study, the nitrate reduction performance and the intracellular metabolism by a psychrotolerant aerobic denitrifying bacteria, named Pseudomonas psychrophila RNC-1, were systematically investigated at different temperatures (10 °C, 20 °C, 30 °C) and different sulfamethoxazole (SMX) concentrations (0 mg/L, 0.1 mg/L, 0.5 mg/L, 1.0 mg/L, and 5.0 mg/L). The results showed that strain RNC-1 performed satisfactory nitrate removal at 10 °C and 20 °C, but its growth was significantly inhibited at 30 °C. Nitrate removal by strain RNC-1 was slightly promoted in the presence of 0.5 mg/L SMX, whereas it was significantly suppressed with 5.0 mg/L SMX. Nitrogen balance analysis indicated that assimilatory nitrate reduction and dissimilatory aerobic denitrification jointly dominated in the nitrate removal process of strain RNC-1, in which the inhibition effected on assimilation process was much higher than that on the aerobic denitrification process under SMX exposure. Further transcriptomics and proteomics analysis revealed that the psychrotolerant mechanism of strain RNC-1 could be attributed to the up-regulation of RNA translation, energy metabolism, ABC transporters and the over-expression of cold shock proteins, while the down-regulation of oxidative phosphorylation pathway was the primary reason for the deteriorative cell growth at 30 °C. The promotion of nitrate reduction with 0.5 mg/L SMX was related to the up-regulation of amino acid metabolism pathways, while the down-regulation of folate cycle, glycolysis/gluconeogenesis and bacterial chemotaxis pathways were responsible for the inhibition effect at 5.0 mg/L SMX. This work provides a mechanistic understanding of the metabolic adaption of strain RNC-1 under different stress, which is of significance for its application in nitrogen contaminated wastewater treatment processes.

Nitrogen Removal Characteristics of a Cold-Tolerant Aerobic Denitrification Bacterium, Pseudomonas sp. 41

Nitrogen pollution of surface water is the main cause of water eutrophication, and is considered a worldwide challenge in surface water treatment. Currently, the total nitrogen (TN) content in the effluent of wastewater treatment plants (WWTPs) is still high at low winter temperatures, mainly as a result of the incomplete removal of nitrate (NO3−-N). In this research, a novel aerobic denitrifier identified as Pseudomonas sp. 41 was isolated from municipal activated sludge; this strain could rapidly degrade a high concentration of NO3−-N at low temperature. Strain 41 completely converted 100 mg/L NO3−-N in 48 h at 15 °C, and the maximum removal rate reached 4.0 mg/L/h. The functional genes napA, nirS, norB and nosZ were successfully amplified, which provided a theoretical support for the aerobic denitrification capacity of strain 41. In particular, the results of denitrification experiments showed that strain 41 could perform aerobic denitrification under the catalysis of NAP. Nitrogen balance analysis revealed that strain 41 degraded NO3−-N mainly through assimilation (52.35%) and aerobic denitrification (44.02%), and combined with the gene amplification results, the nitrate metabolism pathway of strain 41 was proposed. Single-factor experiments confirmed that strain 41 possessed the best nitrogen removal performance under the conditions of sodium citrate as carbon source, C/N ratio 10, pH 8, temperature 15–30 °C and rotation speed 120 rpm. Meanwhile, the bioaugmentation test manifested that the immobilized strain 41 remarkably improved the denitrification efficiency and shortened the reaction time in the treatment of synthetic wastewater.

Heterotrophic nitrification and aerobic denitrification process: Promising but a long way to go in the wastewater treatment

The traditional biological nitrogen removal (BNR) follows the conventional scheme of sequential nitrification and denitrification. In recent years, novel processes such as anaerobic ammonia oxidation (anammox), complete oxidation of ammonia to nitrate in one organism (comammox), heterotrophic nitrification and aerobic denitrification (HN-AD), and dissimilatory nitrate reduction to ammonium (DNRA) are gaining tremendous attention after the discovery of metabolically versatile bacteria. Among them, HN-AD offers several advantages because individual bacteria could achieve one-stage nitrogen removal under aerobic conditions in the presence of organic carbon. In this review, besides classical BNR processes, we summarized the existing literature on HN-AD bacteria which have been isolated from diverse habitats. A particular focus was given on the diversity and physiology of HN-AD bacteria, influences of physiological and biochemical factors on their growth, nitrogen removal performances, as well as limitations and strategies in unraveling HN-AD metabolic pathways. We also presented case studies of HN-AD application in wastewater treatment facilities, pointed out forthcoming challenges of HN-AD in these systems, and presented modulation strategies for HN-AD application in engineering. This review may help improve the existing design of wastewater treatment plants by harnessing HN-AD bacteria for effective nitrogen removal.

Nitrate removal by alkali-resistant Pseudomonas sp. XS-18 under aerobic conditions: Performance and mechanism

To improve poor nitrate removal by microorganisms under strong alkaline conditions, a new type of aerobic nitrification-reducing bacteria was isolated in this study. Using nitrogen balance and genome information, the capacity of Pseudomonas XS-18 to remove nitrate and the mechanism of alkali tolerance were analyzed. At pH 11.0, XS-18 could remove 12.17 mg N/(L·h) nitrate. At C/N ratios of 13.0 and 25 °C, nitrite and ammonia nitrogen were barely enriched. XS-18 could reduce nitrate through dissimilation and assimilation, and 21.74% and 77.39% of nitrate was converted into cellular components and organic nitrogen, respectively. Meanwhile, functional genes (nirBD, nasAB, gdhA, glnA, and gltBD) associated with nitrogen metabolism were determined. In addition, Na⁺/H⁺ antiporters (MnhACDEFG, PhaACDEFG, NhaCD and TrkAH) and a cell surface protein (SlpA) from the XS-18 genome, as well as compatible solutes that help stabilize intracellular pH, were also characterized. XS-18 possessed significant potential in alkaline wastewater treatment.

Hypothermia Pseudomonas taiwanensis J488 exhibited strong tolerance capacity to high dosages of divalent metal ions during nitrogen removal process

The nitrogen metabolic pathways of Pseudomonas taiwanensis J488 have not been confirmed from genomic function analysis and its divalent metal ion resistance remains poorly understood. In this study, the key denitrifying gene of Pseudomonas taiwanensis J488, nirB, was determined by draft genome sequencing. The nitrification of ammonium was insensitive to high concentrations of Ca(II), Mn(II), Zn(II), and Cd(II). Similarly, complete nitrite removal was achieved despite Mn(II) and Zn(II) reaching concentrations up to 30 mg/L. Furthermore, the efficiency of nitrate removal was significantly enhanced by 1.33%, 3.33%, 5.99%, and 1.53% with the addition of 0.5 mg/L Ca(II), 20 mg/L Mn(II), 5 mg/L Zn(II), and 2 mg/L Cd(II), respectively, comparison with the control. The bacterial growth in both nitrifying and denitrifying processes was substantially promoted by various dosages of divalent metal ions. These results indicate that divalent metal ions would not severely limit the capacity of strain J488 to purify nitrogen-polluted wastewater.

The promotion and inhibition effect of graphene oxide on the process of microbial denitrification at low temperature

This study found that graphene oxide (GO) improved microbial denitrification at low temperatures (~12 °C), and the optimal concentration was 10 mg/L as the removal rate of NO₃-N increased by 17%. At the optimal concentration, GO improved the electron transport system activity of the microbes and enhanced the activity of nitrate reductase and nitrite reductase while exhibited low microbial toxicity. The addition of GO increased the content of tightly bound extracellular polymeric substances (EPS). The results of fluorescence spectrometer indicated that GO accelerated the renewal of bound EPS (B-EPS). Fourier Transform infrared spectroscopy (FTIR) results showed that GO affected the secondary structure of the protein in B-EPS, making B-EPS more hydrophobic and promoting microbial aggregation. B-EPS affected by GO can promote the electron transfer process of microorganisms. However, high concentration (>25 mg/L) of GO may inhibit denitrification by competing for electrons, which was not conducive to denitrification thermodynamically.

Heterotrophic nitrification and aerobic denitrification by a novel Acinetobacter sp. TAC-1 at low temperature and high ammonia nitrogen

A novel strain was isolated from swinewastewater and identified as Acinetobacter sp. TAC-1 based on its phylogenetic and phenotypic characteristics. The strain TAC-1 was found to have a high ability to metabolize ammonium-N under low temperature condition. The strain TAC-1 could remove approximately 94.6% of ammonium-N (400 mg/L), 93.3% of nitrate-N (400 mg/L) and 42.4% of nitrite-N (400 mg/L) at 5 °C. The functional genes nitrate reductase gene (narG) and nitrite reductase gene (nirK, nirS) were successfully amplified by qPCR, further evidencing the heterotrophic nitrification and aerobic denitrification capability of Acinetobacter sp. TAC-1. The transcriptome data confirmed that the membrane transport protein and unsaturated fatty acid dehydrogenase-related genes of the strain TAC-1 were significantly up-regulated at 5 °C, enabling it to survive low temperatures. The high nitrogen removal ability at 5 °C makes this strain have a good application prospect.

Toxic Effect of Ammonium Nitrogen on the Nitrification Process and Acclimatisation of Nitrifying Bacteria to High Concentrations of NH4-N in Wastewater

The aim of the conducted research was to assess the effectiveness of the nitrification process, at different concentrations of ammonium nitrogen, in biologically treated wastewater in one of the largest municipal and industrial wastewater treatment plants in Poland. The studies also attempted to acclimate nitrifying bacteria to the limited concentration of ammonium nitrogen and determined the efficiency of nitrification under the influence of acclimated activated sludge in the biological wastewater treatment system. The obtained results indicate that the concentration of ammonium nitrogen above 60.00 mg·dm−3 inhibits nitrification, even after increasing the biomass of nitrifiers. The increase in the efficiency of the nitrification process in the tested system can be obtained by using the activated sludge inoculated with nitrifiers. For this purpose, nitrifiers should be preacclimated, at least for a period of time, allowing them to colonize the activated sludge. The acclimated activated sludge allows reducing the amount of ammonium nitrogen in treated sewage by approx. 35.0%. The process of stable nitrification in the biological treatment system was observed nine days after introducing the acclimated activated sludge into the aeration chamber.