Insight into the denitrification mechanism of Bacillus subtilis JD-014 and its application potential in bioremediation of nitrogen wastewater

FoxO signaling pathway stimulation by Bacillus smithii XY1 contributes to alleviating copper-induced neurotoxicity

Increasingly copper pollution in the environment exacerbates the risk of neurodegenerative diseases. It is necessary to look for effective targets and safe methods for protecting from copper-induced neurotoxicity. Here we firstly explored the impact of copper-exposure on expression profiles in zebrafish. Copper reduced embryo hatching, increased mortality and caused embryonic developmental abnormalities and behavioral dysfunction in juveniles. Transcriptomic analysis revealed that differential genes related to neuron were highly associated with oxidative stress especially enriched to FoxO pathway. Through further validation in Caenorhabditis elegans, copper resulted in nematode neurodegenerative movement disorders and neuronal damage, along with increased levels of reactive oxygen species (ROS) as well as decreased expressions of antioxidant-related enzymes and downstream genes which was also involved in FoxO signaling pathway. Bacillus smithii XY1, a novel strain with an excellent antioxidative activity, showed a great alleviative effect on copper-induced neurotoxicity that was related to FoxO stimulation, being a potential candidate for copper pollution management. Overall, these results suggested that FoxO pathway activation can regard as a strategy for mitigating neurotoxicity caused by copper and B. smithii XY1 with excellent tolerance and outstanding antioxidation specially targeted for FoxO has a promising application in controlling copper contamination.

Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions

The acceleration of the nitrogen cycle and the nitrogen excess observed in some coastal waters has increased interest into understanding the biochemical and molecular basis of nitrogen metabolism in various microorganisms. To investigate nitrogen metabolism of a novel heterotrophic nitrification and aerobic denitrification bacterium Klebsiella aerogenes strain (B23) under nitrogen-rich conditions, we conducted physiological and transcriptomic high-throughput sequencing analyses on strain B23 cultured on potassium nitrate-free or potassium nitrate-rich media. Overall, K. aerogenes B23 assimilated 82.47% of the nitrate present into cellular nitrogen. Further, 1,195 differentially expressed genes were observed between K. aerogenes B23 cultured on potassium nitrate-free media and those cultured on potassium nitrate-rich media. Gene annotation and metabolic pathway analysis of the transcriptome were performed using a series of bioinformatics tools, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Non-Redundant Protein Database annotation. Accordingly, the nitrogen metabolism pathway of K. aerogenes B23 was analyzed; overall, 39 genes were determined to be involved in this pathway. Differential expression analysis of the genes involved in the nitrogen metabolism pathway demonstrated that, compared to the control, FNR, NarK/14945, fdx, gshA, proB, proA, gapA, argH, artQ, artJ, artM, ArgR, GAT1, prmB, pyrG, glnS, and Ca1 were significantly upregulated in the nitrogen-treated K. aerogenes B23; these genes have been established to be involved in the regulation of nitrate, arginine, glutamate, and ammonia assimilation. Further, norV, norR, and narI were also upregulated in nitrogen-treated K. aerogenes B23; these genes are involved in the regulation of NO metabolism. These differential expression results are important for understanding the regulation process of key nitrogen metabolism enzyme genes in K. aerogenes B23. Therefore, this study establishes a solid foundation for further research into the expression regulation patterns of nitrogen metabolism-associated genes in K. aerogenes B23 under nitrogen-rich conditions; moreover, this research provides essential insight into how K. aerogenes B23 utilizes nutritional elements.

Bioinformatic Approach to Investigate Larvae Gut Microbiota Cellulosimicrobium protaetiae via Whole-Genome Analysis

The insect larvae Protaetia brevitarsis seulensis have recently been researched as a nutritious food source and concentrated on their environmental impacts. Therefore, their gut microbiota has been studied to elucidate their effects and roles on the environment. Of the abundance of bacterial genus identified based on the 16S rRNA genes from isolates of the gut of insect larva Protaetia brevitarsis seulensis, six of the prominent genus were identified as Bacillus (40.2%), Cellulosimicrobium (33.5%), Microbacterium (2.8%), Streptomyces (3%), Krasilnikoviella (17.5%), and Isoptericola (3%) and their similarity of 16S rRNA blast changed from 99 to 100%. Cellulosimicrobium protaetiae BI34T showed strong denitrification and cellulose degradation activity. The newly complete genome sequence of BI34T and the genomes of five species was published in the genus Cellulosimicrobium with emphasis on the denitrification and secondary metabolite genes. In order to elucidate the relationship between the strain BI34T and the host insect larva, the whole-genome sequence was analyzed and compared with the genomes of five strains in the same genus, Cellulosimicrobium, loaded from GenBank. Our results revealed the composition of the gut microbiota of the insect larvae and analyzed the genomic data for the new strain to predict its characteristics and to understand the nitrogen metabolism pathway.

Microbially induced calcium precipitation driven by denitrification: Performance, metabolites, and molecular mechanisms

Microbially induced calcium precipitation (MICP) driven by denitrification has attracted extensive attention due to its application potential in nitrate removal from calcium-rich groundwater. However, little research has been conducted on this technique at the molecular level. Here, Pseudomonas WZ39 was used to explore the molecular mechanisms of nitrate-dependent MICP and the effects of Ca²⁺ on bacterial transcriptional regulation and metabolic response. The results exhibited that appropriate Ca²⁺ concentration (4.5 mM) can promote denitrification and the production of ATP, EPSs, and SMPs. Genome-wide analysis showed that the nitrate-dependent MICP was accomplished through heterotrophic denitrification and CO₂ capture. During this process, EPS biosynthesis and Ca²⁺ signaling regulation were involved in the nucleation template supply and Ca²⁺ homeostasis balance. Untargeted transcriptome- and metabolome-association analyses revealed that the addition of Ca²⁺ triggered the significant up-regulation in several key pathways, such as transmembrane transporter and channel activities, amino acid metabolism, fatty acid biosynthesis, and carbon metabolism, which played a momentous role in the mineral nucleation and energy provision. The detailed information provided novel insights for understanding the active control of bacteria on MICP, and has great significance for deepening the cognition of groundwater remediation using nitrate-dependent MICP technique.

Insights into the shift of microbial community related to nitrogen cycle, especially N2O in vanadium-polluted soil

Soil is a vital contributor to the production of nitrous oxide (N₂O), a potent greenhouse gas, through the nitrogen cycle, which can be influenced by accumulated vanadium (V) in soil but it is less pronounced. This work investigated the response of soil N₂O fluxes along with major nitrogen cycle products (ammonium, nitrate, and nitrite) to different vanadium contents (0, 200, 500, 800, and 1100 mg V/kg), and the underlying microbial mechanisms. N₂O fluxes was significantly influenced at high V content (1100 mg V/kg) due to its corresponding high water-soluble V content. Microbial composition and their correlations with nitrogen cycle products showed that microbes in dominant phyla (Actinobacteriota and Proteobacteria) and genus (Nocardioides, Lysobacter, Sphingomonas, and Marmoricola) might be the important contributor to N₂O fluxes regardless of the V content. Moreover, high V contents (800, and 1100 mg V/kg) could enrich microbes involved in nitrogen cycle, but weaken their correlations with nitrogen-related products, such as in genus Bacillus, and change microbial correlation with N₂O from associated with nitrate and nitrite to ammonium. Meanwhile, functional gene predication results showed that denitrifying genes nirKS and nosZ were negatively and positively correlated with V contents, respectively. These all further suggested that the shift of possible N₂O metabolic pathways induced mainly by water-soluble V might be the underlying reason for N₂O fluxes. These findings promote an understanding of the potential effect of metal pollution on N₂O fluxes in soil.

Bacillus coagulans XY2 ameliorates copper-induced toxicity by bioadsorption, gut microbiota and lipid metabolism regulation

Excessive copper pollutes the environment and endangers human health, attracting plenty of global attention. In this study, a novel strain named Bacillus coagulans XY2 was discovered to have a great copper tolerance and adsorption capacity. B. coagulans XY2 might maintain copper homeostasis through multisystem synergies of copper resistance, sulfur metabolism, Fe-S cluster assembly, and siderophore transport. In mice, by promoting the expression of SREBF-1 and SREBF-2 and their downstream genes, B. coagulans XY2 significantly inhibited the copper-induced decrease in weight growth rate, ameliorated dyslipidemia, restored total cholesterol and triglyceride contents both in serum and liver. Furthermore, B. coagulans XY2 recovered the diversity of gut microbiota and suppressed the copper-induced reduction in the ratio of Firmicutes to Bacteroidota. Serum metabolomics analysis showed that the alleviating effect of B. coagulans XY2 on copper toxicity was mainly related to lipid metabolism. For the first time, we demonstrated mechanisms of copper toxicity mitigation by B. coagulans XY2, which was related to self-adsorption, host copper excretion promotion, and lipid metabolism regulation. Moreover, working model of B. coagulans XY2 on copper homeostasis was predicted by whole-genome analysis. Our study provides a new solution for harmfulness caused by copper both in human health and the environment.

Simultaneous nitrogen removal via heterotrophic nitrification and aerobic denitrification by a novel Lysinibacillus fusiformis B301

Simultaneous nitrogen removal via heterotrophic nitrification and aerobic denitrification (HN-AD) has received widespread attention in biological treatment of wastewater. This study reported a novel Lysinibacillus fusiformis B301 strain, which effectively removed nitrogenous pollutants via HN-AD in one aerobic reactor with no nitrite accumulated. It exhibited the optimal nitrogen removal efficiency under 30°C, citrate as the carbon source and C/N ratio of 15. The maximum nitrogen removal rates were up to 2.11 mgNH₄ ⁺ -N/(L·h), 1.62 mgNO₃ ^- -N/(L·h), and 1.41 mgNO₂ ^- -N/(L·h), respectively, when ammonium, nitrate, and nitrite were employed as the only nitrogen source under aerobic conditions. Ammonium nitrogen was preferentially consumed via HN-AD in the coexistence of three nitrogen species, and the removal efficiencies of total nitrogen were up to 94.26%. Nitrogen balance analysis suggested that 83.25% of ammonium was converted to gaseous nitrogen. The HD-AD pathway catalyzed by L. fusiformis B301 followed NH 4 + → N H 2 OH → NO 2 - → NO 3 - → NO 2 - → N 2 , supported by the results of key denitrifying enzymatic activities. PRACTITIONER POINTS: The novel Lysinibacillus fusiformis B301 exhibited the outstanding HN-AD ability. The novel Lysinibacillus fusiformis B301 simultaneously removed multiple nitrogen species. No nitrite accumulated during the HN-AD process. Five key denitrifying enzymes were involved in the HN-AD process. Ammonium nitrogen (83.25%) was converted to gaseous nitrogen by the novel strain.

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.

Nitrogen Removal Characteristics of a Marine Denitrifying Pseudomonas stutzeri BBW831 and a Simplified Strategy for Improving the Denitrification Performance Under Stressful Conditions

A marine aerobic denitrifying bacterium was isolated and identified as Pseudomonas stutzeri BBW831 from the seabed silt of Beibu Gulf in China. According to the genome analysis, P. stutzeri BBW831 possessed a total of 14 genes (narG, narH, narI, narJ, napA, napB, nirB, nirD, nirS, norB, norC, norD, norQ, and nosZ) responsible for fully functional enzymes (nitrate reductase, nitrite reductase, nitric oxide reductase, and nitrous oxide reductase) involved in the complete aerobic denitrification pathway, suggesting that it had the potential for reducing nitrate to the final N₂. Denitrification results showed that P. stutzeri BBW831 exhibited efficient nitrogen removal characteristics. Within 12 h, the NO₃^--N removal efficiency and rate reached 94.64% and 13.09 mg·L^-1·h^-1 under 166.10 ± 3.75 mg/L NO₃^--N as the sole nitrogen source, and removal efficiency of the mixed nitrogen (50.50 ± 0.55, 62.28 ± 0.74, and 64.26 ± 0.90 mg/L of initial NH₄⁺-N, NO₃^--N, and NO₂^--N, respectively) was nearly 100%. Furthermore, a simplified strategy, by augmenting the inoculation biomass, was developed for promoting the nitrogen removal performance under high levels of NO₂^--N and salinity. As a result, the removal efficiency of the initial NO₂^--N up to approximately 130 mg/L reached 99.46% within 8 h, and the NO₃^--N removal efficiency achieved at 59.46% under the NaCl concentration even up to 50 g/L. The C/N ratio of 10 with organic acid salt such as trisodium citrate and sodium acetate as the carbon source was most conducive for cell growth and nitrogen removal by P. stutzeri BBW831, respectively. In conclusion, the marine P. stutzeri BBW831 contained the functional genes responsible for a complete aerobic denitrification pathway (NO₃^--N → NO₂^--N → NO → N₂O → N₂), and had great potential for the practical treatment of high-salinity nitrogenous mariculture wastewater.

Complete genome analysis of Pseudomonas furukawaii ZS1 isolated from grass carp (Ctenopharyngodon idellus) culture water

Pseudomonas furukawaii ZS1, isolated from grass carp (Ctenopharyngodon idellus) culture water, exhibits efficient aerobic nitrate reduction without nitrite accumulation; however, the molecular pathway underlying this aerobic nitrate reduction remains unclear. In this study, we constructed a complete genome map of P. furukawaii ZS1 and performed a comparative genomic analysis with a reference strain. The results showed that P. furukawaii ZS1 genome was 6 026 050 bp in size and contained 5427 predicted protein-coding sequences. The genome contained all the necessary genes for the dissimilatory nitrate reduction to ammonia pathway but lacked those for the assimilatory nitrate reduction pathway; additionally, genes that convert ammonia to organic nitrogen were also identified. The presence of putative genes associated with the nitrogen and oxidative phosphorylation pathways implied that ZS1 can perform respiration and nitrate reduction simultaneously under aerobic conditions, so that nitrite is rapidly consumed for detoxication by denitrification. The aim of this study is to indicate the great potential of strain ZS1 for future full-scale applications in aquaculture. This work provided insights at the molecular level on the nitrogen metabolic pathways in Pseudomonas species. The understanding of nitrogen metabolic pathways also provides significant molecular information for further Pseudomonas species modification and development.

Mutagenesis of high-efficiency heterotrophic nitrifying-aerobic denitrifying bacterium Rhodococcus sp. strain CPZ 24

Breeding high-efficiency heterotrophic nitrifying-aerobic denitrifying (SND) bacteria is important for the removal of biological nitrogen in wastewater treatment. In this study, a high-efficiency SND mutant strain, ΔRhodococcus sp. CPZ 24, was obtained by ultraviolet-diethyl sulfate compound mutagenesis. The maximum nitrification and denitrification rates were 3.77 and 1.37 mg·L^-1·h^-1, respectively 30.30 % and 17.10 % higher than those of wild bacteria. Biolog technology and network model analysis revealed that ΔCPZ 24 significantly improved the utilisation ability and metabolic activity of organic carbon sources. Furthermore, the expression levels of the nitrogen removal function genes nxrA, nosZ, amoA, and norB in strain ΔCPZ 24 increased significantly. In actual sewage, mutant bacteria ΔCPZ 24 have a 95.05 % ammonia-nitrogen degradation rate and a 96.67 % nitrate-nitrogen degradation rate. These results suggested that UV-DES compound mutation was a successful strategy to improve the nitrogen removal performance of SND bacteria in wastewater treatment.

High nitrite-nitrogen stress intensity drives nitrite anaerobic oxidation to nitrate and inhibits methanogenesis

Nitrite is an important intermediate in nitrogen metabolism. We explored the effect of nitrite-nitrogen stress intensity (NNSI) on nitrite metabolism and methanogenesis in anaerobic digestion. The results showed that the NNSI regulated microbial diversity, composition, and functions, and microbial community assembly was primarily shaped by stochastic processes. Moreover, the NNSI was negatively correlated with α-diversity and positively correlated with non-metric multi-dimensional scaling distance. Denitrification gradually increased with increasing NNSI; however, methanogenesis was gradually inhibited, which was primarily due to the inhibition of the aceticlastic methanogenesis pathway (i.e., Methanosaeta) and methylotrophic methanogenesis pathway (i.e., Candidatus_Methanofastidiosum). High NNSI (1882 ± 98.99 mg/L NO₂^--N) promoted nitrite anaerobic oxidation to nitrate and was favorable for dissimilatory nitrate reduction to ammonia (DNRA). We present evidence for the microbial transformation of nitrite under anaerobic conditions, with potential geochemical and evolutionary importance. As nitrogen oxides were already present on early Earth, our finding presents the possibility of a nitrogen cycle before the evolution of oxygenic photosynthesis.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

Biological nitrogen removal from stormwater in bioretention cells: a critical review

Excess nitrogen in stormwater degrades surface water quality via eutrophication and related processes. Bioretention has been recognized as a highly effective low-impact development (LID) technology for the management of high runoff volumes and reduction of nitrogen (N) pollutants through various mechanisms. This paper provides a comprehensive and critical review of recent developments on the biological N removal processes occurring in bioretention systems. The key plant- and microbe-mediated N transformation processes include assimilation (N uptake by plants and microbes), nitrification, denitrification, and anammox (anaerobic ammonia oxidation), but denitrification is the major pathway of permanent N removal. Overall, both laboratory- and field-scale bioretention systems have demonstrated promising N removal performance (TN: >70%). The phyla Bacteroidetes and Proteobacteria are the most abundant microbial communities found to be enriched in biofilter media. Furthermore, the denitrifying communities contain several functional genes (e.g., nirK/nirS, and nosZ), and their concentrations increase near the surface of media depth. The N removal effectiveness of bioretention systems is largely impacted by the hydraulics and environmental factors. When a bioretention system operates at: low hydraulic/N loading rate, containing a saturation zone, vegetated with native plants, having deeper and multilayer biofilter media with warm climate temperature and wet storm events periods, the N removal efficiency can be high. This review highlights shortcomings and current knowledge gaps in the area of total nitrogen removal using bioretention systems, as well as identifies future research directions on this topic.

A Novel Regulator Participating in Nitrogen Removal Process of Bacillus subtilis JD-014

Aerobic denitrification is considered as a promising biological method to eliminate the nitrate contaminants in waterbodies. However, the molecular mechanism of this process varies in different functional bacteria. In this study, the nitrogen removal characteristics for a newly isolated aerobic denitrifier Bacillus subtilis JD-014 were investigated, and the potential functional genes involved in the aerobic denitrification process were further screened through transcriptome analysis. JD-014 exhibited efficient denitrification performance when having sodium succinate as the carbon source with the range of nitrate concentration between 50 and 300 mg/L. Following the transcriptome data, most of the up-regulated differentially expressed genes (DEGs) were associated with cell motility, carbohydrate metabolism, and energy metabolism. Moreover, gene nirsir annotated as sulfite reductase was screened out and further identified as a regulator participating in the nitrogen removal process within JD-014. The findings in present study provide meaningful information in terms of a comprehensive understanding of genetic regulation of nitrogen metabolism, especially for Bacillus strains.

An Exploration of Seaweed Polysaccharides Stimulating Denitrifying Bacteria for Safer Nitrate Removal

Excessive use of nitrogen fertilizer in intensively managed agriculture has resulted in abundant accumulation of nitrate in soil, which limits agriculture sustainability. How to reduce nitrate content is the key to alleviate secondary soil salinization. However, the microorganisms used in soil remediation cause some problems such as weak efficiency and short survival time. In this study, seaweed polysaccharides were used as stimulant to promote the rapid growth and safer nitrate removal of denitrifying bacteria. Firstly, the growth rate and NO₃⁻-N removal capacity of three kinds of denitrifying bacteria, Bacillus subtilis (BS), Pseudomonas stutzeri (PS) and Pseudomonas putida (PP), were compared. The results showed that Bacillus subtilis (BS) had a faster growth rate and stronger nitrate removal ability. We then studied the effects of Enteromorpha linza polysaccharides (EP), carrageenan (CA), and sodium alginate (AL) on growth and denitrification performance of Bacillus subtilis (BS). The results showed that seaweed polysaccharides obviously promoted the growth of Bacillus subtilis (BS), and accelerated the reduction of NO₃⁻-N. More importantly, the increased NH₄⁺-N content could avoid excessive loss of nitrogen, and less NO₂⁻-N accumulation could avoid toxic effects on plants. This new strategy of using denitrifying bacteria for safely remediating secondary soil salinization has a great significance.