Nitrogen Metabolism Genes Research Articles

Novel strategies for enhancing energy metabolism and wastewater treatment in algae-bacteria symbiotic system through carbon dots-induced photogenerated electrons: The definitive role of accelerated electron transport

The nitrogen removal efficiency of the algae-bacteria symbiotic system (ABSS) remains challenging due to competition for light capture and insufficient electron donors in aquaculture wastewater. To overcome this bottleneck issue, we first identified and reported the introduction of photogenerated electrons into ABSS by coupling them with carbon dots (CDs). The energy metabolism (21.52 %-56.25 %) and pollutant degradation efficiency (89.36 %-96.42 %) of ABSS/CDs surpassed the biochemical limit observed in traditional ABSS. Notably, the addtion of CDs facilitated an opening of the plastoquinone-pool (PQ-pool) valve and accelerated electron transfer rates, enabling photogenerated electrons to selectively target light-harvesting complexs as activation sites, thereby mobilizing photosynthesis and respiratory system activity to enhance nicotinamide adenine dinucleotide reduced (NADH) and adenosine triphosphate (ATP) production while promoting tricarboxylic acid (TCA) and Calvin cycle processes. In simulated swine wastewater treatment, ABSS/CDs achieved higher removal rates for the chemical oxygen demand (COD), total nitrogen (TN) and ammonium-nitrogen (NH4+-N) (100 %, 99.23 % and 98.62 % respectively) compared to pure culture systems alone. Network-based analysis revealed that ABSS/CDs improved microbial community structure stability within the photobioreactor while demonstrating efficient coupling between fungi, nitrifying bacteria, and denitrifying bacteria for enhanced performance in nitrogen removal processes. The upregulation of nitrogen metabolism and PQ-pool genes maintains efficient electron transport rates and contributes to nitrogen removal. This study expands our understanding of the physiological aptitudes of ABSS and provides valuable insights into applying CDs photoelectrons for enhanced wastewater treatment.

Functional Genes and Metabolic Pathways of Nitrogen Metabolism Microorganisms in Lake Sediments：A Case Study of Hongfeng Lake, Guizhou Province

The nitrogen cycle is of great importance for material circulation and energy flow in lake ecosystems. It is driven by microorganisms in lake sediments and can contribute to balancing lake ecosystems. In this study, physical and chemical properties of the sediments sampled from Hongfeng Lake in Guizhou Province were assayed and analyzed using metagenomics to reveal relevant microorganisms, functional genes, metabolic pathways, and their relationships throughout nitrogen metabolism. The results showed that bacteria were dominant, and the top three relative abundant genera were Thiobacillus （16.64%）, Rubrivivax（9.43%）, and Nitrospira （7.09%）. Only six pathways, including nitrogen fixation, nitrification, denitrification, assimilatory nitrate reduction, dissimilatory nitrate reduction, and complete nitrification, were detected in total, of which denitrification and dissimilatory nitrate reduction were the primary processes, but anaerobic ammonia oxidation was not detected. Bacteria and archaea participated in these six pathways, while eukaryotes only functioned in dissimilatory nitrate reduction, denitrification, and complete nitrification. Ammonia nitrogen, nitrate nitrogen, and total phosphorus, as main environmental factors affecting the distribution of functional genes for nitrogen metabolism, differentiated with each other in their respective real-world conditions. A positive correlation （95.04%） was observed between the functional genes and microorganisms, and narG, narZ, and nxrA possessed the highest abundance and the highest host genes. On this basis, these findings are expected to further elucidate the nitrogen cycle of typical karst lakes in Guizhou Province.

Effects of straws on greenhouse gas emissions in the ectopic fermentation system

Straws are commonly used padding materials in the ectopic fermentation system, but their effects on greenhouse gas emissions are not well understood. This study compared the effects of rape, rice and corn straws on the fermentation performance of the ectopic fermentation system. Compared with corn straw, the treatment groups with rape straw and rice straw significantly increased the alpha diversity of the fermentation system, and simultaneously mitigated the cumulative emissions of CO2 and N2O by up to 32.4% and 93.9%, respectively. The CO2 and N2O peak emission in the treatment group with corn straw reached 1.4 × 106 and 36.2 mg/m2/d, respectively. CH4 peak emission was one order of magnitude lower than that of N2O in the ectopic fermentation system. Redundancy analysis showed that Pseudoxanthomonas sp000510725 was the key specie that positively affect the fermentation temperature, CO2 and N2O emissions in the fermentation system. Nitrogen metabolism genes, such as nosZ, nirK, and nirS were more abundant in the surface layer of the fermentation system, indicating more active nitrogen metabolism in this region, and the core zone could be the primary source of N2O emissions. Those findings indicated that rape and rice straw can be potential padding materials for mitigating greenhouse gas emissions in large-scale ectopic fermentation system.

Removal of nitrate nitrogen by aerobic denitrification granular sludge under strongly alkaline conditions: Performance and mechanism

Aerobic granular sludge (AGS) technology faces challenges in treating strongly alkaline wastewater because high pH affects sludge settleability and microbial metabolic activity. In this study, aerobic denitrification granular sludge (ADGS) was cultivated with strongly autoaggregating aerobic denitrifying bacteria as the sludge source at an influent pH of 11.0 under aerobic conditions. The formation characteristics of ADGS and its pollutant removal efficiency under strongly alkaline conditions were explored. Compared with ADGS cultivated under neutral conditions, ADGS cultivated under strongly alkaline conditions resulted in superior particle formation rates, settleability, particle strengths and particle stabilities. Nitrate nitrogen was almost completely removed at a pH of 11.0 under aerobic conditions. Protein, polysaccharides and humic acid in extracellular polymeric substances (EPS) under strongly alkaline conditions were involved in the ADGS formation process. In addition, the presence of metallic elements in the EPS and inorganic nuclei in the sludge facilitated the formation of ADGS. The strongly alkaline environment enriched the alkali-resistant aerobic denitrifying bacteria, such as unclassified_f__Rhodobacteraceae, Tessaracoccus, Halomonas, and Pseudofulvimonas, as well as specialized alkali-resistant genera. Furthermore, the strongly alkaline environment increased the abundance of key enzymes involved in carbon metabolism and upregulated the expression of nitrogen metabolism genes in the ADGS to maintain their metabolic activity. In addition, the microorganisms upregulated genes that encoded reverse transporter protein genes (mnhACEFG, nhaACP, and phaACDEFG) and K+ uptake protein genes (trkAHG) and secreted greater amounts of acidic functional groups and free amino groups to help maintain intracellular and extracellular osmolality and acid–base homeostasis under strongly alkaline stress. This research provides a possible option and innovative strategy for the management of highly alkaline nitrate-containing wastewater.

429 Maternal rate of gain and one-carbon metabolites supplementation alters the gene expression profile of fetal brain during early gestation in beef heifers

Abstract Maternal nutritional plane during pregnancy may leave lifelong impacts on offspring in beef cattle. Given that, we hypothesized that the supplementation of one-carbon metabolites (OCM) during pregnancy would mitigate the negative effects of maternal rate of gain through brain gene expression regulation in early developing bovine fetuses. The objective of this study was to evaluate the effects of OCM supplementation and maternal rate of gain on gene expression in the developing fetal brain in gestating beef heifers. Herein, Angus crossbred heifers (n = 72, body weight = 406 ± 33 kg) were randomly assigned to 2 × 2 factorial arrangement of treatments with two levels of maternal rate of gain (CON, 0.60 kg/d; and RES, -0.23 kg/d) each with or without OCM supplementation (+OCM, and -OCM). Heifers were fed individually and were bred using female-sexed semen from a single sire. The OCM supplementation included rumen-protected choline (44.4 g/d) and methionine (7.4 g/d) in corn carrier fed daily and weekly injections of folate (320 mg) and vitamin B12 (20 mg). The -OCM heifers received the corn carrier and saline injections. The treatments started at the time of breeding and continued until d 63 of gestation when pregnant heifers (n = 29) were slaughtered to collect fetal brain tissues for RNA sequencing. The fetal brain phenotypic data were analyzed using MIXED procedures of SAS, indicating that restricted nutrition affected the fetal right hemisphere weight (P < 0.05), and there was a strong tendency for overall fetal brain weight (0.05 < P < 0.1) to be affected as well. Brain transcriptomics data were analyzed using STAR aligner and a total of 177 differentially expressed genes (DEGs, FDR < 0.05) were identified across all treatment comparisons using DESeq2. Most of the DEGs were either isoforms of spliceosomal non-coding RNAs or micro-RNAs (miRNAs) associated with biological processes (FDR < 0.1) like mRNA processing, cellular nitrogen metabolism, lipid metabolism, and post-transcriptional gene silencing. The key miRNAs upregulated in the brain tissue of restricted fetuses without OCM supplementation, bta-mir-2375, bta-mir-876, and bta-mir-196a-1, were found to be associated with early embryogenesis and essential cellular regulatory processes. Conversely, in restricted fetuses with OCM supplementation, upregulated miRNAs such as bta-mir-216b, bta-mir-2285dd, and bta-mir-1298 were linked to early embryonic development, muscular development, and lipid metabolism in cattle. Both phenotypic and transcriptomics data here revealed that the maternal rate of gain altered fetal brain development, with differences seemingly compensated by OCM supplementation. USDA is an equal opportunity provider and employer.

Insight into response mechanism of aerobic granular sludge to combined nanoparticle stress: Nitrogen removal, microbial community and heavy metal resistance genes

Multiple nanoparticles presented in wastewater treatment plants can produce comprehensive ecotoxicity. In this study, copper oxide nanoparticles (nCuO) and zinc oxide nanoparticles (nZnO) were investigated for their co-toxicity to aerobic granular sludge (AGS) systems. The combined stress of nCuO and nZnO performed significant antagonistic effects on nitrogen removal both under acute and chronic stress. Under chronic stress, nCuO and nZnO co-existence performed significant antagonistic effects on cell membrane, adenosine triphosphate (ATP) activity and microbial community structure. PICRUSt analysis indicated that nCuO (15 mg/L) co-existence alleviated nZnO (10 mg/L) inhibition on energy production and membrane transport metabolic pathways. In addition, nCuO addition to single nZnO weakened the toxicity of nZnO to nitrogen metabolism, glucose metabolism, and electron transfer genes, contributing to an alleviation in nitrogen removal inhibition. As compared with individual stress, combined stress decreased Cu(II) release from nCuO, but increased Zn(II) release from nZnO. The combination of nCuO and nZnO increased zinc resistance gene amplification and czcC gene proportion, and promoted Zn(II) efferent from cells, also with AGS resistance.

Innovative application of basalt fibers as biological carrier in constructed wetland-microbial fuel cell for improvement of performance under perfluorooctanoic acid exposure

Basalt fiber (BF) was filled in constructed wetland-microbial fuel cell (CW-MFC) as bio-carrier for enhancement of operation performance under perfluorooctanoic acid (PFOA) exposure. In this study, although PFOA caused significant decline of ammonium removal by 7.5–7.7 %, slight promotion on nitrogen and phosphorus removal was observed with BF filling, compared to control. PFOA removal also increased by 1.7–3.4 % in BF filling group. Besides, improved electrochemical performance was discovered with BF filling, in which the highest power density increased by 86.6 % than control, even under PFOA stress. Enhanced stability and performance of CW-MFC resulted from stimulation of functional bacteria on electrodes like Dechloromonas, Thauera, Zoogloea, Gemmobacter, and Pseudomonas, which were further enriched on BF carrier. Higher abundance of nitrogen metabolism and related genes on electrodes and BF carrier was also discovered with BF filling. This study offered new findings on application of BF in CW-MFC systems with PFOA exposure.

Response of Relationship Between Microplastic Abundance and Nitrogen Metabolism Function Microorganisms and Genes in Water

The impact of microplastics (MPs) as a new type of pollutant on water pollution has become a research hotspot. To explore the response relationship between the abundance of MPs and nitrogen metabolism function in a freshwater environment, Lake Ulansuhai was used as the research object; the abundance of MPs in the water was detected using a Zeiss microscope, and the distribution characteristics of nitrogen metabolism functional bacteria and functional genes in the water were analyzed using metagenomics sequencing. The correlation analysis method was used to explore the relationship between the abundance of MPs and nitrogen metabolism functional microorganisms and nitrogen metabolism functional genes. The results showed that the presence of MPs in freshwater environments had a higher impact on Cyanobacteria and Firmicutes as the dominant phyla, and the presence of MPs promoted their enrichment and growth. Among the dominant bacterial genera, MPs promoted the growth of Mycobacterium and inhibited Candidatus_Planktopila more significantly, further indicating that in freshwater environments, MPs affected normal nitrogen metabolism by affecting microbial communities, and pathways such as carbon and nitrogen fixation and denitrification were important pathways for MPs to affect nitrogen metabolism. From the perspective of nitrogen metabolism functional genes, it was found that the abundance of MPs significantly affected some functional genes during nitrification (pmoA-amoA, pmoB-amoB, and pmoC-amoC), denitrification (nirK and napA), and dissimilatory nitrate reduction (nrfA) processes (P < 0.05). Moreover, the influence of MPs abundance on different functional genes in the same pathway of nitrogen metabolism varied, making the impact of MPs on aquatic environments very complex; thus, its harm to the water environment cannot be underestimated.

Unraveling the effects and mechanisms of antibiotics on aerobic simultaneous nitrogen and phosphorus removal by Acinetobacter indicus CZH-5

The effects of antibiotics, such as tetracycline, sulfamethoxazole, and ciprofloxacin, on functional microorganisms are of significant concern in wastewater treatment. This study observed that Acinetobacter indicus CZH-5 has a limited capacity to remove nitrogen and phosphorus using antibiotics (5 mg/L) as the sole carbon source. When sodium acetate was supplied (carbon/nitrogen ratio = 7), the average removal efficiencies of ammonia-N, total nitrogen, and orthophosphate-P increased to 52.46 %, 51.95 %, and 92.43 %, respectively. The average removal efficiencies of antibiotics were 84.85 % for tetracycline, 39.32 % for sulfamethoxazole, 18.85 % for ciprofloxacin, and 23.24 % for their mixtures. Increasing the carbon/nitrogen ratio to 20 further improved the average removal efficiencies to 72.61 % for total nitrogen and 97.62 % for orthophosphate-P (5 mg/L antibiotics). Additionally, the growth rate and pollutant removal by CZH-5 were unaffected by the presence of 0.1–1 mg/L antibiotics. Transcriptomic analysis revealed that the promoted translation of aceE, aarA, and gltA genes provided ATP and proton -motive forces. The nitrogen metabolism and polyphosphate genes were also affected. The expression of acetate kinase, dehydrogenase, flavin mononucleotide enzymes, and cytochrome P450 contributed to antibiotic degradation. Intermediate metabolites were investigated to determine the reaction pathways.

Orphan response regulator NnaR is critical for nitrate and nitrite assimilation in Mycobacterium abscessus.

Mycobacterium abscessus (Mab) is an opportunistic pathogen afflicting individuals with underlying lung disease such as Cystic Fibrosis (CF) or immunodeficiencies. Current treatment strategies for Mab infections are limited by its inherent antibiotic resistance and limited drug access to Mab in its in vivo niches resulting in poor cure rates of 30-50%. Mab's ability to survive within macrophages, granulomas and the mucus laden airways of the CF lung requires adaptation via transcriptional remodeling to counteract stresses like hypoxia, increased levels of nitrate, nitrite, and reactive nitrogen intermediates. Mycobacterium tuberculosis (Mtb) is known to coordinate hypoxic adaptation via induction of respiratory nitrate assimilation through the nitrate reductase narGHJI. Mab, on the other hand, does not encode a respiratory nitrate reductase. In addition, our recent study of the transcriptional responses of Mab to hypoxia revealed marked down-regulation of a locus containing putative nitrate assimilation genes, including the orphan response regulator nnaR (nitrate/nitrite assimilation regulator). These putative nitrate assimilation genes, narK3 (nitrate/nitrite transporter), nirBD (nitrite reductase), nnaR, and sirB (ferrochelatase) are arranged contiguously while nasN (assimilatory nitrate reductase identified in this work) is encoded in a different locus. Absence of a respiratory nitrate reductase in Mab and down-regulation of nitrogen metabolism genes in hypoxia suggest interplay between hypoxia adaptation and nitrate assimilation are distinct from what was previously documented in Mtb. The mechanisms used by Mab to fine-tune the transcriptional regulation of nitrogen metabolism in the context of stresses e.g. hypoxia, particularly the role of NnaR, remain poorly understood. To evaluate the role of NnaR in nitrate metabolism we constructed a Mab nnaR knockout strain (MabΔnnaR ) and complement (MabΔnnaR+C ) to investigate transcriptional regulation and phenotypes. qRT-PCR revealed NnaR is necessary for regulating nitrate and nitrite reductases along with a putative nitrate transporter. Loss of NnaR compromised the ability of Mab to assimilate nitrate or nitrite as sole nitrogen sources highlighting its necessity. This work provides the first insights into the role of Mab NnaR setting a foundation for future work investigating NnaR's contribution to pathogenesis.

Ca(H2PO4)2 and MgSO4 activated nitrogen-related bacteria and genes in thermophilic stage of compost

This study was conducted to investigate the effects of Ca(H2PO4)2 and MgSO4 on the bacterial community and nitrogen metabolism genes in the aerobic composting of pig manure. The experimental treatments were set up as control (C), 1% Ca(H2PO4)2 + 2% MgSO4 (CaPM1), and 1.5% Ca(H2PO4)2 + 3% MgSO4 (CaPM2), which were used at the end of composting for potting trials. The results showed that Ca(H2PO4)2 and MgSO4 played an excellent role in retaining nitrogen and increasing the alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), and available potassium (AK) contents of the composts. Adding Ca(H2PO4)2 and MgSO4 changed the microbial community structure of the compost. The microorganisms associated with nitrogen retention were activated. The complexity of the microbial network was enhanced. Genetic prediction analysis showed that the addition of Ca(H2PO4)2 and MgSO4 reduced the accumulation of nitroso-nitrogen and the process of denitrification. At the same time, despite the reduction of genes related to nitrogen fixation, the conversion of ammonia to nitrogenous organic compounds was promoted and the stability of nitrogen was increased. Mantel test analysis showed that Ca(H2PO4)2 and MgSO4 can affect nitrogen transformation-related bacteria and thus indirectly affect nitrogen metabolism genes by influencing the temperature, pH, and organic matter (OM) of the compost and also directly affected nitrogen metabolism genes through PO43− and Mg2+. The pot experiment showed that composting with 1.5% Ca(H2PO4)2 + 3% MgSO4 produced the compost product that improved the growth yield and nutrient content of cilantro and increased the fertility of the soil. In conclusion, Ca(H2PO4)2 and MgSO4 reduces the loss of nitrogen from compost, activates nitrogen-related bacteria and genes in the thermophilic phase of composting, and improves the fertilizer efficiency of compost products.Key points• Ca(H2PO4)2 and MgSO4 reduced the nitrogen loss and improved the compost effect• Activated nitrogen-related bacteria and altered nitrogen metabolism genes• Improved the yield and quality of cilantro and fertility of soil

Effects of crayfish shell powder and bamboo-derived biochar on nitrogen conversion, bacterial community and nitrogen functional genes during pig manure composting

This study investigated the effects of crayfish shell powder (CSP) and bamboo-derived biochar (BDB) on nitrogen metabolism, bacterial community and nitrogen functional genes during pig manure composting. Four treatments were established: CP (with no additives), TP1 (5 % BDB), TP2 (5 % CSP) and TP3 (2.5 % BDB + 2.5 % CSP). Compared to CP, the germination index (GI) of TP reached > 85 % 10 days earlier. Meanwhile, TP3 reduced NH3 and N2O emissions by 42.90 % and 65.9 %, respectively, while increased TN (total nitrogen) concentration by 5.43 g/kg. Furthermore, additives changed the bacterial structure and formed a beneficial symbiotic relationship with essential N-preserving bacteria, thereby enhancing nitrogen retention throughout the composting process. Metagenomic analysis revealed that additives upregulated nitrification genes and downregulated denitrification and nitrate reduction genes, ultimately improving nitrogen cycling and mitigating NH3 and N2O emissions. In conclusion, the results confirmed that TP3 was the most effective treatment in reducing nitrogen loss.

Insights into the effects of exogenous folate on the recovery of SPNA system after starvation: Performance, microbial community and metabolism

To investigate the effects of folate addition on the recovery process of the single-stage partial nitritation-anammox (SPNA) system, two continuous stirred tank reactors (CSTRs), named R1 (adding folate) and R2 (control group), were operated for 105 days at room temperatures. The highest nitrogen removal rate (NRR) observed in R1 was 0.47 kg N/(m3·d) with the addition of 3.0 mg/L folate. Additionally, the activities of HZO and HZS in R1 were higher than those in R2. The relative abundance of Candidatus Brocadia reached 23.7% in R1 and 18.2% in R2. Moreover, the relative abundance of nitrogen metabolism genes and carbon metabolism genes increased with folate addition. However, 3.0 mg/L folate addition reduced the relative abundance of nirK/S and the activity and growth of ammonia-oxidizing bacteria, which was not conducive to continually improving the NRR. This study provided a novel perspective on improving the activity and abundance of anammox bacteria during the restoration process.

Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress.

Mycobacterium avium complex (MAC), including Mycobacterium intracellulare is a member of slow-growing mycobacteria and contributes to a substantial proportion of nontuberculous mycobacterial lung disease in humans affecting immunocompromised and elderly populations. Adaptation of pathogens in hostile environments is crucial in establishing infection and persistence within the host. However, the sophisticated cellular and molecular mechanisms of stress response in M. intracellulare still need to be fully explored. We aimed to elucidate the transcriptional response of M. intracellulare under acidic and oxidative stress conditions. At the transcriptome level, 80 genes were shown [FC] ≥ 2.0 and p < 0.05 under oxidative stress with 10mM hydrogen peroxide. Specifically, 77 genes were upregulated, while 3 genes were downregulated. In functional analysis, oxidative stress conditions activate DNA replication, nucleotide excision repair, mismatch repair, homologous recombination, and tuberculosis pathways. Additionally, our results demonstrate that DNA replication and repair system genes, such as dnaB, dinG, urvB, uvrD2, and recA, are indispensable for resistance to oxidative stress. On the contrary, 878 genes were shown [FC] ≥ 2.0 and p < 0.05 under acidic stress with pH 4.5. Among these genes, 339 were upregulated, while 539 were downregulated. Functional analysis highlighted nitrogen and sulfur metabolism pathways as the primary responses to acidic stress. Our findings provide evidence of the critical role played by nitrogen and sulfur metabolism genes in the response to acidic stress, including narGHIJ, nirBD, narU, narK3, cysND, cysC, cysH, ferredoxin 1 and 2, and formate dehydrogenase. Our results suggest the activation of several pathways potentially critical for the survival of M. intracellulare under a hostile microenvironment within the host. This study indicates the importance of stress responses in M. intracellulare infection and identifies promising therapeutic targets.

The global nitrogen regulator GlnR is a direct transcriptional repressor of the key gluconeogenic gene pckA in actinomycetes.

The GlnR regulator of actinomycetes controls nitrogen metabolism genes and many other genes involved in carbon, phosphate, and secondary metabolisms. Currently, the known GlnR-regulated genes in carbon metabolism are involved in the transport of carbon sources, the assimilation of short-chain fatty acid, and the 2-methylcitrate cycle, although little is known about the relationship between GlnR and the TCA cycle and gluconeogenesis. Here, based on the biochemical and genetic results, we identified GlnR as a direct transcriptional repressor of pckA, the gene that encodes phosphoenolpyruvate carboxykinase, a key enzyme for gluconeogenesis, thus highlighting that GlnR plays a central and complex role for dynamic orchestration of cellular carbon, nitrogen, and phosphate fluxes and bioactive secondary metabolites in actinomycetes to adapt to changing surroundings.

Metagenomic analysis reveals gene taxonomic and functional diversity response to microplastics and cadmium in an agricultural soil

Both microplastics (MPs) and heavy metals are common soil pollutants and can interact to generate combined toxicity to soil ecosystems, but their impact on soil microbial communities (e.g., archaea and viruses) remains poorly studied. Here, metagenomic analysis was used to explore the response of soil microbiome in an agricultural soil exposed to MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and/or Cd. Results showed that MPs had more profound effects on microbial community composition, diversity, and gene abundances when compared to Cd or their combination. Metagenomic analysis indicated that the gene taxonomic diversity and functional diversity of microbial communities varied with MPs type and dose. MPs affected the relative abundance of major microbial phyla and genera, while their coexistence with Cd influenced dominant fungi and viruses. Nitrogen-transforming and pathogenic genera, which were more sensitive to MPs variations, could serve as the indicative taxa for MPs contamination. High-dose PLA treatments (10%, w/w) not only elevated nitrogen metabolism and pathogenic genes, but also enriched copiotrophic microbes from the Proteobacteria phylum. Overall, MPs and Cd showed minimal interactions on soil microbial communities. This study highlights the microbial shifts due to co-occurring MPs and Cd, providing evidence for understanding their environmental risks.

Biological nitrogen fixation maintains carbon/nitrogen balance and photosynthesis at elevated CO2.

Understanding crop responses to elevated CO2 is necessary to meet increasing agricultural demands. Crops may not achieve maximum potential yields at high CO2 due to photosynthetic downregulation, often associated with nitrogen limitation. Legumes have been proposed to have an advantage at elevated CO2 due to their ability to exchange carbon for nitrogen. Here, the effects of biological nitrogen fixation (BNF) on the physiological and gene expression responses to elevated CO2 were examined at multiple nitrogen levels by comparing alfalfa mutants incapable of nitrogen fixation to wild-type. Elemental analysis revealed a role for BNF in maintaining shoot carbon/nitrogen (C/N) balance under all nitrogen treatments at elevated CO2, whereas the effect of BNF on biomass was only observed at elevated CO2 and the lowest nitrogen dose. Lower photosynthetic rates at were associated with the imbalance in shoot C/N. Genome-wide transcriptional responses were used to identify carbon and nitrogen metabolism genes underlying the traits. Transcription factors important to C/N signalling were identified from inferred regulatory networks. This work supports the hypothesis that maintenance of C/N homoeostasis at elevated CO2 can be achieved in plants capable of BNF and revealed important regulators in the underlying networks including an alfalfa (Golden2-like) GLK ortholog.

Association between oxidative stress and chronic orofacial pain and potential druggable targets: Evidence from a Mendelian randomization study.

Oxidative stress indicators affect chronic orofacial pain (COFP), but how to reduce these effects is uncertain. 11 oxidative stress biomarkers were collected as exposures, while four forms of COFP were chosen as outcomes for Mendelian randomization (MR) study. The effect estimates between oxidative stress and COFP were calculated using inverse variance-weighted MR (IVW-MR). Then, functional mapping and annotation (FUMA) was utilized in order to carry out SNP-based functional enrichment analyses. In addition, the IVW-MR method was applied to combine effect estimates when using genetic variants associated with oxidative stress biomarkers as an instrument for exploring potential druggable targets. The results indicated that oxidative stress biomarkers (causal OR of uric acid (UA), 0.998 for myofascial pain, 95% CI 0.996-1.000, p < .05; and OR of glutathione transferase (GST), 1.002 for dentoalveolar pain, 95% CI 1.000-1.003, p < .05) were significantly linked with the probability of COFP. Functional analysis also demonstrated that UA and myofascial pain genes were prominent in nitrogen and uracil metabolism, while GST and dentoalveolar pain genes were enriched in glutathione metabolism. Also, the study provided evidence that solute carrier family 2 member 9 (SLC2A9) and glutathione S-transferase alpha 2 (GSTA2) cause discomfort in the myofascial pain (OR = 1.003, 95% CI 1.000-1.006; p < .05) and dentoalveolar region (OR = 1.001, 95% CI 1.000-1.002; p < .05), respectively. In conclusion, this MR study indicates that genetically predicted myofascial pain was significantly associated with decreased UA and dentoalveolar pain was significantly associated with increased GST level. SLC2A9 inhibitor and GSTA2 inhibitor were novel chronic orofacial pain therapies and biomarkers, but clinical trials are called to examine if these oxidative biomarkers have the protective effect against orofacial pain, and further research are needed to explore the underlying mechanisms.

Microbiome comparisons reveal the core microorganisms and key nitrogen metabolic pathway involved in industrial nitrogen fertilizer wastewater treatment plants

Microbiomes from municipal wastewater treatment plants (WWTPs) have been widely investigated, but less attention has been paid to those in the industrial WWTPs. To compare the microbiomes involved in nitrogen fertilizer wastewater treatment, four WWTPs with different concentrations and types of pollutants, processes, and geographic locations were chosen. Diversity results revealed that microbial community was similar within the same WWTP, but different among the four WWTPs. CPCoA further demonstrated these differences (P = 0.022), implying that the diverse manufactured products acted as electron donors to create distinct ecological niches for denitrification. However, bacterial composition and functional profile were similar among four WWTPs (P > 0.05), and their abundance differed and fluctuated. More than 80 % of the dominant genera detected were present in all four WWTPs. And the core bacteria identified were Hyphomicrobium, Acinetobacter, Pedomicrobium, Methyloversatilis, Gp16, Thauera, and Moorella respectively, accounting for 19.524 % of total bacterial abundance. Forty-five nitrogen metabolism genes were active in four nitrogen cycle pathways (nitrification, assimilatory nitrate reduction, dissimilatory nitrate reduction, denitrification). The key genes were amoC (0.30 %), nasA (5.35 %), nirA (2.17 %), nirB (6.04 %), nirD (5.82 %), narG (3.87 %), narH (4.65 %), nirK (3.90 %), norB (3.32 %), nosZ (2.80 %). Hyphomicrobium, Thauera, Afipia, and Paracocccus were the hosts of denitrification genes, synergistically treating the nitrogen fertilizer wastewater to meet the discharge standard. These results suggested that microbial community structure in the nitrogen fertilizer industry is similar, helping further the understanding of the microbiota at an industry level though more samples are required to verify this.

Metagenomic analysis of the microbial communities and associated network of nitrogen metabolism genes in the Ryukyu limestone aquifer.

While microbial biogeochemical activities such as those involving denitrification and sulfate reduction have been considered to play important roles in material cycling in various aquatic ecosystems, our current understanding of the microbial community in groundwater ecosystems is remarkably insufficient. To assess the groundwater in the Ryukyu limestone aquifer of Okinawa Island, which is located in the southernmost region of Japan, we performed metagenomic analysis on the microbial communities at the three sites and screened for functional genes associated with nitrogen metabolism. 16S rRNA amplicon analysis showed that bacteria accounted for 94-98% of the microbial communities, which included archaea at all three sites. The bacterial communities associated with nitrogen metabolism shifted by month at each site, indicating that this metabolism was accomplished by the bacterial community as a whole. Interestingly, site 3 contained much higher levels of the denitrification genes such as narG and napA than the other two sites. This site was thought to have undergone denitrification that was driven by high quantities of dissolved organic carbon (DOC). In contrast, site 2 was characterized by a high nitrate-nitrogen (NO3-N) content and a low amount of DOC, and this site yielded a moderate amount of denitrification genes. Site 1 showed markedly low amounts of all nitrogen metabolism genes. Overall, nitrogen metabolism in the Ryukyu limestone aquifer was found to change based on environmental factors.