Frontiers in Microbiology最新文献

{"title":"The quality of the organic materials determines its carbon conversion efficiency in tropical latosol.","authors":"Shuhui Song, Siru Liu, Yanan Liu, Lei Shi, Huayong Li, Weiqi Shi, Haiyang Ma","doi":"10.3389/fmicb.2025.1573984","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1573984","url":null,"abstract":"<p><strong>Introduction: </strong>Tropical regions are characterized by high temperatures and abundant rainfall, which facilitate rapid carbon mineralization. However, research on soil organic carbon conversion efficiency (Esoc) in these areas is currently constrained by a lack of robust data support.</p><p><strong>Methods: </strong>This study used nylon - bags with typical tropical organic materials (pineapple leaf (PAL), banana stems (BAS), coconut husk (CCH), and organic fertilizer (OF)) to explore how mixing straw with latosol impacts soil organic carbon conversion efficiency (Esoc) and products, and to understand the relationships among Esoc, material composition (glycolipid, hemicellulose, cellulose, lignin), and enzyme activity.</p><p><strong>Results: </strong>CCH had the highest Esoc, from 37.79% to 96.87%, followed by OF with 26.71%-63.12%. The Esoc of PAL and BAS was 34.57% and 25.32% at 90 days, and 7.59% and 2.55% at 1080 days. The main factor that determines the difference in carbon conversion efficiency is the composition of organic materials. Compared with CK treatment, the soil organic carbon for PAL and BAS at 90_days was mainly O-alkyl-C, anomertic-C, and N-alkyl/methoxyl-C, with an unstable structure. The decomposition products of CCH mainly consisted of anomertic-C, aromatic-C, O-alkyl-C, carbonyl-C, and N-alkyl/methoxyl-C. The increased organic carbon in OF - mixed soil was mainly N-alkyl/methoxyl-C and anomertic-C. In the short-term (90 days), PAL, BAS, and OF increased the quantity and diversity of soil microorganisms, as well as the activities of xylosidase and cellobiohydrolase. CCH mainly enhanced soil phenol oxidase activity and maintained microbial biomass stabilityin the long-term (1080 days).</p><p><strong>Discussion: </strong>This study revealed the changes of microbial diversity and enzyme activity under different organic materials. The promotion effects of PAL and BAS on microbial biomass, diversity and enzyme activity in the short term and the maintenance effects of CCH on the stability of microbial biomass in the later period were investigated, which provided a new basis for further exploring the function and mechanism of microorganisms in soil ecosystems.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1573984"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sorghum-peanut intercropping under salt stress mediates rhizosphere microbial community shaping in sorghum by affecting soil sugar metabolism pathways.","authors":"Xia Shao, Chunmei Yang, Yuxuan Chen, Chang Liu, Chunjuan Liu, Xiaolong Shi, Yufei Zhou","doi":"10.3389/fmicb.2025.1589415","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1589415","url":null,"abstract":"<p><p>Soil salinization is a substantial impediment to agricultural production, and investigating sustainable mitigation measures is essential for addressing food security. We conducted a two-year pot experiment to investigate the shaping mechanism of sorghum rhizosphere microbial community in sorghum-peanut intercropping system under salt stress. The experiment comprised four treatments: sole-cropped sorghum under normal soil conditions (NSS), intercropped sorghum under normal soil conditions (NIS), sole-cropped sorghum under salt-stress conditions (SSS), and intercropped sorghum under salt-stress conditions (SIS). The sorghum rhizosphere soil metabolites were examined using GC-MS, and the rhizosphere microbial community was characterized through metabolome sequencing. We identified 123 metabolites across treatments, with significant differences between normal and salt-stress soil conditions. The major metabolite classes included carbohydrates, alcohols, and acids. Key carbohydrates, including fructose and sucrose, were significantly reduced in the SIS than in SSS, NSS, and NIS treatments. Metabolic pathway analyses revealed that these differences were primarily associated with \"Fructose and mannose metabolism,\" \"Starch and sucrose metabolism\" and \"ABC transporter.\" Metabolome analyses revealed significant differences in microbial community structure across diverse soil conditions and cropping patterns. At phylum level, Proteobacteria, Gemmatimonadetes, and Verrucomicrobia predominated, with their relative abundance experiencing substantial changes under salt stress. SIS facilitated the enrichment of specific genera (<i>Rhodanobacter</i>), which were associated with soil health and stress tolerance. Additionally, the responses of rare microbial taxa to salt stress and intercropping varied, with specific rare microbial taxa (<i>Rhizopus</i>) exhibiting relative abundance under salt stress. Correlation analysis of metabolites and microbial taxa revealed that certain carbohydrates were significantly positively correlated with specific microbial phyla (Cyanobacteria and Nitrospirae) while demonstrating a significant negative correlation with Planctomycetota and Bacteroidota. These correlations indicate that sorghum intercropped with peanuts can promote the enrichment of microbial taxa under salt stress, thereby enhancing soil metabolic functions and stress tolerance by optimizing the rhizosphere microbial community. This study reveals the mechanism through which sorghum-peanut intercropping under salt stress influences the composition of sorghum's rhizosphere microbial community by modulating soil sugar metabolism pathways. This finding provides a new perspective on sustainable agricultural practices in saline soils and emphasizes the pivotal role of plant-metabolite-microbe interactions in abiotic stress mitigation.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1589415"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying potential novel widespread determinants of bacterial pathogenicity using phylogenetic-based orthology analysis.","authors":"Sara Ribeiro, Karine Alves, Julien Nourikyan, Jean-Pierre Lavergne, Simon de Bernard, Laurent Buffat","doi":"10.3389/fmicb.2025.1494490","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1494490","url":null,"abstract":"<p><strong>Introduction: </strong>The global rise in antibiotic resistance and emergence of new bacterial pathogens pose a significant threat to public health. Novel approaches to uncover potential novel diagnostic and therapeutic targets for these pathogens are needed.</p><p><strong>Methods: </strong>In this study, we conducted a large-scale, phylogenetic-based orthology analysis (OA) to compare the proteomes of pathogenic to humans (HP) and non-pathogenic to humans (NHP) bacterial strains across 734 strains from 514 species and 91 families.</p><p><strong>Results: </strong>Using a dedicated workflow, we identified 4,383 hierarchical orthologous groups (HOGs) significantly associated with the HP label, many of which are linked to critical factors such as stress tolerance, metabolic versatility, and antibiotic resistance. Both known virulence factors (VFs) and potential novel widespread pathogenicity determinants were uncovered, supported by both statistical testing and complementary protein domain analysis.</p><p><strong>Discussion: </strong>By integrating curated strain-level pathogenicity annotations from BacSPaD with phylogeny-based OA, we introduce a novel approach and provide a novel resource for bacterial pathogenicity research.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1494490"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transfection of unmodified oligodeoxynucleotide with polyethylenimine reduces the level of hepatitis B surface antigen.","authors":"Junyu Lin, Jing Li","doi":"10.3389/fmicb.2025.1600679","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1600679","url":null,"abstract":"<p><strong>Introduction: </strong>The delivery of nucleic acid into cells using polyethylenimine (PEI) as non-viral carrier is a potential candidate technique for the treatment of hepatitis B virus (HBV) infection.</p><p><strong>Methods: </strong>In the present study, PEI was used as cationic polymers and transfected with unmodified oligodeoxynucleotides in cell cultures and the BALB/c mouse model to investigate its efficiency in blocking HBV surface antigen (HBsAg) secretion.</p><p><strong>Results and discussion: </strong>PEI/oligonucleotide complexes selectively inhibited HBsAg secretion in the culture supernatant, while there were no evident alterations in HBeAg and HBV DNA levels, thereby suggesting its potential inhibitory activity against the production of HBsAg. The complexes formed by PEI with double-stranded decoy oligonucleotides also suppressed HBsAg secretion but showed no expected interference with the intermediate levels of HBV transcription or replication. Furthermore, PEI/plasmid-DNA complexes demonstrated no influence on the expression levels of HBsAg, thus highlighting the specific effects of PEI/oligonucleotides exerted on HBsAg release. PEI-oligonucleotides transfection prior to the viral inoculation impaired HBV infection in HepG2-NCTP cells. Importantly, the PEI/oligonucleotide complex also induced the decline of HBsAg in hydrodynamically injected BALB/c mice. These findings demonstrate that transfection of PEI/oligonucleotide complexes can help effectively reduce HBsAg level and may offer a new potential avenue for the development of anti-HBV treatment.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1600679"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synergistic effects of <i>Trichoderma</i> and biochar on the biocontrol of two soil-borne phytopathogens in chickpeas.","authors":"Ranjna Kumari, Vipul Kumar, Bhupendra Koul, Mohammad Abul Farah, Awdhesh Kumar Mishra","doi":"10.3389/fmicb.2025.1583114","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1583114","url":null,"abstract":"<p><strong>Introduction: </strong>This study aims to identify and characterize four <i>Trichoderma</i> isolates using molecular techniques, Fourier transform infrared spectroscopy (FTIR), and volatile organic compounds (VOC) profiling.</p><p><strong>Methods: </strong>The antagonistic activity of these isolates was assessed against <i>Fusarium oxysporum</i> f. sp. <i>ciceri</i> (FOC) and <i>Sclerotium rolfsii</i> (SR) using a dual culture technique. The synergistic effect of <i>Trichoderma harzianum</i> (accession no. PP256488) combined with biochar (BC) was evaluated for plant growth enhancement and disease suppression. Four <i>Trichoderma</i> isolates (<i>T. harzianum, T. asperellum, T. virens</i>, and <i>T. lixii</i>) were identified through ITS region analysis, VOC profiling, and FTIR spectroscopy.</p><p><strong>Results: </strong>Molecular analysis confirmed their distinct identities, and GC-MS analysis revealed 37 VOCs out of 162 with antipathogenic properties. Unique FTIR peaks were recorded at 3271.96 cm^-1 for <i>T. virens</i>, 2800-2900 cm^-1 for <i>T. asperellum</i>, and 2850-2950 cm^-1 for both <i>T. lixii</i> and <i>T. harzianum</i>. Scanning electron microscopy (SEM) analysis of <i>T. harzianum</i> revealed mycoparasitic structures, including hyphal coils, penetration holes, and appressoria, indicating effective pathogen interaction. The combined application of <i>Trichoderma</i> and biochar (T9) significantly enhanced root length (9.23 cm), plant height (26.03 cm), and root mass (43.33 g) in chickpea plants. Moreover, treatments (T9) and (T10) reduced the disease incidence in chickpeas, decreasing fusarium wilt by 27% and collar rot by 33%, respectively.</p><p><strong>Conclusion: </strong>This sustainable approach exhibits the potential of combined application of <i>Trichoderma</i> and biochar which can enhance plant growth and reduce disease incidence, and improve food security.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1583114"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel lncRNA YIL163C enhances genomic stability and antifungal resistance via the DNA damage response in <i>Saccharomyces cerevisiae</i>.","authors":"Xueting Wang, Xuemei Li, Duoyun Li, Yiying Zhang, Bing Bai, Bao Chai, Zewen Wen","doi":"10.3389/fmicb.2025.1571797","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1571797","url":null,"abstract":"<p><strong>Introduction: </strong>Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators in cellular processes, including the DNA damage response (DDR). In <i>Saccharomyces cerevisiae</i>, DDR is critical for maintaining genomic integrity under stress, mediated by proteins like Mec1 and Rad53. However, the involvement of lncRNAs in DDR pathways, remains largely unexplored. This study investigates the function of a novel lncRNA, YIL163C, in promoting cell survival and genomic stability under DNA damage conditions.</p><p><strong>Methods: </strong>Genetic suppressor screening was employed to assess the role of YIL163C in rescuing lethality in <i>mec1Δ sml1Δ</i> and <i>rad53Δ sml1Δ</i> exposed to DNA damage. Proteomic and phosphoproteomic analyses were conducted to evaluate changes in protein abundance and phosphorylation states. The impact of YIL163C on DDR and antifungal drug tolerance, specifically to 5-fluorocytosine, was also examined.</p><p><strong>Results: </strong>Overexpression of YIL163C was found to rescue lethality in <i>mec1Δ sml1Δ</i> and <i>rad53Δ sml1Δ</i> under DNA damage conditions. Proteomic analyses revealed that YIL163C modulates pathways related to DNA replication, ER stress response, and ribosome biogenesis, enhancing cellular resilience to HU-induced stress. Additionally, YIL163C reduced sensitivity to 5-fluorocytosine, indicating a role in antifungal drug tolerance. Phosphoproteomic data suggested YIL163C influences phosphorylation states, potentially acting downstream of the Mec1-Rad53 signaling pathway.</p><p><strong>Conclusion: </strong>This study provides new insights into the regulatory mechanisms of lncRNAs in DDR, with broader implications for antifungal therapy and genomic stability research, emphasizing the role of lncRNAs in stress responses beyond traditional protein-centric mechanisms.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1571797"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of antibiotic resistance genes and virulence factors in organic managed tea plantation soils in southwestern China by metagenomics.","authors":"Taobing Yu, Lang Cheng, Qing Zhang, Jida Yang, Huadong Zang, Zhaohai Zeng, Yadong Yang","doi":"10.3389/fmicb.2025.1580450","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1580450","url":null,"abstract":"<p><p>Sustainable organic management practices have gained significant attentions for its potential health and environmental benefits. However, the spread of antibiotic resistance genes (ARGs) and virulence factors (VFs) in soils, plants, and agricultural products has severely limited the development of organic managements on agriculture. At present, the distribution and assembly of ARGs and VFs in organic managed tea plantation systems remains largely unknown. Here, we used metagenomic analysis to explore soil microbial taxa, ARGs and VFs in 20 years of conventional managed (CM) and organic managed (OM) tea plantation soils. Results showed that total abundance of ARGs in OM was 16.9% (<i>p</i> < 0.001) higher than that in CM, and the increased ARGs were <i>rpoB2</i>, <i>evgS</i>, <i>MuxB</i>, <i>TaeA</i>, and <i>efrA</i>. As for VFs, OM significantly increased the abundance of adherence, stress protein and actin-based motility compared to CM. Moreover, OM increased the relative abundance of soil microbial taxa harboring ARGs and VFs, which were <i>Streptomyces</i>, <i>Pseudomonas</i>, and <i>Terrabacter</i>, compared to CM. Network analysis suggested that OM increased the positive interactions of microbial taxa-ARGs, microbial taxa-VFs and ARGs-VFs compared to CM. Impact of stochastic process on the assembly of soil microbial taxa, ARGs and VFs in OM was stronger than that in CM. Overall, these findings provide a basis for integrating ARGs, VFs and pathogen hosts to assess the ecological and health risks in long-term organic managed soils, and increased efforts need to be done in reducing ARGs, VFs and bacterial pathogens in fertilizers for organic managements on agriculture.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1580450"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biodegradable hydrogels and microbial consortia as a treatment for soil dysbiosis.","authors":"Renee A Davis, Korena K Mafune, Mari K H Winkler","doi":"10.3389/fmicb.2025.1565940","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1565940","url":null,"abstract":"<p><p>Terrestrial microbial communities drive many soil processes and can be pushed into a state of dysbiosis upon disturbance. This dysregulation negatively impacts soil biogeochemical cycles, which threatens plant and soil health. Effective treatment of soil dysbiosis requires simultaneous restoration of multiple system components, addressing both the physical structure of soil and its microbial communities. Hydrogels with microbial consortia simultaneously remedy soil hydrodynamics while promoting microbial reestablishment. The purpose of this review is to shed light on soil management practices through the lens of soil dysbiosis. This is important to address not only for soil health and crop productivity, but also to mitigate climate change through improved soil carbon sequestration and reduced greenhouse gas emissions. This review positions hydrogels and microbes as tools for the treatment of soil dysbiosis, contributing to agricultural and climate resilience.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1565940"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A six-year retrospective study on the causative agents of onychomycosis in China: the emergence of dematiaceous fungi.","authors":"Xin Ye, Jun Tian, Wanqing Liao, Weihua Pan, Zhe Liu, Jiaming Zhang, Li Yang, Lei Zhang","doi":"10.3389/fmicb.2025.1582147","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1582147","url":null,"abstract":"<p><strong>Introduction: </strong>Onychomycosis, a common nail disease, is caused by a diverse range of pathogens worldwide. However, the epidemiology and pathogen profile of onychomycosis in China remain insufficiently characterized. This study aimed to investigate these aspects in a large Chinese hospital.</p><p><strong>Methods: </strong>A six-year retrospective analysis was conducted at a tertiary hospital in China, where nail samples from 298 patients who were clinically suspected of onychomycosis were cultured and analyzed to identify causative agents and clinical features.</p><p><strong>Results: </strong>Of the 298 samples, 51.00% (152) were positive for fungal infection. Young adults (18-30 years) comprised the majority of the patients, with a man-to-woman ratio of 1:1.45. Dermatophytes were the most prevalent causative agents (36.18%), followed by yeasts (28.29%) and non-dermatophyte molds (NDMs) (28.29%). Among dermatophytes, <i>Trichophyton</i> species (34.9%) were the most frequently identified, followed by <i>Candida</i> (21.7%) and dematiaceous fungi (8.6%). Dermatophytes were the predominant pathogens in the patients aged 18-50 years. The toenails (63.04%) were more commonly affected than the fingernails (36.96%), with bilateral toenail involvement (34.07%) being the most frequent.</p><p><strong>Conclusion: </strong>While dermatophytes remain the leading cause of onychomycosis in China, non-dermatophyte molds, particularly dematiaceous fungi, are emerging as significant pathogens. These organisms present unique treatment challenges and warrant increased clinical attention.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1582147"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiomics-based analysis of the mechanism of ammonia reduction in <i>Sphingomonas</i>.","authors":"Wang Mingcheng, Liu Daoqi, Xia Huili, Wang Gailing, Liu Chaoying, Guo Yanan, Guo Aizhen","doi":"10.3389/fmicb.2024.1437056","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1437056","url":null,"abstract":"<p><p>Ammonia is the primary component of malodorous substances in chicken farms. Currently, the microbial ammonia reduction is considered a potential method due to its low cost, high safety, and environmental friendliness. <i>Sphingomonas</i> sp. Z392 can significantly reduce the ammonia level in broiler coops. However, the mechanisms of ammonia nitrogen reduction by <i>Sphingomonas</i> sp. Z392 remain unclear. To explore the mechanisms of ammonia reduction by <i>Sphingomonas</i> sp. Z392, the transcriptome and metabolome analysis of <i>Sphingomonas</i> sp. Z392 under high ammonium sulfate level were conducted. It was found that the transcription levels of genes related to purine metabolism (<i>RS01720</i>, <i>RS07605</i>, <i>purM</i>, <i>purC</i>, <i>purO</i>) and arginine metabolism (<i>glsA</i>, <i>argB</i>, <i>argD</i>, <i>aguA</i>, <i>aguB</i>) were decreased under high ammonium sulfate environment, and the levels of intermediate products such as ornithine, arginine, IMP, and GMP also were also decreased. In addition, the <i>ncd2</i> gene in nitrogen metabolism was upregulated, and intracellular nitrite content increased by 2.27 times than that without ammonium sulfate. These results suggested that under high ammonium sulfate level, the flux of purine and arginine metabolism pathways in <i>Sphingomonas</i> sp. Z392 might decrease, while the flux of nitrogen metabolism pathway might increase, resulting in increased nitrite content and NH₃ release. To further verify the effect of the <i>ncd2</i> gene on ammonia removal, <i>ncd2</i> was successfully overexpressed and knocked out in <i>Sphingomonas</i> sp. Z392. <i>ncd2</i> Overexpression exhibited the most ammonia reduction capability, the ammonia concentration of <i>ncd2</i> overexpression group decreased by 43.33% than that of without <i>Sphingomonas</i> sp. group, and decreased by 14.17% than that of <i>Sphingomonas</i> sp. Z392 group. In conclusion, <i>Sphingomonas</i> sp. Z392 might reduce the release of NH₃ by reducing the flux of purine and arginine metabolisms, while enhancing ammonia assimilation to form nitrite. In this context, <i>ncd2</i> might be one of the key genes to reduce ammonia.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1437056"},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}