Frontiers in Microbiology最新文献

{"title":"Harnessing beneficial soil bacteria to promote sustainable agriculture and food security: a one health perspective.","authors":"Carlos Sabater, Madalina Neacsu, Sylvia H Duncan","doi":"10.3389/fmicb.2025.1638553","DOIUrl":"10.3389/fmicb.2025.1638553","url":null,"abstract":"<p><p>Harnessing beneficial soil bacteria for use in agricultural practices offers an exciting and promising pathway to achieving sustainable farming. Soil microbes, including bacteria and fungi, play a pivotal role in nutrient cycling, enhancing soil structure, and promoting plant growth. Certain plant growth-promoting bacteria, such as <i>Bacillus</i> and <i>Paenibacillus</i> species, are particularly notable for their ability to improve nutrient uptake, suppress pathogens, and enhance plant resilience to environmental stress. By employing these natural bacterial species, farmers can rely less on chemical fertilisers and pesticides, helping the environment and improving soil health. Moreover, soil bacteria may possess potent enzymes systems for breaking down complex carbohydrates, so that the simpler sugars can be used to nourish plants. Genome mining of soil representatives can be used to design novel consortia of soil bacteria (including <i>Paenibacillus odorifer, P. xylanilyticus</i> and <i>Streptococcus cellostaticus</i>) to cover the maximum number of complementary enzyme activities acting on cellulosic and hemi cellulosic materials. Similarly, the combination of these strains and <i>Arthobacter humicola</i> could be of great interest to maximize the metabolisation of lignocellulosic substrates and to reduce and re-valorise food waste from the food production cycle. Soil bacteria play a pivotal role in advancing One Health by mediating interactions across human, animal, and environmental health. Future research and development should focus on optimizing microbial delivery to different soils and also understanding the complex interactions within the soil microbiome to maximize their benefits in diverse farming systems.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1638553"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232040","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":"Harnessing beneficial bacteria to remediate antibiotic-polluted agricultural soils: integrating source diversity, bioavailability modulators, and ecological impacts.","authors":"Oluwaseyi Samuel Olanrewaju, Cornelius Carlos Bezuidenhout","doi":"10.3389/fmicb.2025.1635233","DOIUrl":"10.3389/fmicb.2025.1635233","url":null,"abstract":"<p><p>Antibiotic contamination in agricultural soils, primarily from manure application and wastewater irrigation, has emerged as a critical threat to food security, environmental health, and public safety due to the proliferation and persistence of antibiotic-resistant genes. This review examines the diverse sources and ecological impacts of antibiotics in soil, including their alteration of microbial community structures, promotion of horizontal gene transfer, and subsequent risks to plant and human health. It further evaluates how soil properties, such as pH, organic matter content, and texture, influence the bioavailability of antibiotics and modulate their degradation dynamics. Emphasis is placed on the bioremediation potential of beneficial bacteria, detailing key mechanisms such as enzymatic biodegradation, biosorption, biofilm formation, and the formation of synergistic microbial consortia capable of utilizing antibiotics as nutrient sources. In addition, the manuscript critically discusses the regulatory, technological, and scalability challenges inherent to deploying microbial bioremediation strategies, including integrating gene editing and systems biology approaches under a One Health framework. By synthesizing molecular insights with environmental and policy considerations, this review provides a comprehensive assessment of current bioremediation strategies and outlines future directions to mitigate the ecological and health risks associated with antibiotic pollution in agricultural ecosystems.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1635233"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232081","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":"Soil viruses drive carbon turnover during subtropical secondary forest succession.","authors":"Xingyi Chen, Danting Yu, Yuting Yan, Chengyu Yuan, Jizheng He","doi":"10.3389/fmicb.2025.1633379","DOIUrl":"10.3389/fmicb.2025.1633379","url":null,"abstract":"<p><strong>Introduction: </strong>Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.</p><p><strong>Methods: </strong>We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.</p><p><strong>Results: </strong>Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.</p><p><strong>Discussion: </strong>These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1633379"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231932","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":"Growth, physiology, and metabolism of <i>Halomonas meridiana</i> in aqueous ammonium sulfate with implications for icy moon astrobiology.","authors":"Cassie M Hopton, Peter Nienow, Charles S Cockell","doi":"10.3389/fmicb.2025.1642998","DOIUrl":"10.3389/fmicb.2025.1642998","url":null,"abstract":"<p><p>The discovery of extraterrestrial reservoirs of liquid water has motivated missions to icy moons Europa and Titan. Tentative evidence of ammonium sulfate ((NH₄)₂SO₄) has been detected on the surface of Europa, and (NH₄)₂SO₄ could be a prominent constituent of the Titan subsurface ocean. While <math> <msubsup><mrow><mtext>NH</mtext></mrow> <mrow><mn>4</mn></mrow> <mrow><mo>+</mo></mrow> </msubsup> </math> acts as a nitrogen source for many organisms, detrimental impacts of (NH₄)₂SO₄ fertilizer have been documented in bacteria. Consequently, the presence of (NH₄)₂SO₄ within icy moon environments may constrain the capacity of these environments to support life. In this study, the bacterial survival limits and physiological response to aqueous (NH₄)₂SO₄ were assessed using the extremophile <i>Halomonas meridiana</i> Slthf1. Growth assays demonstrated concentrations exceeding 0.25 M (NH₄)₂SO₄ led to a measurable slowing of the growth rate. Cell density remained comparable to control conditions up to 0.75 M (NH₄)₂SO₄ at which a decline was observed. Contrary to existing hypotheses, alterations to cell density were not determined by pH, osmolarity, salinity, ionic strength, or water activity of the aqueous (NH₄)₂SO₄ solution. Furthermore, neither <math> <msubsup><mrow><mtext>NH</mtext></mrow> <mrow><mn>4</mn></mrow> <mrow><mo>+</mo></mrow> </msubsup> </math> nor <math> <msubsup><mrow><mtext>SO</mtext></mrow> <mrow><mn>4</mn></mrow> <mrow><mn>2</mn> <mo>-</mo></mrow> </msubsup> </math> alone accounted for these alterations. Metabolite profiling revealed that exposure to (NH₄)₂SO₄ reduced the abundance of glutamine compared to control, indicating an alteration to nitrogen, carbon, and energy metabolism. Active catabolism was suggested by reduced levels of purine metabolites and amino acids. Metabolites within the methylaspartate cycle were detected. We discuss these results with regards to the potential for habitability in aqueous extraterrestrial (NH₄)₂SO₄ environments as well as terrestrial environments in which (NH₄)₂SO₄ fertilizer is applied.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1642998"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232084","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":"The influence of particle activated carbon on heavy metal passivation and antibiotic degradation in various organic fertilizers.","authors":"Zifang Chi, Yuru Li, Huai Li","doi":"10.3389/fmicb.2025.1686052","DOIUrl":"10.3389/fmicb.2025.1686052","url":null,"abstract":"<p><p>This study investigated the effects of different particle sizes of activated carbon [small particle activated carbon (S-AC, 2-4 mm), medium particle activated carbon (M-AC, 3-6 mm), and large particle activated carbon (B-AC, 5-8 mm)] on the physicochemical properties of organic fertilizers (chicken manure, sheep manure, cow manure and pig manure), the passivation of heavy metals, and the degradation of antibiotics. The results showed that the addition of particle activated carbon could increase the pH value of organic fertilizers, reduce the cation exchange capacity (CEC) value, and its fragmentation led to an increase in organic matter in organic fertilizers, but had no significant effect on the electrical conductivity (EC) value. The small particle activated carbon (S-AC) had high mechanical strength (compressive strength 4.014 MPa), low loss rate, and high recovery rate, showing the best remediation performance. After adding S-AC, the removal rates of total copper (Cu) and zinc (Zn) in organic fertilizers reached 23.71-28.57% and 15.41-17.81% respectively, and the maximum passivation rates of exchangeable fraction Cu and Zn were 61.31 and 29.10%. At the same time, S-AC significantly promoted the degradation of antibiotics, with the degradation rates of tetracycline (TC) and ciprofloxacin (CIP) reaching 81.38-85.81% and 76.53-80.59% within 30 days.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1686052"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232005","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":"Apoptosis and autophagy promote <i>Babesia microti</i> infection in tick midguts: insights from transcriptomic and functional RNAi studies.","authors":"Songqin Chen, Shanming Hu, Fengjun Gong, Haotian Zhu, Yongzhi Zhou, Jie Cao, Houshuang Zhang, Yanan Wang, Jinlin Zhou","doi":"10.3389/fmicb.2025.1632974","DOIUrl":"10.3389/fmicb.2025.1632974","url":null,"abstract":"<p><strong>Introduction: </strong>Ticks are the primary vectors of <i>Babesia</i> sp, with the midgut as the initial site of pathogen invasion following blood feeding. Elucidating the molecular interactions between tick midguts and <i>Babesia</i> is essential for developing targeted strategies to control tick-borne babesiosis. However, studies in this field remain limited.</p><p><strong>Methods: </strong>To investigate tick-pathogen interactions, we employed RNA-seq to profile gene expression, and qRT-PCR served to validate key findings. Apoptosis and autophagy were assessed via TUNEL staining and Transmission Electron Microscopy (TEM). Furthermore, RNA interference (RNAi) and pharmacological modulation were employed to evaluate the impact of ticks on pathogen load.</p><p><strong>Results: </strong>Our RNA-seq analysis identified 540 and 569 Differentially Expressed Genes (DEGs) in infected midguts at 0 and 4 d post-engorgement, respectively. These DEGs were enriched in pathways related to metabolic processes, immunity, and cellular processes. To clarify the functional relevance of these findings, the roles of apoptosis and autophagy during infection were further evaluated. Quantitative Real-Time PCR (qRT-PCR) analysis revealed significant upregulation of apoptosis-related genes (<i>caspase-7, caspase-8</i>, and <i>caspase-9</i>) and autophagy genes (<i>ATG5, ATG8, and ATG12</i>) in response to <i>B. microti</i> infection. TUNEL assay and Transmission Electron Microscopy (TEM) analysis demonstrated that <i>B. microti</i> infection significantly induced apoptosis and autophagosome formation in tick midgut tissues. Functional assays demonstrated that RNA interference (RNAi)-mediated knockdown of caspase-7, caspase-9, and ATG5 significantly reduced the <i>burden of B. microti</i>. Conversely, pharmacological induction of autophagy using rapamycin increased <i>B. microti</i> load, whereas inhibition with 3-methyladenine (3-MA) decreased <i>B. microti</i> load.</p><p><strong>Discussion: </strong>These findings underscore the critical roles of apoptosis and autophagy in facilitating <i>B. microti</i> infection within tick midguts, highlighting these pathways as potential molecular targets for disrupting the transmission of tick-borne <i>Babesia</i> infections.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1632974"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231921","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":"Sitagliptin ameliorates microbial dysbiosis and enhances gut barrier integrity in streptozotocin-induced type 2 diabetic rats.","authors":"Ying Chang, Yuanjiang Zhou, Fanlin Zhou, Jie Liang, Yu Li, Mingyuan Tian","doi":"10.3389/fmicb.2025.1655522","DOIUrl":"10.3389/fmicb.2025.1655522","url":null,"abstract":"<p><strong>Background: </strong>Sitagliptin, a dipeptidyl peptidase-4 (DPP-4) inhibitor, has demonstrated efficacy in the management of type 2 diabetes mellitus (T2DM). This study aimed to investigate the effects of sitagliptin on gut microbial composition and gut barrier integrity in a streptozotocin (STZ)-induced rat model of T2DM.</p><p><strong>Methods: </strong>Sprague-Dawley rats were randomly divided into four groups (<i>n</i> = 6 per group): a T2DM group induced by high-fat diet (HFD) and STZ injection; a T2DM group treated with oral sitagliptin at 10 mg/kg/day for 12 weeks (T2DM-Sit); a normal diet control group (ND); and a normal diet group treated with sitagliptin (ND-Sit). Fecal samples were collected for 16S rRNA gene sequencing to analyze gut microbial composition and diversity. Intestinal tissues were assessed for tight junction protein expression via immunohistochemistry and western blot.</p><p><strong>Result: </strong>Alpha index metrics, including observed feature number and Shannon index, were significantly decreased in the T2DM group compared to the ND group. Sitagliptin treatment led to a significant restoration of these indices. Principal coordinate analysis based on Bray-Curtis distances revealed distinct clustering between the ND and T2DM groups, with sitagliptin shifting the microbial profile of diabetic rats toward that of healthy controls. Sitagliptin treatment increased the relative abundance of <i>Lactobacillus, Ruminococcus, Streptococcus, Klebsiella, Clostridium_IV</i>, and <i>Romboutsia</i>, while reducing levels of <i>Alloprevotella</i> and <i>Parasutterella</i>, effectively reversing the dysbiotic changes observed in T2DM. Additionally, sitagliptin modulated microbial metabolic pathways, restructured the gut microbial network, and promoted short-chain fatty acid production. Histological and western blot analysis revealed enhanced expression of the tight junction protein ZO-1 and increased numbers of mucin-secreting goblet cells, indicating improved gut barrier integrity.</p><p><strong>Conclusion: </strong>Sitagliptin effectively ameliorates gut microbial dysbiosis and restores intestinal barrier function in STZ-induced T2DM rats. These findings provide novel insights into the gut-related therapeutic effects of sitagliptin and underscore its potential in restoring gut homeostasis in T2DM.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1655522"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491974/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231929","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":"Anaerobic gut fungi as biocatalysts: metabolic and physiological analysis of anaerobic gut fungi under diverse cultivation conditions.","authors":"Kevin Edward Schulz, Dominik Scholz, Anto Rafael Sikirić, Daniela Rambow, Anke Neumann, Katrin Ochsenreither","doi":"10.3389/fmicb.2025.1662047","DOIUrl":"10.3389/fmicb.2025.1662047","url":null,"abstract":"<p><strong>Background: </strong>Anaerobic gut fungi, known for their diverse carbohydrate-active enzymes and hydrogen production, have promising potential for the valorization of lignocellulosic materials. Despite being classified nearly 50 years ago and re-categorized into the phylum <i>Neocallimastigomycota</i> in 2007, their growth conditions and metabolism remain largely underexplored. This study investigates the metabolic responses of <i>Aestipascuomyces dupliciliberans, Caecomyces churrovis, Khyollomyces ramosus, Orpinomyces joyonii, Pecoramyces ruminantium</i>, and <i>Neocallimastix cameroonii</i> under various conditions, including different growth temperatures, wheat straw particle sizes, alternative carbon sources, and cultivation methods.</p><p><strong>Results: </strong>Strain-specific differences were observed in temperature tolerance and metabolite production. Optimal growth occurred at 39 °C, while hydrogen production peaked at 41 °C in <i>N. cameroonii, P. ruminantium</i>, and <i>C. churrovis</i>. Larger wheat straw particles (2-3 mm) partially enhanced hydrogen yields, and soluble carbon sources such as glucose and cellobiose were efficiently metabolized, whereas xylose led to stress responses and low hydrogen output, particularly in <i>K. ramosus</i> and <i>O. joyonii</i>. High sugar concentrations triggered overflow metabolism, with increased lactate and formate production in <i>A. dupliciliberans</i> and <i>N. cameroonii</i>, while <i>K. ramosus</i>, lacking lactate dehydrogenase, accumulated formate and succinate. Fed-batch cultivation did not improve yields, likely due to substrate overfeeding and end-product inhibition. Biowaste substrates such as cucumber, carrot, and potato peels were effectively degraded and supported fungal growth. Notably, a novel morphological growth form was observed in <i>O. joyonii</i> under starvation conditions, suggesting a stress-induced developmental transition.</p><p><strong>Conclusion: </strong>This study provides valuable insights into the growth and physiology of anaerobic gut fungi and complements existing genomic data. The robustness of the process with respect to temperature, carbon source and substrate properties was evaluated, improving the understanding of anaerobic gut fungi cultivation and handling.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1662047"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231967","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":"Issues on microbial soil remediation: a case of Cd detoxification by <i>Bacillus</i> strains for alleviating heavy metal stress in crop plants.","authors":"Yini Shi, Xianyang Feng, Zhongke Sun, Boyuan Zhang, Chengwei Li","doi":"10.3389/fmicb.2025.1665354","DOIUrl":"10.3389/fmicb.2025.1665354","url":null,"abstract":"","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1665354"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231634","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":"Geographic variation in fungal diversity associated with leaf spot symptoms of <i>Coffea arabica</i> in Yunnan, China.","authors":"Xingfei Fu, Haohao Yu, Yaqi Li, Guiping Li, Xiaofei Bi, Yanan Li, Faguang Hu, Wenjiang Dong","doi":"10.3389/fmicb.2025.1568029","DOIUrl":"10.3389/fmicb.2025.1568029","url":null,"abstract":"<p><p>In China, the small grain coffee plants (<i>Coffea arabica</i>) are mainly cultivated in Yunnan province, yet the diversity of associated fungi remains poorly characterized. In this study we collected symptomatic leaves from 16 locations across Pu'er City and Xishuangbanna Dai Autonomous Prefecture (<i>n</i> = 48 samples, triplicate controls). Fungal communities were analyzed via ITS amplicon sequencing (Illumina MiSeq). We identified 3,638 fungal OTUs, dominated by Ascomycota (92%), including pathogens (<i>Colletotrichum gloeosporioides, Cercospora coniogrammes</i>), saprophytes, and beneficial entomopathogens (<i>Lecanicillium, Simplicillium</i>). The fungal communities showed significant geographical variation, with Pu'er City exhibiting a higher relative abundance of pathogenic fungi such as <i>Colletotrichum gloeosporioides</i> and <i>Cercospora coniogrammes</i>, while Xishuangbanna had a greater presence of beneficial entomopathogenic fungi such as <i>Lecanicillium</i> and <i>Simplicillium</i>. We classified abundant fungal OTUs into 48 different species colonizing leaves of coffee plants. Our core microbiome analysis revealed the presence of <i>Cercospora coniogrammes</i> (2%), the <i>Fusarium equiseti</i> of <i>Nectriaceae</i> family (5%), and the novel pathogenic fungi <i>Colletotrichum gloeosporioides</i> and <i>Cercospora coniogrammes.</i> Interestingly, we also identified the anti-phytopathogenic fungi belonging to the genus <i>Simplicillium</i> (9%) and entomopathogenic fungi known as <i>lecanicillium</i> (11%). This first report of <i>C. coniogrammes</i> and <i>C. gloeosporioides</i> in Yunnan coffee highlights the need for region-specific disease management. The prevalence of entomopathogenic fungi in Xishuangbanna suggests untapped biocontrol potential. Our data provide a foundation for monitoring leaf-associated fungi to improve crop resilience.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1568029"},"PeriodicalIF":4.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231928","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}