Applied and Environmental Microbiology最新文献

{"title":"RkMsn4, a zinc finger transcription factor, regulates carotenoid and lipid metabolism to enhance tolerance to environmental stress in <i>Rhodosporidium kratochvilovae</i>.","authors":"Meixia He, Mingjing Yang, Xinyan Xiong, Yuxuan Gan, Jingwen Qiu, Yuan Chen, Qi Zhang","doi":"10.1128/aem.00647-26","DOIUrl":"https://doi.org/10.1128/aem.00647-26","url":null,"abstract":"<p><p>Red yeasts serve as indispensable microbial resources for the production of carotenoids and lipids; however, environmental stress factors often limit their performance during industrial fermentation. The zinc-finger transcription factors Msn2/Msn4 act as central regulators of stress responses in yeasts. However, researchers have not yet systematically elucidated the similarities and differences in the mechanisms underlying the regulatory effects of Msn2/Msn4 under different stress conditions. In this study, we compared the shared and stress-specific regulatory functions of RkMsn4 in <i>Rhodosporidium kratochvilovae</i> YM25235 under conditions of glucose starvation, 15 °C low temperature, and 4% NaCl salt stress. RkMsn4 contributed to the activity of the oxidative defense systems, including antioxidant enzymes, carotenoids, and glutathione, and the remodeling of membrane lipids, including phospholipids and unsaturated fatty acids (UFAs) across all three stress conditions. Additionally, RkMsn4 regulated stress-specific metabolic regulation by modulating branched-chain amino acid (BCAA) and aromatic amino acid (AAA) metabolism under glucose starvation conditions and promoting the utilization of exogenous sucrose and fructose under salt stress. By conducting weighted gene co-expression network analysis (WGCNA), we identified candidate genes potentially associated with carotenoid and lipid metabolism. These findings provide practical insights for improving tolerance to stress and metabolic productivity of red yeasts in industrial bioprocesses.IMPORTANCERed yeasts are important microorganisms for the production of carotenoids and lipids, but their performance is often limited by environmental stress. Understanding how red yeasts respond to environmental stress is crucial for advancing their application in industrial fermentation. This study reveals the stress response mechanisms mediated by the transcription factor RkMsn4 in <i>Rhodosporidium kratochvilovae</i> YM25235 under glucose starvation, low temperature, and salt stress, as well as its regulatory role in carotenoid and lipid metabolism. These findings provide valuable insights for enhancing the stress resistance and productivity of red yeasts in industrial applications.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0064726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149023736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Composting dairy cattle manure significantly reduces antibiotic-resistant bacteria with no biochar impact.","authors":"Getahun E Agga, Annesly Netthisinghe, Paul Woosley, William Strunk, Karamat R Sistani","doi":"10.1128/aem.01258-26","DOIUrl":"10.1128/aem.01258-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;In two randomized controlled field studies, we investigated the effect of biochar-amended dairy manure composting on the concentrations and prevalence of generic and antibiotic-resistant &lt;i&gt;E. coli&lt;/i&gt; and enterococci. Fresh dairy manure mixed with sawdust and biochar was randomly distributed into plastic reactors and composted for 6 months. Pre-compost (biochar, sawdust, fresh dairy manure), manure mixture, and final compost samples were cultured for enumeration and prevalence. While biochar and sawdust were not significant sources, fresh dairy manure was the major contributor of bacteria to the initial manure mixture. Biochar amendment did not significantly reduce bacterial load beyond that could be achieved by composting alone. Spring-summer composting was more effective than fall-winter composting. While &lt;i&gt;E. coli&lt;/i&gt; was more prone, enterococci were more likely to survive composting. Dairy manure composting eliminated bacteria (3rd generation cephalosporin-resistant [3GC&lt;sup&gt;r&lt;/sup&gt;] and extended spectrum beta-lactamase-producing [ESBL]-&lt;i&gt;E. coli&lt;/i&gt;) resistant to critically important and highest priority antibiotics for human health and significantly reduced the prevalence and concentrations of other investigated bacteria. 3GC&lt;sup&gt;r&lt;/sup&gt;- and ESBL-&lt;i&gt;E. coli&lt;/i&gt; from fresh dairy manure were multidrug resistant and carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CTX-M&lt;/sub&gt; genes, a widely distributed ESBL gene type. By whole-genome sequencing, ESBL-&lt;i&gt;E. coli&lt;/i&gt; from experiment 1 (fall-winter) had diverse resistance profiles, sequence types, plasmid profiles, virulence factor genes, and more &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CTX-M&lt;/sub&gt; genes (CTX-M-1, CTX-M-32, and CTX-M-55). However, those from experiment 2 (spring-summer) were clonal and carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CTX-M-55&lt;/sub&gt; only. In conclusion, dairy manure composting effectively removes antibiotic resistant bacteria of public health importance, with no added effect of biochar amendment.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Composting is a microbially mediated decomposition of organic matter into a nutrient-rich product for use as fertilizer. Biochar, obtained from the pyrolysis of biomass including animal manure, has been used for soil amendment. Beyond its nutrient stabilizing potential, composting has been shown to reduce bacterial load in animal manure. However, its effect with or without a biochar addition was not evaluated under a randomized controlled field trial. Biochar was nearly bacteriologically \"sterile,\" and the sawdust used as a bulking agent had low concentrations of innocuous bacteria indicating that dairy manure was the main source of bacteria to the pre-compost mixture. Biochar did not have an extra effect on the bacterial load beyond composting alone. Composting during spring/summer is more effective than fall/winter. Furthermore, it is more effective against gram-negatives than gram-positive bacteria. Importantly, composting effectively eliminated multidrug-resistant bacteria of critical importance to","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0125826"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148720006","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":"Sodium ion stress accelerates cell lysis in <i>Bacillus coagulans</i> by exacerbating energy deficit during carbon source transition.","authors":"Zhihao Liu, Yingping Zhuang, Yonghong Wang, Guan Wang","doi":"10.1128/aem.01314-26","DOIUrl":"10.1128/aem.01314-26","url":null,"abstract":"<p><p>The choice of pH neutralizer plays a critical role in determining the performance of industrial lactic acid fermentation. This study investigated the distinct phenotypic and metabolic responses of <i>Bacillus coagulans</i> during batch fermentation with mixed carbon sources (glucose and trehalose) when using sodium hydroxide versus calcium hydroxide for pH control. Compared to calcium hydroxide, sodium hydroxide resulted in a slightly lower lactic acid yield and induced significant cell lysis during the carbon source transition. Metal ion experiments confirmed that sodium ion stress is the primary factor responsible for extensive cell lysis. Omics analysis indicated that under sodium hydroxide conditions, cells require more energy to resist stress. To meet this demand, cells downregulated cellular growth and sodium ion uptake systems, while upregulating carbon source transport. However, during carbon source transition, cellular resource reallocation resulted in insufficient carbon source uptake, leading to stagnation of glycolysis and amino acid metabolism. The resulting energy deficit triggered upregulation of cellular hydrolases, ultimately causing population-wide cell lysis. In contrast, calcium hydroxide as a neutralizer does not impose sodium stress and contributes to maintaining cell wall stability under carbon source deficiency. This study contributes to the understanding of cellular regulatory mechanisms in response to different neutralizers, and provides insights for metabolic engineering and process optimization.IMPORTANCEpH neutralizer selection critically determines cell survival and process efficiency in industrial fermentation. Our study demonstrates that sodium hydroxide, although effective for pH control, imposes severe sodium ion stress that synergizes with the inherent energy vulnerability of cells during carbon source transition, triggering catastrophic population-wide lysis in <i>Bacillus coagulans</i>. Through integrated physiology, ion experiments, and multi-omics analyses, we reveal that the underlying cause is an energy crisis arising from the conflict between stress defense and metabolic reallocation. In contrast, calcium hydroxide not only avoids sodium stress but also confers structural and thermal stability to cells, thereby preserving cell density and improving carbon utilization. These findings shift the perspective on neutralizers from mere pH regulators to key determinants of cellular energy economy and survival. Our study thus offers a rational basis for neutralizer selection, strain engineering toward ion resistance, and the design of robust fermentation processes, with direct implications for the sustainable and cost-effective production of lactic acid and other microbial metabolites.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0131426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148672908","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":"Cellulose-fueled extracellular electron transfer in termite gut microbes.","authors":"Xiao Deng, Akihiro Okamoto","doi":"10.1128/aem.01272-26","DOIUrl":"10.1128/aem.01272-26","url":null,"abstract":"<p><p>Termites decompose billions of tons of lignocellulosic material annually through the cellulolytic metabolism of their gut microbiota. However, the mechanisms by which cellulose degradation drives anaerobic metabolism of the gut microbiome remain poorly understood. Here, we demonstrate cellulose-driven extracellular electron transfer (EET) in both a termite gut-derived gram-positive cellulolytic bacterium, <i>Ruminiclostridium cellobioparum</i> subsp. <i>termitidis</i> CT1112, and the termite gut microbiome. CT1112 cells produced current in the presence of cellulose or cellobiose as the electron donor under potentiostatic conditions. This activity was strongly dependent on self-secreted redox mediators. EET was markedly impaired when stationary-phase CT1112 developed a thickened, multilayered cell wall, reducing accessibility to exogenously added redox mediators, such as riboflavin, and small redox-active molecules, such as diaminobenzidine. As a proof of concept, current production from cellulose was also observed in the termite gut microbiome, together with increases in the relative abundances of Bacillota, Bacteroidota, and Pseudomonadota. These results support the presence of EET-capable bacteria in the termite gut and suggest that EET contributes to redox balance within the steep redox gradients of the gut. Our study expands the environmental relevance of EET in carbon cycling and highlights termite-derived microbiomes as promising platforms for bioelectrochemical applications, including cellulolytic microbial fuel cells.IMPORTANCETermites play major roles in carbon cycling in tropical ecosystems by decomposing lignocellulosic biomass with the help of their gut microbiota. However, the microbial physiology underlying this highly efficient cellulose conversion remains poorly understood. Here, we show that both a cellulolytic termite gut isolate and the termite gut microbiome are capable of extracellular electron transfer (EET) using cellulose and its derivatives as electron donors. These findings suggest that cellulose degradation in the termite gut is coupled to extracellular redox processes, expanding our understanding of how this globally important process proceeds in anaerobic environments. They also raise the possibility that EET contributes to redox homeostasis within the gut microenvironment and open new avenues for investigating the electrochemical physiology of termite gut microbes, including their ability to reduce dietary iron(III) minerals and their potential to participate in syntrophic interspecies electron transfer. Moreover, this work highlights termite-derived microbes as promising platforms for developing efficient cellulose-to-electricity conversion technologies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0127226"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148824343","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":"Comparative analysis reveals distinct microbial community profiles and assembly mechanisms in sediments of coastal wetland ecosystems.","authors":"Linqiong Wang, Zhen Chen, Xinle Li, Zhe Zhao","doi":"10.1128/aem.01159-26","DOIUrl":"https://doi.org/10.1128/aem.01159-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Coastal wetland ecosystems (CWEs), including mangroves, saltmarshes, and seagrasses, support vital biogeochemical cycles mediated by microbes, yet their global microbial diversity, distribution, and potential functions remain elusive. Thus, we analyzed 1,381 16S rRNA gene amplicon data sets targeting the V3-V4 and V4 regions to examine microbial diversity and assembly processes across these habitats. Results revealed significant differences in microbial diversity and composition among these ecosystems, with mangroves exhibiting the highest richness and diversity. The habitat-specific indicator taxa were Rhodothermia, Anaerolineaceae, and SBR1031 in mangroves, &lt;i&gt;Flavobacteriaceae&lt;/i&gt;, &lt;i&gt;Burkholderiales&lt;/i&gt;, and &lt;i&gt;Woeseiaceae&lt;/i&gt; in saltmarshes, and &lt;i&gt;Desulfosarcinaceae&lt;/i&gt;, &lt;i&gt;Pseudomonadaceae&lt;/i&gt;, &lt;i&gt;Firmicutes&lt;/i&gt;, and &lt;i&gt;Bacillales&lt;/i&gt; in seagrasses through linear discriminant analysis effect size (LEfSe) and random forest analyses. Co-occurrence network analysis revealed a robust structure comprising 1,521 nodes and 64,463 edges, dominated by &lt;i&gt;Gammaproteobacteria&lt;/i&gt;, &lt;i&gt;Desulfobacteria&lt;/i&gt;, &lt;i&gt;Bacteroidia&lt;/i&gt;, and &lt;i&gt;Desulfobulbia&lt;/i&gt;. KEGG-based functional prediction revealed distinct functional profiles across CWEs. Mangrove communities exhibited higher predicted potentials for carbon fixation and complex hydrocarbon metabolism, whereas seagrass communities showed higher potentials for sulfate metabolism. Saltmarsh communities were enriched in predicted functions related to the degradation of certain aromatic compounds. Using iCAMP, drift was most pronounced in seagrass communities (63.10%), whereas its contribution was lower but remained substantial in mangroves and saltmarshes. Deterministic processes also contributed considerably to community assemblies in mangroves (43.04%) and saltmarshes (44.42%). This underscores the dependence of dominant assembly processes on local environmental contexts. Our findings establish a basis for elucidating the structure and function of microbial communities in CWEs, offering insights for future hypothesis-driven research and enhancing predictive capacity amid growing anthropogenic and climatic pressures.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Coastal wetlands, including mangroves, saltmarshes, and seagrasses, protect shorelines and play a critical role in regulating the global climate. Microbial communities maintain the stability and essential functions of these ecosystems. This study provided the first comprehensive global map of microbial communities in the three ecosystems. By analyzing over 1,381 samples, the results revealed that different habitats relied on different diversity, composition, and dominant taxa. Mangroves showed the highest richness and diversity. KEGG-based functional predictions suggested that microbial communities in the CWEs shared core predicted metabolic functions but differed in their predicted functional potentials. The null model revealed that the assembly process of","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0115926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149023715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Poultry handling-related stress alters membrane composition, extracellular vesicle production, survival, and virulence in <i>Campylobacter jejuni</i> Bf.","authors":"Jeanne Malet-Villemagne, Rochelle D'Mello, Yingxi Li, Zoran Minic, Karine Gloux, Florence Dubois-Brissonnet, Bastien Prost, Audrey Solgadi, Christine Péchoux, Vlad Costache, Marianne De Paepe, Zhu Zhang, Gilles Tessier, Jasmina Vidic","doi":"10.1128/aem.01265-26","DOIUrl":"10.1128/aem.01265-26","url":null,"abstract":"<p><p>We investigated the adaptation of the aerotolerant <i>Campylobacter jejuni</i> Bf strain to conditions mimicking the poultry slaughter process. We showed that <i>C. jejuni</i> Bf survives and actively multiplies under combined thermal and oxidative stress. Stress exposure induces cell rounding, loss of motility, remodeling of membrane composition, decreased membrane fluidity, and metabolic reprogramming with increased intracellular ATP levels. While maintaining the lipid composition of its plasma membrane, <i>C. jejuni</i> modulates the lipid composition of its extracellular vesicles when exposed to stress. Notably, stressed <i>C. jejuni</i> cells release extracellular vesicles with increased toxicity toward the epithelial barrier of Caco-2 cells, potentially facilitating invasion of the gut epithelium.IMPORTANCE<i>Campylobacter</i> infections are one of the leading causes of foodborne gastroenteritis worldwide. <i>Campylobacter</i> readily enters the food chain and is transmitted to humans, primarily through the consumption of contaminated poultry meat. The high prevalence of aerotolerant human <i>Campylobacter jejuni</i> isolates suggests a correlation between their ability to survive under aerobic conditions, virulence, and resistance to harsh stress conditions. However, the underlying mechanism remains unclear. Our results show that <i>C. jejuni</i> extracellular vesicles are part of a survival strategy that links environmental adaptation with pathogenicity.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0126526"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148757300","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":"MclX modulates the process of mother cell lysis by SpoIIID in <i>Bacillus thuringiensis</i>.","authors":"Yanrong Xu, Xin Zhang, Ruibin Zhang, Dongshu Wang, Shaomi Dai, Xiaowen Du, Shuyuan Guo, Fuping Song","doi":"10.1128/aem.00215-26","DOIUrl":"10.1128/aem.00215-26","url":null,"abstract":"<p><p>Cell differentiation is essential for the survival and adaptation of organisms. In <i>Bacillus</i> species, sporulation is a tightly coordinated program that culminates in mother cell lysis, a critical step for spore release. Despite its importance, the mechanisms modulating the process remain poorly understood. Here, we show that MclX regulates mother cell lysis by inhibiting SpoIIID, a sporulation-specific transcription factor that represses <i>cwlC</i>, which encodes a key hydrolase required for lysis. SpoIIID directly binds to the <i>cwlC</i> promoter, and its overexpression during sporulation markedly delays both the onset and progression of mother cell lysis. These findings support a model in which MclX modulates SpoIIID to control <i>cwlC</i> expression and lysis process. Collectively, this work defines a previously unrecognized MclX-SpoIIID-<i>cwlC</i> regulatory axis, providing new insight into the control of late sporulation events and the process of mother cell lysis.</p><p><strong>Importance: </strong>Mother cell lysis is a critical step in <i>Bacillus</i> sporulation, yet its regulation remains poorly understood. Here, we identify <i>mclX</i> as an upstream factor that modulates the onset and progression of mother cell lysis in <i>Bacillus thuringiensis</i>. MclX reduces SpoIIID levels, which in turn directly represses <i>cwlC</i> expression. These findings provide new insight into the regulatory network governing lysis process and advance our understanding of bacterial cell differentiation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0021526"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148705233","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":"Correction for Cheng et al., \"Preparation of sodium alginate-coated microencapsulated phage vB_SalP_SE29 and evaluation of its therapeutic effect on <i>Salmonella</i> enteritidis infection\".","authors":"Yan Cheng, Jiahao Yu, Xiaochen Ren, Ruiqi Liang, Bingmei Du, Jinhong Li, Sayed Haidar Abbas Raza, Wuwen Sun, Dongxing Zhang, Lei Zhang","doi":"10.1128/aem.01329-26","DOIUrl":"10.1128/aem.01329-26","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0132926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148676898","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":"Soilless farming system design impacts the diversity and composition of microbiota.","authors":"Auja Bywater, Aline Novaski Seffrin, Jordan E Bisanz, Francesco Di Gioia, Jasna Kovac","doi":"10.1128/aem.01167-26","DOIUrl":"10.1128/aem.01167-26","url":null,"abstract":"<p><p>Controlled environment agriculture (CEA), including soilless farming systems, is expanding to improve food security and resource efficiency. However, little is known about how different soilless farming system designs influence microbial populations that may be relevant to plant health and food safety. This study investigated the effects of soilless system type on microbial load and bacterial community composition in nutrient solution and on bok choy leaves over two growing cycles. Soilless systems, including deep water culture (DWC), Kratky (KR), nutrient film technique (NFT), ebb and flow (EF), and drip irrigation (DI), were evaluated. Significant differences in aerobic plate count (APC) in nutrient solution were observed among system types, with the DI system exhibiting the highest counts across both cycles. Increased nutrient solution pH was negatively associated with APC, whereas temperature did not significantly affect microbial concentrations. APC on bok choy leaves at harvesting was not significantly different by system type. Bacterial community composition in nutrient solution significantly varied by system type, temperature, growing cycles, and sampling day. Microbial alpha diversity also varied significantly by system type. Core microbiota analysis identified <i>Acidovorax</i>, <i>Legionella</i>, and <i>Caulobacter</i> as both core and hub taxa, with <i>Acidovorax</i> being the only genus detected across all samples. These findings indicate that microbial dynamics differ among soilless system designs and across growing cycles, suggesting that factors not monitored in this study strongly influence microbial community composition. Furthermore, we identified core and hub bacterial genera warranting further investigation of their function in CEA and their impact on plant health and food safety.IMPORTANCEThis study demonstrated that microbial load and community composition in hydroponic production varied by soilless system type and between growing cycles. We found that system design had a significant effect on community composition. Furthermore, the community compositions differed between growing cycles, suggesting that factors not measured in this study significantly shaped the community structure. Drip irrigation systems exhibited higher microbial loads compared to other systems. Leaf-associated microbial load showed insignificant differences across systems and growing cycles, likely due to limited contact with nutrient solutions. <i>Acidovorax</i> was detected across all samples, warranting further investigation of its role in hydroponic systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0116726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148668234","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 dual methane production mechanism mediated by enzymatic catalysis and the Fenton reaction in the wood-rotting fungus <i>Schizophyllum commune</i>.","authors":"Mengshi Zhao, Yu Xiao, Shuang Leng, Jiasong Fang, Changhong Liu","doi":"10.1128/aem.01298-26","DOIUrl":"10.1128/aem.01298-26","url":null,"abstract":"<p><p>Understanding biological sources of methane is critical for elucidating the global methane cycle and addressing climate change. While traditional research has predominantly focused on prokaryotic methanogens, emerging evidence suggests that eukaryotes, particularly fungi, can produce methane through both enzymatic and non-enzymatic pathways. However, no eukaryotic organism has been documented to possess both pathways simultaneously. Here, we provide preliminary evidence suggesting that the wood-decaying fungus <i>Schizophyllum commune</i> strain 20R-7-F01, isolated from sediment approximately 2 km below the seafloor, employs dual mechanisms for methane production. By comparing wild-type strains with mct1 (methyl chloride transferase 1) and dh3 (dehalogenase 3) deficient strains under iron-replete (50 μM Fe³⁺, to facilitate Fenton reactions) and iron-free conditions, we estimated that enzymatic pathways account for roughly 82%-85% of total methane production. The remaining ~15%-18% of methane output is consistent with a contribution from Fenton-type chemistry, and this quantitative partitioning of pathway contributions was derived from cross-condition yield comparisons. Environmental factors such as oxygen, temperature, and substrate type significantly influence enzymatic efficiency, whereas the efficacy of the non-enzymatic pathway depends on the concentration of methyl donors, particularly dimethyl sulfoxide. Additionally, both pathways are activated by hydrogen peroxide, indicating that reactive oxygen species positively regulate methane synthesis. This study reveals a novel co-existing \"enzymatic-Fenton\" mechanism for methane production in fungi, highlighting their crucial role in the global methane budget and carbon cycling.IMPORTANCEMethane is a key driver of climate change, yet our understanding of its biological sources has long been limited to bacteria and archaea. Here, we reveal that a fungus, <i>Schizophyllum commune</i> 20R-7-F01, isolated from deep below the seafloor, produces methane through two distinct mechanisms operating simultaneously: an enzymatic pathway and a Fenton reaction-driven non-enzymatic pathway. This dual system, previously unreported in any eukaryote, redefines the potential contribution of fungi to the global methane budget. Our findings challenge the traditional prokaryote-centric view of methanogenesis and open new avenues for understanding methane cycling in oxygen-rich and iron-rich environments, with implications for climate modeling and carbon cycle research.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0129826"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148824266","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}