Journal of Applied Microbiology最新文献

{"title":"Integration of genome mining and HiTES reveals secondary metabolic potential in marine-derived Aspergillus sp. WHUF0304.","authors":"Hua-Wei Lv, Xiao-Ting Liu, Yi-Jiang Zhou, Bin Wei, Meng-Di Zhu, Ti-Ti Ying, Hai Cai, Mahmoud Emam, Hong Wang, Xing-Nuo Li","doi":"10.1093/jambio/lxag226","DOIUrl":"10.1093/jambio/lxag226","url":null,"abstract":"<p><strong>Aims: </strong>Marine-derived Aspergillus species are prolific producers of bioactive secondary metabolites, yet the majority of their biosynthetic gene clusters (BGCs) remain silent. This study aimed to integrate genome mining with high-throughput elicitor screening (HiTES) to unlock the metabolic potential of Aspergillus sp. WHUF0304 and identify elicitors that promote the accumulation of previously undetected metabolites.</p><p><strong>Methods and results: </strong>A high-quality genome of Aspergillus sp. WHUF0304 was assembled and annotated using multiple functional databases, revealing substantial secondary metabolic potential. antiSMASH analysis identified diverse BGCs, including NRPS/indole-related clusters potentially associated with indole diketopiperazine biosynthesis. A HiTES-inspired elicitor screening strategy was then applied to evaluate 42 small molecules for their ability to alter the metabolite profile of this strain. Among the tested elicitors, fluconazole was identified as the optimal inducer, triggering the production of several indole diketopiperazine-related differential metabolites. Subsequent activity-guided isolation led to the identification of a bioactive indole diketopiperazine dimer, cristatumin E, which exhibited antibacterial activity against Escherichia coli and Bacillus subtilis with minimum inhibitory concentrations (MICs) of 32 µg mL-1 and 256 µg mL-1, respectively.</p><p><strong>Conclusions: </strong>These findings demonstrate that integrating genomic and functional approaches effectively activates silent BGCs in marine fungi. The fluconazole-associated accumulation and subsequent isolation of cristatumin E, a bioactive indole diketopiperazine dimer, highlight the potential of elicitor-mediated activation to expand the detectable metabolite profile of Aspergillus sp. WHUF0304.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bentonite compaction shapes microbial communities but abiotic processes dominate carbon steel corrosion in repository conditions.","authors":"Kateřina Černá, Saqlain Saqib Mukhtar, Richard Bureš, Jakub Říha, Veronika Hlavackova, Jan Stoulil","doi":"10.1093/jambio/lxag215","DOIUrl":"10.1093/jambio/lxag215","url":null,"abstract":"<p><strong>Aims: </strong>The long-term safety of deep geological repositories (DGRs) for high-level radioactive waste relies on the corrosion resistance of metal canisters embedded in bentonite buffers. Microbiologically influenced corrosion (MIC) is considered a potential threat to metal canisters in DGRs, yet the effect of bentonite compaction on corrosion processes remains poorly understood. This study evaluated microbial and abiotic contributions to carbon steel corrosion and corrosion localization in bentonite under repository-relevant conditions.</p><p><strong>Methods and results: </strong>Carbon steel corrosion was investigated in bentonite Černý Vrch under slurry and compacted conditions (1200, 1400, and 1600 kg m⁻³) during 3-11 months of anaerobic incubation. Corrosion was assessed by weight-loss measurements, X-ray diffraction, and microscopy, while microbial communities were analysed using 16S rRNA gene sequencing and digital PCR. Sterile and low-biomass systems often exhibited higher corrosion rates than biotic treatments, indicating that abiotic processes predominated in bentonite systems. Bentonite prevented localized corrosion and promoted uniform surface alteration. Corrosion was most pronounced in compacted bentonite (1.6 g cm⁻³), despite reduced microbial activity. Bentonite dry density was the primary driver of microbial community composition in compacted systems, suppressing many taxa associated with steel colonization in slurries, although sulfate-reducing Desulfosporosinus remained abundant.</p><p><strong>Conclusions: </strong>Under the investigated conditions, bentonite compaction restricted microbial activity and suppressed many candidate MIC taxa but did not suppress abiotic corrosion. Corrosion rates were often lower in biotic than in sterile treatments, indicating that microbial activity may, under certain conditions, mitigate corrosion and should be considered alongside corrosion-promoting processes when evaluating repository-relevant bentonite systems.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148818437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulatory mechanisms of synthetic microbial communities on rhizosphere microecology to alleviate continuous monoculture obstacles of medicinal plants.","authors":"Yiling Zuo, Zihang Su, Jia Guo, Meng Zhou, Yu Wang, Zhiyu Ni","doi":"10.1093/jambio/lxag205","DOIUrl":"10.1093/jambio/lxag205","url":null,"abstract":"<p><p>Driven by industrial policies and market expansion, China has formed the world's largest medicinal plant cultivation industry. However, sustainable herbal production is seriously hindered by continuous monoculture obstacles (CMOs), which arise from prolonged single-species successive cultivation and manifest as comprehensive soil degradation featuring autotoxic allelochemical buildup, unbalanced rhizosphere microbiota, impaired soil physicochemical conditions, and frequent soil-borne pathogen outbreaks. Such adverse alterations lower soil enzyme activity, disrupt microbial community homeostasis, and severely impair both the yield and bioactive constituent quality of medicinal plants. Synthetic microbial communities (SynComs), experimentally assembled from defined microbial isolates via precise cultivation and controlled assembly, exhibit promising potential to regulate plant metabolism, optimize nutrient cycling, and boost plant stress tolerance, and thus may serve as a feasible strategy to mitigate medicinal plant CMOs. This review took rhizosphere microecology as its core research perspective and summarized CMOs' status, SynComs' significance, construction methods, and their mechanisms in reshaping rhizosphere microecology-focusing on root exudates, nutrient cycling, and microbiome dynamics. SynComs adjust root exudates, participate in carbon/nitrogen/phosphorus cycling, enhance stress/pathogen resistance, and strengthen root immunity via signaling pathways (e.g. jasmonic acid). Existing experimental evidence indicated SynComs may partially repair plant-microbe communication networks impaired under continuous monoculture. Future research should prioritize innovative SynCom designs with keystone microbes, improved assembly techniques, and deeper rhizosphere mechanistic studies to advance sustainable medicinal plant production.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148760385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterologous surface display of Serratia marcescens-derived laccase and its decolorization performance toward Azo dyes.","authors":"Fumin Tan, Ying Pan, Qifeng Li, Enguo Fan, Cuijuan Gao","doi":"10.1093/jambio/lxag232","DOIUrl":"10.1093/jambio/lxag232","url":null,"abstract":"<p><strong>Aims: </strong>Laccase represents a high-value green catalyst with extensive industrial application prospects. The aim of this study is to construct a laccase surface-displaying recombinant strain LacA-BL21 by fusing LacA from Serratia marcescens with Escherichia coli (E. coli) Ag43 autotransport system, optimize its enzyme production and dye decolorization parameters, verify the surface display system efficiency, and evaluate its potential for industrial wastewater bioremediation.</p><p><strong>Methods and results: </strong>In this study, we generated the surface-displaying strain LacA-BL21 by fusing laccase (LacA) from S. marcescens with the Ag43 autotransport system from E. coli. The enzyme activity results indicate that the recombinant laccase exhibits optimal catalytic activity at 45°C and pH 4.0. Key parameters affecting enzyme production were systematically optimized and LacA-BL21 achieved a maximum laccase activity of 43.66 ± 1.45 U ml-1 in TB medium supplemented with 4% methanol, 1.77 times that of the wild-type strain ZH-5. Furthermore, qRT-PCR (quantitative real-time polymerase chain reaction) analysis demonstrated that the relative transcription level of the target gene in the LacA-BL21 was 1.91-fold higher than that in the wild-type strain ZH-5, verifying the high efficiency of the surface display system for laccase heterologous expression. Dye decolorization assays using simulated wastewater were performed to evaluate the catalytic performance of the recombinant LacA-BL21 system, and the results indicated outstanding decolorization efficacy toward various dye substrates. Following systematic process optimization, the crude preparation containing recombinant LacA achieved an 82.17% decolorization rate for Congo red simulated wastewater within 2 h.</p><p><strong>Conclusion: </strong>This study constructs a surface display system for laccase expression, which exhibits exceptional catalytic efficiency and favorable decolorization capability toward azo dyes, thereby harboring substantial promise for the bioremediation of industrial wastewater.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148919839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Acanthamoeba spp. on rice (Oryza sativa L.) plant growth and rhizobacterial community composition.","authors":"Komal A Chandarana, Saborni Maiti, Abhishek Gupta, Natarajan Amaresan","doi":"10.1093/jambio/lxag177","DOIUrl":"10.1093/jambio/lxag177","url":null,"abstract":"<p><strong>Aims: </strong>This study aimed to evaluate the influence of two amoebae (Acanthamoeba lenticulata (A10) and Acanthamoeba genotype T4 (A23)) on rice growth, nutrient uptake, and rhizobacterial community composition.</p><p><strong>Methods and results: </strong>Rice seedlings were inoculated with either A10 or A23 and grown under greenhouse conditions for 30 d. Plant growth parameters, biomass accumulation, and nutrient contents were determined. Rhizosphere bacterial community diversity and composition were assessed using 16S rRNA gene amplicon sequencing followed by statistical analyses including Tukey's HSD test (P < 0.05). Both amoebae significantly increased root length (33%-36%) compared to uninoculated controls. A10 exerted stronger effects on biomass accumulation, increasing the root fresh weight (136%), shoot fresh weight (94%), root dry weight (325%), and shoot dry weight (188%). Both treatments enhanced nutrient uptake, particularly phosphorus content. Although the bacterial alpha diversity indices did not differ significantly among the treatments; clear shifts in community composition were observed. Amoebae-inoculated soils were enriched in Proteobacteria (65%-75%), whereas Firmicutes dominated the control soils (34%). Several plant-beneficial genera such as Methylobacillus, Methylotenera, Methylobacterium, Sphingomonas, Acinetobacter, and Novosphingobium were more abundant in amoebae-treated rhizospheres.</p><p><strong>Conclusions: </strong>Acanthamoeba species enhanced rice growth and nutrient acquisition by selective restructuring of rhizosphere bacterial communities.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148470660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antibiofilm activity of benzophenone-2 against uropathogenic Escherichia coli.","authors":"Lakshi Sihara Jayasekara, Bharath Reddy Boya, Jin-Hyung Lee, Jintae Lee","doi":"10.1093/jambio/lxag183","DOIUrl":"10.1093/jambio/lxag183","url":null,"abstract":"<p><strong>Aims: </strong>Uropathogenic Escherichia coli (UPEC) is the primary cause of urinary tract infections, with biofilm formation playing a critical role in infection recurrence. The increasing prevalence of multidrug-resistant UPEC underscores the need for alternative strategies that target biofilms without imposing strong evolutionary pressure typical of conventional antibiotics. This study identifies 2,2',4,4'-Tetrahydroxybenzophenone, also known as benzophenone-2 (BP-2), a UV filter widely used in sunscreens and cosmetic products as a promising candidate for repurposing as an antibiofilm agent against UPEC.</p><p><strong>Methods and results: </strong>BP-2 was evaluated for its antibiofilm activity against UPEC, as well as its ability to inhibit key virulence factors, including curli production, rugosity, and motility. Additionally, in vivo, in vitro, and in silico toxicity assessments were performed, along with 3D-QSAR analysis and molecular docking. BP-2 exhibited a minimum inhibitory concentration of 600 μg ml-1 and inhibited over 50% and 80% of UPEC biofilm formation at sub-inhibitory concentrations of 20 and 100 μg ml-1, respectively, without affecting bacterial growth or viability. Furthermore, BP-2 disrupted mature UPEC biofilms, impaired motility, rugose colony formation, and curli biogenesis, and showed antimicrobial activity against other pathogens. qRT-PCR demonstrated downregulation of curli biogenesis and motility related virulence genes while molecular docking suggested inhibition of the curli master regulator CsgD. 3D-QSAR analysis emphasized the role of hydroxyl substitutions at the 2- and 4- positions of the benzophenone scaffold.</p><p><strong>Conclusions: </strong>BP-2 possesses potent antibiofilm activity against UPEC by targeting key virulence factors without affecting bacterial viability and has potential as a promising antibiofilm candidate for the treatment of UPEC-associated infections.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional microorganisms in bioorganic fertilizers: strain screening, application validation, and characterization.","authors":"Weihong Chen, Kailing Zhong, Lechen Li, Yunqing Liu, Hao Wang, Dayi Qian, Hongzhi Ma","doi":"10.1093/jambio/lxag100","DOIUrl":"10.1093/jambio/lxag100","url":null,"abstract":"<p><p>The efficacy of bioorganic fertilizers is strongly dependent on functional microbial strains; however, systematic frameworks for candidate strain acquisition, functional screening, application validation, and strain characterization remain insufficiently developed for bioorganic fertilizer research and product development. This review synthesizes the major functional microbial groups used in bioorganic fertilizers and their mechanisms of action, with particular emphasis on strain selection strategies, functional screening and application-validation pathways, and methods for strain identification and functional characterization. Current evidence indicates that conventional culture-based isolation, oligotrophic screening, extreme-habitat screening, and modern molecular and data-driven approaches each occupy distinct methodological niches. These strategies are respectively suited to pure-culture resource acquisition, discovery of strains adapted to resource-limited environments, identification of stress-tolerant and process-adaptive strains, and candidate discovery coupled with functional analysis. Importantly, optimization of functional strains should not rely solely on single in vitro trait-based screening. Instead, it should integrate formulation-related adaptability, robustness-oriented microbial phenotyping, and application-context validation into a tiered evaluation framework spanning strain acquisition, functional screening, application validation, and strain identification and functional characterization. This review provides a systematic methodological reference for the selection, evaluation, and product development of functional strains for bioorganic fertilizers (BOFs).</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148603315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Streptococcus thermophilus 1131 and Lactobacillus delbrueckii subsp. bulgaricus 2038 induce immune responses via M cell-mediated transcytosis in an in vitro human gut model.","authors":"Fuka Yamazaki, Kyosuke Kobayashi, Toshihiro Sashihara","doi":"10.1093/jambio/lxag157","DOIUrl":"10.1093/jambio/lxag157","url":null,"abstract":"<p><strong>Aims: </strong>This study aimed to elucidate in vitro how orally administered Streptococcus thermophilus 1131 and Lactobacillus delbrueckii subsp. bulgaricus 2038, stimulated immune cells in the gut lamina propria and thereby enhanced the intestinal barrier function, as reported in our previous study.</p><p><strong>Methods and results: </strong>We prepared an M cell model by coculturing small intestinal epithelial cells derived from human induced pluripotent stem cells with Raji cells. In this model, we demonstrated that both strains were incorporated into M cells and translocated to the basolateral side via transcytosis. Evaluation of the immune response using peripheral blood mononuclear cells showed that S. thermophilus 1131, translocated via M cells, induced the secretion of several cytokines, including IL-22 and IL-23.</p><p><strong>Conclusion: </strong>We showed that both strains were transcytosed by M cells in a human gut model. The results suggested that oral administration of both strains induced immune responses by translocating from the gut lumen to the lamina propria via M cells.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148375774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding the interactions and effects of environmental biofilms on SARS-CoV-2 viability on contact surfaces.","authors":"Chendu Bharat Prasad Mosuri, Nick Monday, Sapna Chitlapilly Dass","doi":"10.1093/jambio/lxag200","DOIUrl":"10.1093/jambio/lxag200","url":null,"abstract":"<p><strong>Aims: </strong>To investigate the role of multispecies drain biofilms in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity and persistence on contact surfaces used in meat processing plants.</p><p><strong>Methods and sesults: </strong>Environmental drain biofilms from pork (n = 12) and beef (n = 22) processing plants were grown with and without SARS-CoV-2 on stainless steel (S.S.), polyvinyl chloride (PVC), tile, and galvanized steel (G.S.) at 7°C for 5 days. Biofilm biomass, viral RNA persistence, and viral infectivity were quantified and compared with controls. Surface type significantly influenced viral RNA persistence with PVC, tile, and particularly G.S. supporting increased SARS-CoV-2 RNA persistence relative to virus controls (P < .001), while S.S. consistently showed reduced viral RNA persistence (P < .01). Plaque assays demonstrated that SARS-CoV-2 remained viable on all surfaces after 5 days. Beef drain biofilms on tile and G.S. exhibited two to four-fold higher infectivity than corresponding virus controls (P < .001), while infectivity was reduced in pork drain biofilms on PVC and tile. Viral RNA persistence and infectivity were not consistently correlated, indicating that detection of viral RNA within biofilm matrices does not necessarily reflect infectious virus. SARS-CoV-2 exposure also altered biofilm development in a surface and origin-dependent manner, increasing biomass of pork drain biofilms on PVC and tile (>2-fold; P < .01) while reducing growth of beef drain biofilms on S.S. and G.S. (0.9-1.8 log reductions; P < .01).</p><p><strong>Conclusions: </strong>Drain biofilms may act as transient reservoirs for SARS-CoV-2, with viral persistence governed by the combined effects of surface properties, biofilm structure, and microbial origin.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Food additive titanium dioxide (E171) alters gut microbial metabolic activity and butyrate production in the TIM-2 in vitro colon model.","authors":"","doi":"10.1093/jambio/lxag181","DOIUrl":"https://doi.org/10.1093/jambio/lxag181","url":null,"abstract":"","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":"137 8","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148706676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}