Journal of microbiological methods最新文献

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Microbial biofilms and nanoparticles synergistic interaction: A cutting-edge nano-bioremediation method for environmental cleanup and site restoration 微生物生物膜和纳米颗粒协同作用:一种用于环境清理和现场修复的尖端纳米生物修复方法。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-22 DOI: 10.1016/j.mimet.2026.107406
Manoj Kumar , Meera Goswami , Deepak Pant , Kulamani Parida , Anand Giri
{"title":"Microbial biofilms and nanoparticles synergistic interaction: A cutting-edge nano-bioremediation method for environmental cleanup and site restoration","authors":"Manoj Kumar ,&nbsp;Meera Goswami ,&nbsp;Deepak Pant ,&nbsp;Kulamani Parida ,&nbsp;Anand Giri","doi":"10.1016/j.mimet.2026.107406","DOIUrl":"10.1016/j.mimet.2026.107406","url":null,"abstract":"<div><div>In nature, bacteria have two different growth modes: a unicellular life stage, in which the cells are free-moving (planktonic), and a multicellular life stage wherein the cells are immobile and reside within a biofilm structure, composed of a complex network of extracellular polymeric substances (EPS). The EPS contribute to the distinctive characteristics of the biofilm's lifestyle, environmental degradation, as well as virulence and antibiotic resistance. The present review critically analyses the functional significance of extracellular polymeric substances (EPS), characteristics of biofilms and nanoparticle-biofilm interactions for the removal of emerging environmental contaminants. Nanoparticles can also function as emulsifiers, enhancing bioavailability by providing droplet surfaces that facilitate microbial attachment and promote microbial proliferation. The enhancement of certain biofilms through positive interactions with nanoparticles will enable the design of systems that facilitate the development of cost-effective alternatives of interest, including enhanced bioremediation, biodegradation, oil spill mitigation, and improved microbial fuel cell (MFC) performance. Nano-bioremediation is effective across a wide range of emerging environmental contaminants such as PAHs, chlorinated compounds, pHthalates, plastic heavy metals, etc. and provides a sustainable alternative to conventional remediation approaches.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107406"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Combining isolation chips with velvet transfer for high-throughput primary screening of antibiotic-producing soil-dwelling bacteria 分离芯片与丝绒转移相结合的产抗生素土栖细菌高通量初筛研究。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-17 DOI: 10.1016/j.mimet.2026.107397
Sabina D. Hidat , Joan Masatu , Nelson E. Masota , Rogers Mwakalukwa , Paul Malaba , Joseph Sempombe , Doreen Mloka
{"title":"Combining isolation chips with velvet transfer for high-throughput primary screening of antibiotic-producing soil-dwelling bacteria","authors":"Sabina D. Hidat ,&nbsp;Joan Masatu ,&nbsp;Nelson E. Masota ,&nbsp;Rogers Mwakalukwa ,&nbsp;Paul Malaba ,&nbsp;Joseph Sempombe ,&nbsp;Doreen Mloka","doi":"10.1016/j.mimet.2026.107397","DOIUrl":"10.1016/j.mimet.2026.107397","url":null,"abstract":"<div><div>Antimicrobial resistance (AMR) remains a significant threat to global health, requiring various mitigation strategies. Soil-dwelling microbes have long been a valuable source of novel antibiotics; however, their low cultivability using standard methods has often led to the discovery of known antibiotics. This bottleneck has been partially overcome by using isolation chips (iChips), which enhance the cultivability (both in terms of number and diversity) of soil bacteria. This has created a need to find new screening methods that allow high-throughput screening, are less resource-intensive, and can screen multiple test organisms.</div><div>To address this, soil samples were collected from three different regions of Tanzania, and numerous bacterial soil species colonies were grown in iChips and then transferred to master plates. Replica plates were created using a velvet transfer method and utilized for parallel agar overlay assays against <em>Escherichia coli</em>, <em>Klebsiella pneumoniae</em>, and <em>Staphylococcus aureus</em>. Master plates with 33–62 colonies showing variation in size, morphology, and spatial arrangement were produced by cultivating agar plugs from iChips. Three to four replicates, which preserved these characteristics at the transfer efficiencies of 91.3–100% were obtained without contamination. Zones of inhibition -to-colony diameter ratios ranging 1.15–3.27 were obtained following parallel primary screening against test strains, hence enabling the identification of potential antibiotic producers.</div><div>This is the first report of the combined iChip and velvet transfer workflow that offers a high-throughput, resource-efficient, and scalable method for primary screening of various soil-derived bacteria for antibacterial Natural Products (NPs), while also maintaining the master plates for downstream investigations.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107397"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146003742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A simple preservation method for the short-medium term storage of environmental bacteria 一种简易的环境细菌中短期保存方法。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-30 DOI: 10.1016/j.mimet.2026.107409
John E. Moore , Beverley Cherie Millar
{"title":"A simple preservation method for the short-medium term storage of environmental bacteria","authors":"John E. Moore ,&nbsp;Beverley Cherie Millar","doi":"10.1016/j.mimet.2026.107409","DOIUrl":"10.1016/j.mimet.2026.107409","url":null,"abstract":"<div><div>A novel method is described for the short to medium term storage of environmental bacteria up to six months. Fifty environmental bacteria were employed in this study, which had been previously isolated from green spaces. These organisms comprised of 14 genera (10 Gram negative and 4 Gram positive) [<em>Arthrobacter, Bacillus, Buttiauxella, Carnobacterium, Citrobacter, Enterobacter, Lelliottia, Pectobacterium, Pseudomonas, Rahnella, Serratia, Sporosarcina, Stenotrophomonas, Yersinia</em>] and 16 identified species. Organisms were inoculated onto fresh plates of Standard Plate Count (SPC) agar and incubated aerobically at 30 °C for 72 h. Following this, plates with growth were stacked in metal plate racks and wrapped in plastic with a large autoclave bag and sealed with a cable tie. Plates were stored at 5 °C in the dark for six months, after which they were removed and the colonies checked for viability. All isolates were able to be recovered through passaging onto fresh SPC plates. This method is simple, inexpensive, versatile and widely adaptable and requires minimum preparation/handling/processing, utilising a small laboratory footprint for refrigerator space. Adoption and employment of this simple storage system encourages the routine archiving of environmental isolates for future research purposes.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107409"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146100264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Strain-level typing of Candida albicans and Saccharomyces cerevisiae using Fourier transform infrared spectroscopy and whole-genome sequencing 利用傅里叶变换红外光谱和全基因组测序对白色念珠菌和酿酒酵母进行菌株水平分型。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-22 DOI: 10.1016/j.mimet.2026.107405
Asuka Kashiwaba , Asako Mitani , Takumi Sonoda , Naofumi Shigemune , Hiroki Takahashi
{"title":"Strain-level typing of Candida albicans and Saccharomyces cerevisiae using Fourier transform infrared spectroscopy and whole-genome sequencing","authors":"Asuka Kashiwaba ,&nbsp;Asako Mitani ,&nbsp;Takumi Sonoda ,&nbsp;Naofumi Shigemune ,&nbsp;Hiroki Takahashi","doi":"10.1016/j.mimet.2026.107405","DOIUrl":"10.1016/j.mimet.2026.107405","url":null,"abstract":"<div><div>Rapid, low-cost strain-level typing is essential for source attribution and microbiological control in clinical and industrial settings. Fourier-transform infrared (FT-IR) spectroscopy using IR Biotyper method was previously optimized to achieve an identification level equivalent to that of whole-genome sequencing (WGS) discrimination of <em>Wickerhamomyces anomalus</em>. However, the species of yeast studied were limited; further, studies that have used the results of WGS as a reference for strain identification in yeast remain limited. Therefore, here, the generalizability of this approach to <em>Candida albicans</em> and <em>Saccharomyces cerevisiae</em> was assessed using publicly available whole-genome datasets as references. Single-nucleotide polymorphisms from 29<em>C. albicans</em> and 27 <em>S. cerevisiae</em> genomes were analyzed to build phylograms and select 5 and 4 mutually distant strains for FT-IR. FT-IR spectra were obtained after a standardized 24-h rotational culture in SD liquid medium, with three independent passages per strain. The same and similar strains clustered tightly, and different strains formed non-overlapping clusters; branches for the same and similar strains were &lt; 0.1 on IR dendrograms, whereas branches for distinct strains were &gt; 0.1. The discriminatory ability of FT-IR fully agreed with the WGS-based same/different classifications. Standardized liquid culture likely reduced cell-state heterogeneity, improving reproducibility. These results extend FT-IR strain typing beyond <em>W. anomalus</em>, providing a rapid, low-cost tool for contamination source attribution.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107405"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimization of physicochemical and antimicrobial properties of functional kombucha beverage sweetened with dried fruits using simplex centroid mixture and Plackett-Burman designs 采用单形质心混合和Plackett-Burman设计优化干果加糖功能性康普茶饮料的理化及抗菌性能。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-25 DOI: 10.1016/j.mimet.2026.107408
Lamia Ayed , Haifa Dhif , Souhir Torjmèn , Kamel Chaieb
{"title":"Optimization of physicochemical and antimicrobial properties of functional kombucha beverage sweetened with dried fruits using simplex centroid mixture and Plackett-Burman designs","authors":"Lamia Ayed ,&nbsp;Haifa Dhif ,&nbsp;Souhir Torjmèn ,&nbsp;Kamel Chaieb","doi":"10.1016/j.mimet.2026.107408","DOIUrl":"10.1016/j.mimet.2026.107408","url":null,"abstract":"<div><div>Traditional foods and beverages represent alternative strategies to counteract bacterial virulence. The fermentation of tea, sugar, supplemented with a symbiotic culture of bacteria and yeast (SCOBY) produces kombucha beverage, which offers several health advantages and is similar to soft drinks. This study investigates the effect of various fermentation factors on the growth levels of <em>Lactobacillus</em>, <em>Lactococcus</em>, total phenolic content and antimicrobial activities of Green Tea, Black Tea and Moringa kombucha beverage (GTBTMK) prepared with a starter SCOBY culture. Formulation of kombucha beverage was optimized using a Simplex-Centroid Mixture Design and Plackett-Burman Design. The best optimized kombucha formulation (18.98 g/L; Dried Apricot was 20 g/L; Dried plum was 10 g/L, Dried Grape was 20 g/L,11.763 g/L Green tea, 0.01238 g/L Black tea and 8.1127 g/L Moringa) contain a high phenolic content of 86.79 mg GAE/mL and exhibited a significant antimicrobial activity against <em>Bacillus cereus</em> ATCC 11778, <em>Micrococcus luteus</em> NCIMB 8166 and <em>Enterococcus faecalis</em> ATCC 29212, <em>Candida albicans</em> ATCC 90028, <em>Cryptococcus neoformans</em> ATCC 14116, <em>Aspergillus brasiliensis</em> ATCC 16404 (Inhibition zone more than 20 mm). This research provides new insights into the development of innovative, functional kombucha beverage potentially expanding the spectrum of health-promoting fermented drinks available to consumers.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107408"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146064144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Revelation of DNA aptamer sequences that bind Cyclospora cayetanensis 卡耶坦环孢子虫DNA适体序列的揭示。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-02-01 DOI: 10.1016/j.mimet.2026.107410
John G. Bruno
{"title":"Revelation of DNA aptamer sequences that bind Cyclospora cayetanensis","authors":"John G. Bruno","doi":"10.1016/j.mimet.2026.107410","DOIUrl":"10.1016/j.mimet.2026.107410","url":null,"abstract":"<div><div>This article completes the preliminary work published in the Journal of Fluorescence (PMID: 38109032) that demonstrated both external surface and seemingly internal binding of DNA aptamers to <em>Cyclospora cayetanensis</em> oocysts by disclosing the actual aptamer DNA sequences for public scrutiny and use in experimentation. These aptamer DNA sequences were previously held as trade secrets due to their perceived potential commercial value, but given the inability to generate much commercial interest in the aptamers for diagnostics applications, the author has decided to reveal the sequences so that other researchers may further study aptamer binding to the oocysts especially with regard to the unexpected internal binding. The author also shows that these aptamers appear useful in binding magnetic microbeads to the oocysts in buffer. Thus, perhaps the aptamers can be validated for magnetic separation of oocysts in more complex natural water or sewage samples as well. And finally, the public disclosure of these sequences could be applied to lateral flow test strip, Western blots and ELISA-like or other diagnostic assays. Both the refined and vetted list of highest affinity and most specific aptamer sequences against known <em>Cyclospora cayetanensis</em> proteins and whole oocysts as well as the comprehensive lists of thousands of aptamer sequences from next generation Illumina-based sequencing are disclosed.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107410"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146112785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A review on membrane biofouling during downtime of pharmaceutical water treatment equipment: Risks, mechanisms, and control strategies 制药水处理设备停机期间膜生物污染:风险、机制和控制策略综述。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-02-02 DOI: 10.1016/j.mimet.2026.107415
Zijian Cui, Jun Ma, Yanjun Zhang, Zhenxing Song, Xinxi Xu
{"title":"A review on membrane biofouling during downtime of pharmaceutical water treatment equipment: Risks, mechanisms, and control strategies","authors":"Zijian Cui,&nbsp;Jun Ma,&nbsp;Yanjun Zhang,&nbsp;Zhenxing Song,&nbsp;Xinxi Xu","doi":"10.1016/j.mimet.2026.107415","DOIUrl":"10.1016/j.mimet.2026.107415","url":null,"abstract":"<div><div>Pharmaceutical water is a crucial component in drug manufacturing, as its quality directly affects drug safety and efficacy. This study focuses on membrane biofouling in pharmaceutical water systems during downtime, revealing its unique formation mechanisms: abrupt decreases in flow rate, reduced dissolved oxygen, and nutrient accumulation collectively create favourable conditions for microbial colonization. Biofilm formation not only causes a decline in membrane flux and an increase in transmembrane pressure but may also release harmful substances, such as endotoxins, posing a severe threat to water quality. The study systematically reviews existing control technologies, encompassing conventional methods such as chemical cleaning and backflushing, as well as innovative approaches including electrochemical treatment and cold atmospheric pressure plasma (CAP) technology. Furthermore, this paper prospectively explores future research directions, such as the development of green antifouling agents and the application of intelligent monitoring technologies, providing a scientific basis and technical support for achieving water safety and sustainable development in the pharmaceutical industry.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107415"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Usefulness of approved and newly emerging non-cultural assays for early detection of invasive fungal infections in pediatric patients: A scoping review 批准的和新出现的非培养测定法在儿科患者侵袭性真菌感染早期检测中的有效性:范围综述。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-13 DOI: 10.1016/j.mimet.2026.107389
Jarom Kuhre , Manav Jain , Sheri Hohmann , Elena Y. Enioutina
{"title":"Usefulness of approved and newly emerging non-cultural assays for early detection of invasive fungal infections in pediatric patients: A scoping review","authors":"Jarom Kuhre ,&nbsp;Manav Jain ,&nbsp;Sheri Hohmann ,&nbsp;Elena Y. Enioutina","doi":"10.1016/j.mimet.2026.107389","DOIUrl":"10.1016/j.mimet.2026.107389","url":null,"abstract":"<div><h3>Introduction and objective</h3><div>Invasive fungal infections (IFI) affect millions worldwide, especially the immunocompromised and pediatric patients. The standard fungal culture has low sensitivity and is slow for fungal identification. Rapid and accurate laboratory assays may support early successful treatment. Although the European Organization for Research and Treatment of Cancer/Mycoses Study Group Education and Research Consortium (EORTC/MSGERC) has proposed IFI diagnostic criteria, there are few recommendations for children. This scoping review analyzed the sensitivity, specificity, and positive and negative predictive value of standard and recently developed non-cultural laboratory assays to diagnose IFI in children.</div></div><div><h3>Methods</h3><div>PubMed, Embase, Scopus, and Web of Science were searched from January 1, 2016, to March 23, 2025, for free, full-text publications for pediatric IFI and the EORTC/MSGERC-recommended fungal antigen assays (1,3)-ß-D-glucan and galactomannan. The same databases were searched for articles published before January 30, 2025, for emerging assays, Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), T2Candida, and lateral flow immunoassays (LFA).</div></div><div><h3>Results</h3><div>From the fungal antigen studies reviewed, (1,3)-ß-D-glucan and galactomannan assays exhibit varying rates of sensitivity and specificity, poor positive predictive value, and high negative predictive value. From the emerging assay studies, MALDI-TOF MS had near 100% sensitivity, T2Candida reported high specificity, and only one article reviewed LFA.</div></div><div><h3>Conclusion</h3><div>Despite varying accuracy and reliability, the fungal antigen assays offer the benefits of speed, noninvasive collection, and serial testing. The emerging assays appear faster and more sensitive, but few outcomes were reported. This limits comparisons between emerging laboratory assays and fungal culture.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107389"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145989617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An efficient targeted gene deletion approach for Trichoderma atroviride using Agrobacterium tumefaciens-mediated transformation 农杆菌介导转化的atroviride木霉高效靶向基因缺失方法
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-22 DOI: 10.1016/j.mimet.2026.107407
Mengke Li , Yihong Li , Xiaoyu Zhang, Hui Zhou, Yusheng Liu, Qiuye Liu, Shuqin Xiao
{"title":"An efficient targeted gene deletion approach for Trichoderma atroviride using Agrobacterium tumefaciens-mediated transformation","authors":"Mengke Li ,&nbsp;Yihong Li ,&nbsp;Xiaoyu Zhang,&nbsp;Hui Zhou,&nbsp;Yusheng Liu,&nbsp;Qiuye Liu,&nbsp;Shuqin Xiao","doi":"10.1016/j.mimet.2026.107407","DOIUrl":"10.1016/j.mimet.2026.107407","url":null,"abstract":"<div><div><em>Trichoderma atroviride</em> is well-known biocontrol fungus that plays a crucial role in controlling plant fungal diseases. In this study, the Serine Protease (<em>T. atSp1</em>) gene of <em>T. atroviride</em> was selected as the target gene to investigate the effects of <em>Agrobacterium tumefaciens</em> concentration, conidial concentration, mixing ratio of conidia and <em>Agrobacterium</em> cells, and induction time on transformation efficiency. The optimal knockout system was achieved under conditions that the density of <em>A. tumefaciens</em> was OD<sub>600</sub> = 0.5, the concentration of conidia suspension was 10<sup>6</sup> conidia/mL, the mixture ratio of conidia suspension and <em>A. tumefaciens</em> AGL-1 was 1:1, and the induction time was 0.5 h. The transformation efficiency reached 28.33 to 61.67 transformants per 10<sup>6</sup> conidia under the optimized conditions. The Δ<em>T. atSp1</em> was successfully validated by PCR analysis. Additionally, two genes of <em>T. atEDG1</em> and <em>T. atchi18</em> were also knocked out and verified, further demonstrating the robustness of this ATMT system. This study provides a stable and efficient genetic manipulation protocol for <em>T. atroviride</em>, facilitating further to understand genes function and biocontrol mechanisms.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107407"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ciliates as next-generation bioindicators in pollution-impacted freshwaters: Integrating community signatures with stress-response endpoints 受污染影响的淡水中作为下一代生物指标的纤毛虫:将群落特征与应激反应端点相结合。
IF 1.9 4区 生物学
Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-29 DOI: 10.1016/j.mimet.2026.107412
Sandeep Antil , Govindhasamay R. Varatharajan , Jean Claude Ndayishimiye , Pascaline Nyirabuhoro , Damir Saldaev , Santosh Kumar , Ravi Toteja , Seema Makhija , Antonietta La Terza , Yuri A. Mazei
{"title":"Ciliates as next-generation bioindicators in pollution-impacted freshwaters: Integrating community signatures with stress-response endpoints","authors":"Sandeep Antil ,&nbsp;Govindhasamay R. Varatharajan ,&nbsp;Jean Claude Ndayishimiye ,&nbsp;Pascaline Nyirabuhoro ,&nbsp;Damir Saldaev ,&nbsp;Santosh Kumar ,&nbsp;Ravi Toteja ,&nbsp;Seema Makhija ,&nbsp;Antonietta La Terza ,&nbsp;Yuri A. Mazei","doi":"10.1016/j.mimet.2026.107412","DOIUrl":"10.1016/j.mimet.2026.107412","url":null,"abstract":"<div><div>Aquatic ecosystems are increasingly threatened by diverse pollutants that compromise ecological integrity and impair ecosystem functioning. Conventional physicochemical monitoring methods are insufficient to detect early biological responses or cumulative stress. Bioindicators offer a biologically integrative, cost-effective, and ecologically meaningful alternative. This review synthesizes current knowledge on established and emerging bioindicator groups, with a critical appraisal of ciliates (Phylum Ciliophora), whose short generation times, trophic versatility, and suitability for both morphological and molecular assays position them as promising next-generation indicators of freshwater ecosystem health. We identify a clear research gap: although numerous primary studies document dose-dependent cytotoxic, oxidative-stress, and behavioural responses in ciliates, but no comprehensive review has consolidated these findings or outlined how ciliates can be operationalized in biomonitoring frameworks. The objectives of this review are to (i) compile and evaluate ciliate-based assays ranging from microscopy to qRT-PCR and multi-omics approaches, (ii) compare ciliates with other bioindicator taxa, and (iii) introduce a novel, empirically testable Ciliate Community Index (CCI) that integrates community composition, morphological integrity, and fold-change–based molecular biomarker responses into a single, unified assessment framework. Literature synthesis reveals consistent early-warning signals, such as motility impairment, vacuolization, and antioxidant responses, demonstrating the feasibility of multi-tiered monitoring while also underscoring the need for standardized protocols and field validation. We conclude that, with appropriate calibration and methodological harmonization, the CCI has strong potential to serve as a sensitive and scalable tool for assessing metal-impacted freshwater ecosystems.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107412"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146097179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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