Suzanne L. Warring, Hazel M. Sisson, Peter C. Fineran, Mojgan Rabiey
{"title":"Strategies for the biocontrol Pseudomonas infections pre-fruit harvest","authors":"Suzanne L. Warring, Hazel M. Sisson, Peter C. Fineran, Mojgan Rabiey","doi":"10.1111/1751-7915.70017","DOIUrl":"10.1111/1751-7915.70017","url":null,"abstract":"<p>The efficiency of global crop production is under threat from microbial pathogens which is likely to be worsened by climate change. Major contributors to plant disease are <i>Pseudomonas syringae</i> (<i>P. syringae</i>) pathovars which affect a variety of important crops. This opinion piece focuses on <i>P. syringae</i> pathovars <i>actinidiae</i> and <i>syringae</i>, which affect kiwifruit and stone fruits, respectively. We discuss some of the current control strategies for these pathogens and highlight recent research developments in combined biocontrol agents such as bacteriophages and combinations of bacteriophages with known anti-microbials such as antibiotics and bacteriocins.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 10","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370446","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}
Phuong Ha Vu, Dang Huy Nguyen, Tung Son Vu, Anh Hien Le, Trang Quynh Thi Tran, Yen Thi Nguyen, Thuy Thu Thi Nguyen, Linh Dam Thi Mai, Ha Viet Thi Bui, Hanh My Tran, Huy Quang Nguyen, Thao Kim Nu Nguyen, Bao Gia Truong, Huyen Thanh Thi Tran, Hai The Pham
{"title":"Biodegradation of DDT using multi-species mixtures: From genome-mining prediction to practical assessment","authors":"Phuong Ha Vu, Dang Huy Nguyen, Tung Son Vu, Anh Hien Le, Trang Quynh Thi Tran, Yen Thi Nguyen, Thuy Thu Thi Nguyen, Linh Dam Thi Mai, Ha Viet Thi Bui, Hanh My Tran, Huy Quang Nguyen, Thao Kim Nu Nguyen, Bao Gia Truong, Huyen Thanh Thi Tran, Hai The Pham","doi":"10.1111/1751-7915.70021","DOIUrl":"10.1111/1751-7915.70021","url":null,"abstract":"<p>DDT (dichlorodiphenyltrichloroethane) is a commonly used insecticide that is recalcitrant and highly stable in the environment. Currently, DDT residue contamination, especially in agricultural soil, is still a concern in many countries, threatening human health and the environment. Among the approaches to resolve such an issue, novel biodegradation-based methods are now preferred to physicochemical methods, due to the sustainability and the effectiveness of the former. In this study, we explored the possibility of building mixed microbial cultures that can offer improved DDT-degrading efficiencies and be more environmentally transilient, based on genome annotation using the KEGG database and prediction of interactions between single strains using the obtained metabolic maps. We then proposed 10 potential DDT-degrading mixed cultures of different strain combinations and evaluated their DDT degradation performances in liquid, semi-solid and solid media. The results demonstrated the superiority of the mixtures over the single strains in terms of degrading DDT, particularly in a semi-solid medium, with up to 40–50% more efficiency. Not only did the mixed cultures degrade DDT more efficiently, but they also adapted to broader spectra of environmental conditions. The three best DDT-degrading and transilient mixtures were selected, and it turned out that their component strains seemed to have more metabolic interactions than those in the other mixtures. Thus, our study demonstrates the effectiveness of exploiting genome-mining techniques and the use of constructed mixed cultures in improving biodegradation.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306801","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}
Aaron Yip, Owen D. McArthur, Kalista C. Ho, Marc G. Aucoin, Brian P. Ingalls
{"title":"Degradation of polyethylene terephthalate (PET) plastics by wastewater bacteria engineered via conjugation","authors":"Aaron Yip, Owen D. McArthur, Kalista C. Ho, Marc G. Aucoin, Brian P. Ingalls","doi":"10.1111/1751-7915.70015","DOIUrl":"10.1111/1751-7915.70015","url":null,"abstract":"<p>Wastewater treatment plants are one of the major pathways for microplastics to enter the environment. In general, microplastics are contaminants of global concern that pose risks to ecosystems and human health. Here, we present a proof-of-concept for reduction of microplastic pollution emitted from wastewater treatment plants: delivery of recombinant DNA to bacteria in wastewater to enable degradation of polyethylene terephthalate (PET). Using a broad-host-range conjugative plasmid, we enabled various bacterial species from a municipal wastewater sample to express FAST-PETase, which was released into the extracellular environment. We found that FAST-PETase purified from some transconjugant isolates could degrade about 40% of a 0.25 mm thick commercial PET film within 4 days at 50°C. We then demonstrated partial degradation of a post-consumer PET product over 5–7 days by exposure to conditioned media from isolates. These results have broad implications for addressing the global plastic pollution problem by enabling environmental bacteria to degrade PET.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A novel DNA damage detection method based on a distinct DNA damage response system","authors":"Shitong Zhong, Shuang Song, Linjia Wang, Yufeng Liu, Hong Xu, Liangyan Wang, Huizhi Lu, Yuejin Hua","doi":"10.1111/1751-7915.70008","DOIUrl":"https://doi.org/10.1111/1751-7915.70008","url":null,"abstract":"<p>DNA damage occurs when cells encounter exogenous and endogenous stresses such as long periods of desiccation, ionizing radiation and genotoxic chemicals. Efforts have been made to detect DNA damage in vivo and in vitro to characterize or quantify the damage level. It is well accepted that single-stranded DNA (ssDNA) is one of the important byproducts of DNA damage to trigger the downstream regulation. A recent study has revealed that PprI efficiently recognizes ssDNA and cleaves DdrO at a specific site on the cleavage site region (CSR) loop in the presence of ssDNA, which enables the radiation resistance of <i>Deinococcus</i>. Leveraging this property, we developed a quantitative DNA damage detection method in vitro based on fluorescence resonance energy transfer (FRET). DdrO protein was fused with eYFP and eCFP on the N-terminal and C-terminal respectively, between which the FRET efficiency serves as an indicator of cleavage efficiency as well as the concentration of ssDNA. The standard curve between the concentration of ssDNA and the FRET efficiency was constructed, and application examples were tested, validating the effectiveness of this method.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142244541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A novel DNA damage detection method based on a distinct DNA damage response system","authors":"Shitong Zhong, Shuang Song, Linjia Wang, Yufeng Liu, Hong Xu, Liangyan Wang, Huizhi Lu, Yuejin Hua","doi":"10.1111/1751-7915.70008","DOIUrl":"https://doi.org/10.1111/1751-7915.70008","url":null,"abstract":"<p>DNA damage occurs when cells encounter exogenous and endogenous stresses such as long periods of desiccation, ionizing radiation and genotoxic chemicals. Efforts have been made to detect DNA damage in vivo and in vitro to characterize or quantify the damage level. It is well accepted that single-stranded DNA (ssDNA) is one of the important byproducts of DNA damage to trigger the downstream regulation. A recent study has revealed that PprI efficiently recognizes ssDNA and cleaves DdrO at a specific site on the cleavage site region (CSR) loop in the presence of ssDNA, which enables the radiation resistance of <i>Deinococcus</i>. Leveraging this property, we developed a quantitative DNA damage detection method in vitro based on fluorescence resonance energy transfer (FRET). DdrO protein was fused with eYFP and eCFP on the N-terminal and C-terminal respectively, between which the FRET efficiency serves as an indicator of cleavage efficiency as well as the concentration of ssDNA. The standard curve between the concentration of ssDNA and the FRET efficiency was constructed, and application examples were tested, validating the effectiveness of this method.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142244527","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}
Indra Roux, Clara Woodcraft, Nicolau Sbaraini, Amy Pepper, Emily Wong, Joe Bracegirdle, Yit-Heng Chooi
{"title":"Next-generation AMA1-based plasmids for enhanced heterologous expression in filamentous fungi","authors":"Indra Roux, Clara Woodcraft, Nicolau Sbaraini, Amy Pepper, Emily Wong, Joe Bracegirdle, Yit-Heng Chooi","doi":"10.1111/1751-7915.70010","DOIUrl":"https://doi.org/10.1111/1751-7915.70010","url":null,"abstract":"<p>Episomal AMA1-based plasmids are increasingly used for expressing biosynthetic pathways and CRISPR/Cas systems in filamentous fungi cell factories due to their high transformation efficiency and multicopy nature. However, the gene expression from AMA1 plasmids has been observed to be highly heterogeneous in growing mycelia. To overcome this limitation, here we developed next-generation AMA1-based plasmids that ensure homogeneous and strong expression. We achieved this by evaluating various degradation tags fused to the auxotrophic marker gene on the AMA1 plasmid, which introduces a more stringent selection pressure throughout multicellular fungal growth. With these improved plasmids, we observed in <i>Aspergillus nidulans</i> a 5-fold increase in the expression of a fluorescent reporter, a doubling in the efficiency of a CRISPRa system for genome mining, and a up to a 10-fold increase in the production of heterologous natural product metabolites. This strategy has the potential to be applied to diverse filamentous fungi.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233122","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}
Indra Roux, Clara Woodcraft, Nicolau Sbaraini, Amy Pepper, Emily Wong, Joe Bracegirdle, Yit-Heng Chooi
{"title":"Next-generation AMA1-based plasmids for enhanced heterologous expression in filamentous fungi","authors":"Indra Roux, Clara Woodcraft, Nicolau Sbaraini, Amy Pepper, Emily Wong, Joe Bracegirdle, Yit-Heng Chooi","doi":"10.1111/1751-7915.70010","DOIUrl":"https://doi.org/10.1111/1751-7915.70010","url":null,"abstract":"<p>Episomal AMA1-based plasmids are increasingly used for expressing biosynthetic pathways and CRISPR/Cas systems in filamentous fungi cell factories due to their high transformation efficiency and multicopy nature. However, the gene expression from AMA1 plasmids has been observed to be highly heterogeneous in growing mycelia. To overcome this limitation, here we developed next-generation AMA1-based plasmids that ensure homogeneous and strong expression. We achieved this by evaluating various degradation tags fused to the auxotrophic marker gene on the AMA1 plasmid, which introduces a more stringent selection pressure throughout multicellular fungal growth. With these improved plasmids, we observed in <i>Aspergillus nidulans</i> a 5-fold increase in the expression of a fluorescent reporter, a doubling in the efficiency of a CRISPRa system for genome mining, and a up to a 10-fold increase in the production of heterologous natural product metabolites. This strategy has the potential to be applied to diverse filamentous fungi.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233209","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}
Marcel Rüllke, Franziska Meyer, Kevin Schmitz, Hannes Blase, Elisabeth Tamayo, J. Philipp Benz
{"title":"A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi","authors":"Marcel Rüllke, Franziska Meyer, Kevin Schmitz, Hannes Blase, Elisabeth Tamayo, J. Philipp Benz","doi":"10.1111/1751-7915.70012","DOIUrl":"https://doi.org/10.1111/1751-7915.70012","url":null,"abstract":"<p>Filamentous fungi with their diverse inventory of carbohydrate-active enzymes promise a holistic usage of lignocellulosic residues. A major challenge for application is the inherent repression of enzyme production by carbon catabolite repression (CCR). In the presence of preferred carbon sources, the transcription factor CreA/CRE-1 binds to specific but conserved motifs in promoters of genes involved in sugar metabolism, but the status of CCR is notoriously difficult to quantify. To allow for a real-time evaluation of CreA/CRE-1-mediated CCR at the transcriptional level, we developed a luciferase-based construct, representing a dynamic, highly responsive reporter system that is inhibited by monosaccharides in a quantitative fashion. Using this tool, CreA/CRE-1-dependent CCR triggered by several monosaccharides could be measured in <i>Neurospora crassa</i>, <i>Aspergillus niger</i> and <i>Aspergillus nidulans</i> over the course of hours, demonstrating distinct and dynamic regulatory processes. Furthermore, we used the reporter to visualize the direct impacts of multiple CreA truncations on CCR induction. Our reporter thus offers a widely applicable quantitative approach to evaluate CreA/CRE-1-mediated CCR across diverse fungal species and will help to elucidate the multifaceted effects of CCR on fungal physiology for both basic research and industrial strain engineering endeavours.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142231039","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}
Marcel Rüllke, Franziska Meyer, Kevin Schmitz, Hannes Blase, Elisabeth Tamayo, J. Philipp Benz
{"title":"A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi","authors":"Marcel Rüllke, Franziska Meyer, Kevin Schmitz, Hannes Blase, Elisabeth Tamayo, J. Philipp Benz","doi":"10.1111/1751-7915.70012","DOIUrl":"https://doi.org/10.1111/1751-7915.70012","url":null,"abstract":"<p>Filamentous fungi with their diverse inventory of carbohydrate-active enzymes promise a holistic usage of lignocellulosic residues. A major challenge for application is the inherent repression of enzyme production by carbon catabolite repression (CCR). In the presence of preferred carbon sources, the transcription factor CreA/CRE-1 binds to specific but conserved motifs in promoters of genes involved in sugar metabolism, but the status of CCR is notoriously difficult to quantify. To allow for a real-time evaluation of CreA/CRE-1-mediated CCR at the transcriptional level, we developed a luciferase-based construct, representing a dynamic, highly responsive reporter system that is inhibited by monosaccharides in a quantitative fashion. Using this tool, CreA/CRE-1-dependent CCR triggered by several monosaccharides could be measured in <i>Neurospora crassa</i>, <i>Aspergillus niger</i> and <i>Aspergillus nidulans</i> over the course of hours, demonstrating distinct and dynamic regulatory processes. Furthermore, we used the reporter to visualize the direct impacts of multiple CreA truncations on CCR induction. Our reporter thus offers a widely applicable quantitative approach to evaluate CreA/CRE-1-mediated CCR across diverse fungal species and will help to elucidate the multifaceted effects of CCR on fungal physiology for both basic research and industrial strain engineering endeavours.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142231040","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}
Aya Brill, Barak Menagen, Einav Malach, Einat Zelinger, David Avnir, Saul Burdman, Zvi Hayouka
{"title":"Entrapment of antimicrobial compounds in a metal matrix for crop protection","authors":"Aya Brill, Barak Menagen, Einav Malach, Einat Zelinger, David Avnir, Saul Burdman, Zvi Hayouka","doi":"10.1111/1751-7915.70005","DOIUrl":"https://doi.org/10.1111/1751-7915.70005","url":null,"abstract":"<p>Agricultural yields are often limited by damage caused by pathogenic microorganisms, including plant-pathogenic bacteria. The chemical control options to cope with bacterial diseases in agriculture are limited, predominantly relying on copper-based products. These compounds, however, possess limited efficacy. Therefore, there is an urgent need to develop novel technologies to manage bacterial plant diseases and reduce food loss. In this study, a new antimicrobial agent was developed using a doping method that entraps small bioactive organic molecules inside copper as the metal matrix. The food preservative agent lauroyl arginate ethyl ester (ethyl lauroyl arginate; LAE) was chosen as the doped organic compound. The new composites were termed LAE@[Cu]. Bactericidal assays against <i>Acidovorax citrulli</i>, a severe plant pathogen, revealed that LAE and copper in the composites possess a synergistic interaction as compared with each component individually. LAE@[Cu] composites were further characterised in terms of chemical properties and in planta assays demonstrated their potential for further development as crop protection agents.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142231038","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}