Pub Date : 2024-03-26DOI: 10.3390/applmicrobiol4020042
Danielle L. Peters, Bassel Akache, Wangxue Chen, M. McCluskie
The extremophile Halobacterium salinarum is an aerobic archaeon that has adapted to thrive in high-salt environments such as salted fish, hypersaline lakes, and salterns. Halophiles have garnered significant interest due to their unique interactions with bacteriophages known as haloarchaeophages. Studies have identified and characterized prophages in halophilic archaea, such as Haloferax volcanii, Haloquadratum walsbyi, and Haloarcula marismortui. Still, an investigation has yet to be conducted into the presence of prophage elements on Halobacterium salinarum ATCC 33170. This is of particular interest to us as we are using this strain as a source of archaeol, as one of the components of our sulfated lactosyl archaeol (SLA) archaeosome adjuvant. Genomic contigs of strain 33170 were bioinformatically assessed for prophage-like features using BLAST, PHASTER, InterProScan, and PHYRE2. A 7 kb region encoding six genes was identified as an incomplete prophage, and the proteins were further analyzed, revealing high homology to proteins encoded by bacteria, archaea, and an IS200 transposon. Restricting the BLASTp database to viruses resulted in hits to both myo- and siphoviral proteins, which would be unusual for an intact prophage. Additionally, no known phage structural proteins were identified in the search, suggesting a low chance that H. salinarum ATCC 33170 harbors a latent prophage.
{"title":"In Silico Prophage Analysis of Halobacterium salinarum ATCC 33170","authors":"Danielle L. Peters, Bassel Akache, Wangxue Chen, M. McCluskie","doi":"10.3390/applmicrobiol4020042","DOIUrl":"https://doi.org/10.3390/applmicrobiol4020042","url":null,"abstract":"The extremophile Halobacterium salinarum is an aerobic archaeon that has adapted to thrive in high-salt environments such as salted fish, hypersaline lakes, and salterns. Halophiles have garnered significant interest due to their unique interactions with bacteriophages known as haloarchaeophages. Studies have identified and characterized prophages in halophilic archaea, such as Haloferax volcanii, Haloquadratum walsbyi, and Haloarcula marismortui. Still, an investigation has yet to be conducted into the presence of prophage elements on Halobacterium salinarum ATCC 33170. This is of particular interest to us as we are using this strain as a source of archaeol, as one of the components of our sulfated lactosyl archaeol (SLA) archaeosome adjuvant. Genomic contigs of strain 33170 were bioinformatically assessed for prophage-like features using BLAST, PHASTER, InterProScan, and PHYRE2. A 7 kb region encoding six genes was identified as an incomplete prophage, and the proteins were further analyzed, revealing high homology to proteins encoded by bacteria, archaea, and an IS200 transposon. Restricting the BLASTp database to viruses resulted in hits to both myo- and siphoviral proteins, which would be unusual for an intact prophage. Additionally, no known phage structural proteins were identified in the search, suggesting a low chance that H. salinarum ATCC 33170 harbors a latent prophage.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"122 28","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140378832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-25DOI: 10.3390/applmicrobiol4020041
Saja Hamaideh, A. Olaimat, M. Al-Holy, Ahmad Ababneh, H. Shahbaz, M. Abughoush, A. Al-Nabulsi, T. Osaili, M. Ayyash, Richard A. Holley
The transformation of the food chain due to technological advances has had significant implications in regard to food safety. A noteworthy trend in this evolution relates to the emergence of new or previously unseen pathogens within products, thereby altering the landscape of foodborne illness epidemiology. The escalating frequency of these events underscores the need for a comprehensive re-evaluation of preventive strategies. The occurrence of novel species of bacteria, viruses, parasites, and unusual biotoxins from unexpected sources has challenged the previous limits that had been set to prevent foodborne illness outbreaks. The repercussions, ranging from detrimental effects on public health to economic burden, are influenced by a myriad of factors affecting the evolution of foodborne pathogens and emerging ailments. Among these factors are shifts in population demographics and behaviors, especially dietary patterns, as well as climate extremes, advances in more precise pathogen detection, microbial adaptation, evolving agricultural practices, and transformative changes within the food industry. This review critically examines the impact of technological metamorphosis along the food chain, encompassing production, processing, handling, packaging, storage, transportation, and industry demographics on the dynamics influencing the emergence of foodborne pathogens. Additionally, potential solutions to mitigate and manage this escalating issue are proposed.
{"title":"The Influence of Technological Shifts in the Food Chain on the Emergence of Foodborne Pathogens: An Overview","authors":"Saja Hamaideh, A. Olaimat, M. Al-Holy, Ahmad Ababneh, H. Shahbaz, M. Abughoush, A. Al-Nabulsi, T. Osaili, M. Ayyash, Richard A. Holley","doi":"10.3390/applmicrobiol4020041","DOIUrl":"https://doi.org/10.3390/applmicrobiol4020041","url":null,"abstract":"The transformation of the food chain due to technological advances has had significant implications in regard to food safety. A noteworthy trend in this evolution relates to the emergence of new or previously unseen pathogens within products, thereby altering the landscape of foodborne illness epidemiology. The escalating frequency of these events underscores the need for a comprehensive re-evaluation of preventive strategies. The occurrence of novel species of bacteria, viruses, parasites, and unusual biotoxins from unexpected sources has challenged the previous limits that had been set to prevent foodborne illness outbreaks. The repercussions, ranging from detrimental effects on public health to economic burden, are influenced by a myriad of factors affecting the evolution of foodborne pathogens and emerging ailments. Among these factors are shifts in population demographics and behaviors, especially dietary patterns, as well as climate extremes, advances in more precise pathogen detection, microbial adaptation, evolving agricultural practices, and transformative changes within the food industry. This review critically examines the impact of technological metamorphosis along the food chain, encompassing production, processing, handling, packaging, storage, transportation, and industry demographics on the dynamics influencing the emergence of foodborne pathogens. Additionally, potential solutions to mitigate and manage this escalating issue are proposed.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":" 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140384249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-28DOI: 10.3390/applmicrobiol4010031
Jeremy R. Smith, Christine D. Sislak, Pedro Fernandez Mendoza, Laurin Carmichael, Alisha G Lewis, Anqi Chen, G. Jiang, P. Gibney
Plasmid shuttle vectors are a common tool used to study yeast physiology. The majority of yeast plasmids have been optimized for Saccharomyces cerevisiae lab strain compatibility, relying on auxotrophic complementation as their selective property. We sought to construct a series of plasmid shuttle vectors to extend functionality beyond strains with auxotrophic requirements, and test compatibility across a diverse panel of yeasts. We constructed 18 plasmids which were successfully maintained by yeasts from several genera. From a panel of 24 yeast strains, these plasmids were maintained by 18 yeasts, spanning 11 species within the genera Lachancea, Metschnikowia, Pichia, Saccharomyces, and Torulaspora. Additionally, an integrated gene expression reporter was assayed for functional compatibility with the 18 strains. Plasmid-derived gene expression was observed for 13 strains, spanning five species within the Saccharomyces genus, in addition to Torulaspora delbrueckii. These results indicate that this plasmid series is broadly useful for advancements and applications within academia, biotechnology, and the food and fermentation industries for research utilizing diverse Saccharomyces and non-Saccharomyces yeasts.
{"title":"Auxotrophy-Independent Plasmid Shuttle Vectors for Applications in Diverse Yeasts","authors":"Jeremy R. Smith, Christine D. Sislak, Pedro Fernandez Mendoza, Laurin Carmichael, Alisha G Lewis, Anqi Chen, G. Jiang, P. Gibney","doi":"10.3390/applmicrobiol4010031","DOIUrl":"https://doi.org/10.3390/applmicrobiol4010031","url":null,"abstract":"Plasmid shuttle vectors are a common tool used to study yeast physiology. The majority of yeast plasmids have been optimized for Saccharomyces cerevisiae lab strain compatibility, relying on auxotrophic complementation as their selective property. We sought to construct a series of plasmid shuttle vectors to extend functionality beyond strains with auxotrophic requirements, and test compatibility across a diverse panel of yeasts. We constructed 18 plasmids which were successfully maintained by yeasts from several genera. From a panel of 24 yeast strains, these plasmids were maintained by 18 yeasts, spanning 11 species within the genera Lachancea, Metschnikowia, Pichia, Saccharomyces, and Torulaspora. Additionally, an integrated gene expression reporter was assayed for functional compatibility with the 18 strains. Plasmid-derived gene expression was observed for 13 strains, spanning five species within the Saccharomyces genus, in addition to Torulaspora delbrueckii. These results indicate that this plasmid series is broadly useful for advancements and applications within academia, biotechnology, and the food and fermentation industries for research utilizing diverse Saccharomyces and non-Saccharomyces yeasts.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"81 13","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140423641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-27DOI: 10.3390/applmicrobiol4010030
Andrew M. Scollon, Haiqiang Wang, E. Ryser
This study assessed the extent of L. monocytogenes transfer from onions to the surface of a commercial dicer, from inoculated onions to uninoculated onions, and the efficacy of various sanitizers during the subsequent flume washing of diced onions. Spanish yellow onions (Allium cepa L.) were dip-inoculated in a 3-strain avirulent L. monocytogenes cocktail (5.9 or 4.2 log CFU/50 g) and air-dried. After dicing one 2.2 kg batch of onions inoculated at ~5.9 log CFU/50 g followed by ten uninoculated batches of 2.2 kg each, L. monocytogenes progressively decreased from 4.6 to 2.6 log CFU/50 g in baches 1 through 10, respectively. After onions inoculated at ~4.0 log CFU/g were diced and flume washed for 2 min in tap water, electrolyzed water containing 55 ppm free chlorine, 80 ppm free chlorine from a commercial sanitizer, or 80 ppm peroxyacetic acid and dewatered on a mechanical shaker table, L. monocytogenes populations decreased 0.4, 0.3, 1.4, and 1.0 log, respectively, with populations of ~1.2 log CFU/mL in water for all three sanitizers. These findings should be useful in future risk assessments and aid in the development of improved industry guidelines to better enhance the safety of diced onions.
{"title":"Transfer and Inactivation of Listeria monocytogenes during Pilot-Scale Dicing and Flume Washing of Onions","authors":"Andrew M. Scollon, Haiqiang Wang, E. Ryser","doi":"10.3390/applmicrobiol4010030","DOIUrl":"https://doi.org/10.3390/applmicrobiol4010030","url":null,"abstract":"This study assessed the extent of L. monocytogenes transfer from onions to the surface of a commercial dicer, from inoculated onions to uninoculated onions, and the efficacy of various sanitizers during the subsequent flume washing of diced onions. Spanish yellow onions (Allium cepa L.) were dip-inoculated in a 3-strain avirulent L. monocytogenes cocktail (5.9 or 4.2 log CFU/50 g) and air-dried. After dicing one 2.2 kg batch of onions inoculated at ~5.9 log CFU/50 g followed by ten uninoculated batches of 2.2 kg each, L. monocytogenes progressively decreased from 4.6 to 2.6 log CFU/50 g in baches 1 through 10, respectively. After onions inoculated at ~4.0 log CFU/g were diced and flume washed for 2 min in tap water, electrolyzed water containing 55 ppm free chlorine, 80 ppm free chlorine from a commercial sanitizer, or 80 ppm peroxyacetic acid and dewatered on a mechanical shaker table, L. monocytogenes populations decreased 0.4, 0.3, 1.4, and 1.0 log, respectively, with populations of ~1.2 log CFU/mL in water for all three sanitizers. These findings should be useful in future risk assessments and aid in the development of improved industry guidelines to better enhance the safety of diced onions.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140425511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-21DOI: 10.3390/applmicrobiol4010029
S. Ankathi, Utkarsh S. Chaudhari, Robert M. Handler, David R. Shonnard
Anaerobic digestion (AD) involves a set of microbiological reactions and physio-chemical processes to generate biogas, a mixture of predominantly CH4 and CO2. It is commercialized globally; however, AD has limited commercial applications in the U.S. compared to other regions of the world. The main objective of this article is to review different studies on socio-economic and environmental aspects and policies of biogas/biomethane production and to focus on resource availability. The key outcome from this review shows that the anaerobic digestion of food waste and animal manure has great potential to achieve economic and environmental benefits compared to other waste management techniques such as landfilling or conventional manure management. The 12 life cycle assessment (LCA) studies reviewed showed lower impacts for biogas systems and indicated a need for standardization of methodology so that alternative production concepts can be objectively compared. Similarly, economic analyses showed higher profitability for a biogas combined heat and power facility compared to a biomethane facility. By considering a review of the sustainability of biogas, we presented a new multi-criteria sustainable assessment framework that includes three domains: i. resource availability and logistics, ii. process modeling, and iii. impact assessment with primary application to the optimum location and installation of sustainable biogas/biomethane plants in the U.S.
厌氧消化（AD）涉及一系列微生物反应和物理化学过程，以产生沼气（主要是 CH4 和 CO2 的混合物）。厌氧消化已在全球实现商业化，但与世界其他地区相比，厌氧消化在美国的商业应用有限。本文的主要目的是回顾有关沼气/生物甲烷生产的社会经济和环境方面及政策的不同研究，并重点关注资源可用性。综述的主要结果表明，与填埋或传统粪便管理等其他废物管理技术相比，厌氧消化食物垃圾和动物粪便在实现经济和环境效益方面具有巨大潜力。所审查的 12 项生命周期评估（LCA）研究表明，沼气系统受到的影响较小，并指出有必要实现方法标准化，以便客观地比较替代生产概念。同样，经济分析表明，与生物甲烷设施相比，沼气热电联产设施的盈利能力更高。通过对沼气可持续性的审查，我们提出了一个新的多标准可持续评估框架，其中包括三个领域：i. 资源可用性和物流；ii. 过程建模；iii. 影响评估，主要应用于美国可持续沼气/生物甲烷工厂的最佳选址和安装。
{"title":"Sustainability of Biogas Production from Anaerobic Digestion of Food Waste and Animal Manure","authors":"S. Ankathi, Utkarsh S. Chaudhari, Robert M. Handler, David R. Shonnard","doi":"10.3390/applmicrobiol4010029","DOIUrl":"https://doi.org/10.3390/applmicrobiol4010029","url":null,"abstract":"Anaerobic digestion (AD) involves a set of microbiological reactions and physio-chemical processes to generate biogas, a mixture of predominantly CH4 and CO2. It is commercialized globally; however, AD has limited commercial applications in the U.S. compared to other regions of the world. The main objective of this article is to review different studies on socio-economic and environmental aspects and policies of biogas/biomethane production and to focus on resource availability. The key outcome from this review shows that the anaerobic digestion of food waste and animal manure has great potential to achieve economic and environmental benefits compared to other waste management techniques such as landfilling or conventional manure management. The 12 life cycle assessment (LCA) studies reviewed showed lower impacts for biogas systems and indicated a need for standardization of methodology so that alternative production concepts can be objectively compared. Similarly, economic analyses showed higher profitability for a biogas combined heat and power facility compared to a biomethane facility. By considering a review of the sustainability of biogas, we presented a new multi-criteria sustainable assessment framework that includes three domains: i. resource availability and logistics, ii. process modeling, and iii. impact assessment with primary application to the optimum location and installation of sustainable biogas/biomethane plants in the U.S.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"65 S1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140444719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-20DOI: 10.3390/applmicrobiol4010028
Abigail M. Jones, Kyle A. Davis, D. Panaccione
Ergot alkaloids are fungal natural products with important roles in agriculture and medicine. We used heterologous expression and gene knockout approaches to investigate potential roles for the product of a major facilitator superfamily transporter gene (easT) recently found in an ergot alkaloid biosynthetic gene cluster in Aspergillus leporis. A strain of Aspergillus fumigatus previously engineered to accumulate lysergic acid, but which did not convert the precursor agroclavine to lysergic acid efficiently or secrete lysergic acid well, was chosen as an expression host for easT. Expression of easT in this strain resulted in accumulation of significantly more pathway intermediates but no detectable lysergic acid. Secretion of ergot alkaloids was reduced in the easT-expressing strain. EasT localized to discrete vesicle-like structures in the cytosol of A. fumigatus, with no localization detected in the plasma membrane. When easT was knocked out in A. leporis, accumulation of lysergic acid amides was reduced relative to the wild type. There was no negative effect on secretion of ergot alkaloids in the knockout mutant. The data indicate that easT encodes a product that contributes to accumulation of ergot alkaloids, perhaps by transporting intermediates between cellular compartments, but does not have a significant role in secreting ergot alkaloids.
麦角生物碱是真菌天然产物，在农业和医药领域具有重要作用。我们使用异源表达和基因敲除方法研究了最近在雷伯曲霉（Aspergillus leporis）麦角生物碱生物合成基因簇中发现的主要促进剂超家族转运体基因（easT）的产物的潜在作用。我们选择了一株以前被设计为能积累麦角酸但不能有效地将前体农醉素转化为麦角酸或不能很好地分泌麦角酸的烟曲霉作为 easT 的表达宿主。在该菌株中表达 easT 会导致积累更多的途径中间产物，但却检测不到麦角酸。在表达 easT 的菌株中，麦角生物碱的分泌减少。EasT 定位于烟曲霉细胞质中离散的囊泡状结构中，在质膜中未检测到定位。当 EasT 被敲除后，麦角酰酰胺的积累相对于野生型有所减少。敲除突变体对麦角生物碱的分泌没有负面影响。这些数据表明，easT 编码的产物有助于麦角生物碱的积累，可能是通过在细胞区间运输中间产物，但在分泌麦角生物碱方面作用不大。
{"title":"A Major Facilitator Superfamily Transporter Contributes to Ergot Alkaloid Accumulation but Not Secretion in Aspergillus leporis","authors":"Abigail M. Jones, Kyle A. Davis, D. Panaccione","doi":"10.3390/applmicrobiol4010028","DOIUrl":"https://doi.org/10.3390/applmicrobiol4010028","url":null,"abstract":"Ergot alkaloids are fungal natural products with important roles in agriculture and medicine. We used heterologous expression and gene knockout approaches to investigate potential roles for the product of a major facilitator superfamily transporter gene (easT) recently found in an ergot alkaloid biosynthetic gene cluster in Aspergillus leporis. A strain of Aspergillus fumigatus previously engineered to accumulate lysergic acid, but which did not convert the precursor agroclavine to lysergic acid efficiently or secrete lysergic acid well, was chosen as an expression host for easT. Expression of easT in this strain resulted in accumulation of significantly more pathway intermediates but no detectable lysergic acid. Secretion of ergot alkaloids was reduced in the easT-expressing strain. EasT localized to discrete vesicle-like structures in the cytosol of A. fumigatus, with no localization detected in the plasma membrane. When easT was knocked out in A. leporis, accumulation of lysergic acid amides was reduced relative to the wild type. There was no negative effect on secretion of ergot alkaloids in the knockout mutant. The data indicate that easT encodes a product that contributes to accumulation of ergot alkaloids, perhaps by transporting intermediates between cellular compartments, but does not have a significant role in secreting ergot alkaloids.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"485 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140446641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-13DOI: 10.3390/applmicrobiol4010026
Navya Kommu, P. Stothard, Christian Chukwujindu, A. Pathak, Ashvini Chauhan
Soils and sediments from the Savannah River Site (SRS), located in the USA are known to have a long history of co-contamination with radionuclides (mainly uranium) and heavy metals. To better understand the bacterial taxonomic and genomic characteristic of the SRS soil habitat, shotgun metagenomes were obtained from three different levels of contaminated soil—high, medium, and low. Sequences were then assembled and annotated to generate metagenome-assembled genomes (MAGs) using toolkits within the nf-core/mag. The initial analysis resulted in a total of 254 MAGs. After bin refinement and de-replication, 55 MAGs which met the quality standard with a completeness > 75% and contamination < 25%, accounting for 21.67% of all the MAGs, were reconstructed. Further refinement with completeness > 90% and contamination < 10% yielded 24 MAGs (18 from the winter season and 6 from the summer season) spanning 6 bacterial phyla, predominantly Actinomycetota, Proteobacteriota, Bacteroidota, and Cyanobacteria. Overall, the Arthrobacter MAG was found to be robust for further analysis, with over 1749 genes putatively involved in the crucial metabolism of elements viz. nitrogen, phosphorous, and sulfur, and 598 genes encoding enzymes for the resistance of metals including cadmium, zinc, chromium, arsenic, and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium-contaminated soils.
{"title":"Utilizing a Metagenome Assembled Genome Approach Revealed Further Insights into Microbially Mediated Heavy-Metal Resistance in Soils from a Former Nuclear Materials Production Facility","authors":"Navya Kommu, P. Stothard, Christian Chukwujindu, A. Pathak, Ashvini Chauhan","doi":"10.3390/applmicrobiol4010026","DOIUrl":"https://doi.org/10.3390/applmicrobiol4010026","url":null,"abstract":"Soils and sediments from the Savannah River Site (SRS), located in the USA are known to have a long history of co-contamination with radionuclides (mainly uranium) and heavy metals. To better understand the bacterial taxonomic and genomic characteristic of the SRS soil habitat, shotgun metagenomes were obtained from three different levels of contaminated soil—high, medium, and low. Sequences were then assembled and annotated to generate metagenome-assembled genomes (MAGs) using toolkits within the nf-core/mag. The initial analysis resulted in a total of 254 MAGs. After bin refinement and de-replication, 55 MAGs which met the quality standard with a completeness > 75% and contamination < 25%, accounting for 21.67% of all the MAGs, were reconstructed. Further refinement with completeness > 90% and contamination < 10% yielded 24 MAGs (18 from the winter season and 6 from the summer season) spanning 6 bacterial phyla, predominantly Actinomycetota, Proteobacteriota, Bacteroidota, and Cyanobacteria. Overall, the Arthrobacter MAG was found to be robust for further analysis, with over 1749 genes putatively involved in the crucial metabolism of elements viz. nitrogen, phosphorous, and sulfur, and 598 genes encoding enzymes for the resistance of metals including cadmium, zinc, chromium, arsenic, and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium-contaminated soils.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"99 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139840199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-13DOI: 10.3390/applmicrobiol4010026
Navya Kommu, P. Stothard, Christian Chukwujindu, A. Pathak, Ashvini Chauhan
Soils and sediments from the Savannah River Site (SRS), located in the USA are known to have a long history of co-contamination with radionuclides (mainly uranium) and heavy metals. To better understand the bacterial taxonomic and genomic characteristic of the SRS soil habitat, shotgun metagenomes were obtained from three different levels of contaminated soil—high, medium, and low. Sequences were then assembled and annotated to generate metagenome-assembled genomes (MAGs) using toolkits within the nf-core/mag. The initial analysis resulted in a total of 254 MAGs. After bin refinement and de-replication, 55 MAGs which met the quality standard with a completeness > 75% and contamination < 25%, accounting for 21.67% of all the MAGs, were reconstructed. Further refinement with completeness > 90% and contamination < 10% yielded 24 MAGs (18 from the winter season and 6 from the summer season) spanning 6 bacterial phyla, predominantly Actinomycetota, Proteobacteriota, Bacteroidota, and Cyanobacteria. Overall, the Arthrobacter MAG was found to be robust for further analysis, with over 1749 genes putatively involved in the crucial metabolism of elements viz. nitrogen, phosphorous, and sulfur, and 598 genes encoding enzymes for the resistance of metals including cadmium, zinc, chromium, arsenic, and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium-contaminated soils.
{"title":"Utilizing a Metagenome Assembled Genome Approach Revealed Further Insights into Microbially Mediated Heavy-Metal Resistance in Soils from a Former Nuclear Materials Production Facility","authors":"Navya Kommu, P. Stothard, Christian Chukwujindu, A. Pathak, Ashvini Chauhan","doi":"10.3390/applmicrobiol4010026","DOIUrl":"https://doi.org/10.3390/applmicrobiol4010026","url":null,"abstract":"Soils and sediments from the Savannah River Site (SRS), located in the USA are known to have a long history of co-contamination with radionuclides (mainly uranium) and heavy metals. To better understand the bacterial taxonomic and genomic characteristic of the SRS soil habitat, shotgun metagenomes were obtained from three different levels of contaminated soil—high, medium, and low. Sequences were then assembled and annotated to generate metagenome-assembled genomes (MAGs) using toolkits within the nf-core/mag. The initial analysis resulted in a total of 254 MAGs. After bin refinement and de-replication, 55 MAGs which met the quality standard with a completeness > 75% and contamination < 25%, accounting for 21.67% of all the MAGs, were reconstructed. Further refinement with completeness > 90% and contamination < 10% yielded 24 MAGs (18 from the winter season and 6 from the summer season) spanning 6 bacterial phyla, predominantly Actinomycetota, Proteobacteriota, Bacteroidota, and Cyanobacteria. Overall, the Arthrobacter MAG was found to be robust for further analysis, with over 1749 genes putatively involved in the crucial metabolism of elements viz. nitrogen, phosphorous, and sulfur, and 598 genes encoding enzymes for the resistance of metals including cadmium, zinc, chromium, arsenic, and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium-contaminated soils.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139780476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-12DOI: 10.3390/applmicrobiol4010024
Jong-Gyu Kim, Jeong-Yeong Park
Background: Meju is a base material for making soy sauce, soybean paste, and red chili pepper paste, which are representative ingredients of Korean cuisine. Objectives: This study aimed to isolate a predominant bacterial strain of B. subtilis from meju and to observe its inhibitory effects on an aflatoxigenic mold. Methods: We used yellow soybeans (Glycine mar (L) Mert) grown in South Korea, and meju was produced according to the recommended methods of the Korea Food Research Institute. The identification of the strain was conducted based on its morphological and biochemical characteristics and 16S rDNA sequence. Evaluation of the bacterial effect against A. parasiticus ATCC 15517 was done in yeast extract–sucrose broth at 28 °C. Its inhibitory effect was evaluated using two approaches: mycelial weight and aflatoxin production. Aflatoxins were determined using high-performance liquid chromatography. Results: In the meju samples fermented for three months, a B. subtilis strain, K-0924 was identified. At the end of the incubation period of A. parasiticus, dry mycelial weight was significantly reduced by more than 80% (p < 0.01) and total aflatoxin production was inhibited by more than 63% (p < 0.05) in the presence of B. subtilis. Conclusions: These results indicate that B. subtilis K-0924 inhibits the growth and aflatoxin production of toxigenic Aspergillus, which can be contaminated with meju. We could expect more inhibition by other bacteria related to fermentation of meju, and further examination is necessary on species other than B. subtilis.
{"title":"Inhibitory Effects of Bacillus subtilis Isolated from Meju (Fermented Soybean Brick) on the Growth of Aspergillus parasiticus","authors":"Jong-Gyu Kim, Jeong-Yeong Park","doi":"10.3390/applmicrobiol4010024","DOIUrl":"https://doi.org/10.3390/applmicrobiol4010024","url":null,"abstract":"Background: Meju is a base material for making soy sauce, soybean paste, and red chili pepper paste, which are representative ingredients of Korean cuisine. Objectives: This study aimed to isolate a predominant bacterial strain of B. subtilis from meju and to observe its inhibitory effects on an aflatoxigenic mold. Methods: We used yellow soybeans (Glycine mar (L) Mert) grown in South Korea, and meju was produced according to the recommended methods of the Korea Food Research Institute. The identification of the strain was conducted based on its morphological and biochemical characteristics and 16S rDNA sequence. Evaluation of the bacterial effect against A. parasiticus ATCC 15517 was done in yeast extract–sucrose broth at 28 °C. Its inhibitory effect was evaluated using two approaches: mycelial weight and aflatoxin production. Aflatoxins were determined using high-performance liquid chromatography. Results: In the meju samples fermented for three months, a B. subtilis strain, K-0924 was identified. At the end of the incubation period of A. parasiticus, dry mycelial weight was significantly reduced by more than 80% (p < 0.01) and total aflatoxin production was inhibited by more than 63% (p < 0.05) in the presence of B. subtilis. Conclusions: These results indicate that B. subtilis K-0924 inhibits the growth and aflatoxin production of toxigenic Aspergillus, which can be contaminated with meju. We could expect more inhibition by other bacteria related to fermentation of meju, and further examination is necessary on species other than B. subtilis.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"59 16","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139783755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-12DOI: 10.3390/applmicrobiol4010025
Ofélia Godinho, O. Lage, Sandra Quinteira
Antimicrobial resistance is presently one of the leading causes of death worldwide. The surveillance of different environments, namely, wastewater treatment plants (WWTPs), as hotspots of antibiotic-resistant bacteria, has become crucial under the One Health approach. This study aimed to characterize, phenotypically and genotypically, antibiotic-resistant bacteria along a WWTP receiving domestic and industrial sewage. Four sampling sites, representing distinct treatment points of the WWTP, were selected for sampling bacterial isolation in selective media supplemented, or not, with antibiotics, and subsequent antimicrobial susceptibility testing. Antibiotic resistance encoding genes were screened by molecular methods. A total of 50 bacterial isolates were obtained, 50% of which were affiliated with the genus Enterococcus. The antimicrobial susceptibility testing revealed antibiotic phenotypic resistance in isolates obtained from all the four treatment points of the wastewater samples, with resistance to tetracycline (32.5%) and ampicillin (25%) being the most common. Three isolates were found to be multidrug resistant and were affiliated with the genera Citrobacter, Shigella and Klebsiella. Molecular screening revealed the presence of tet(M), blaTEM, blaSHV and blaCTX-M, as well as class 1 integrons carrying dfrA25, ANT(3″)-IIa and aadA6 genes. This study highlights the relevance of bacterial isolation and their antimicrobial susceptibility evaluation in WWTP systems since antibiotic-resistant strains were found from the raw influent to the final effluent discharged into the environment, denoting the need for surveillance and containment measures.
{"title":"Antibiotic-Resistant Bacteria across a Wastewater Treatment Plant","authors":"Ofélia Godinho, O. Lage, Sandra Quinteira","doi":"10.3390/applmicrobiol4010025","DOIUrl":"https://doi.org/10.3390/applmicrobiol4010025","url":null,"abstract":"Antimicrobial resistance is presently one of the leading causes of death worldwide. The surveillance of different environments, namely, wastewater treatment plants (WWTPs), as hotspots of antibiotic-resistant bacteria, has become crucial under the One Health approach. This study aimed to characterize, phenotypically and genotypically, antibiotic-resistant bacteria along a WWTP receiving domestic and industrial sewage. Four sampling sites, representing distinct treatment points of the WWTP, were selected for sampling bacterial isolation in selective media supplemented, or not, with antibiotics, and subsequent antimicrobial susceptibility testing. Antibiotic resistance encoding genes were screened by molecular methods. A total of 50 bacterial isolates were obtained, 50% of which were affiliated with the genus Enterococcus. The antimicrobial susceptibility testing revealed antibiotic phenotypic resistance in isolates obtained from all the four treatment points of the wastewater samples, with resistance to tetracycline (32.5%) and ampicillin (25%) being the most common. Three isolates were found to be multidrug resistant and were affiliated with the genera Citrobacter, Shigella and Klebsiella. Molecular screening revealed the presence of tet(M), blaTEM, blaSHV and blaCTX-M, as well as class 1 integrons carrying dfrA25, ANT(3″)-IIa and aadA6 genes. This study highlights the relevance of bacterial isolation and their antimicrobial susceptibility evaluation in WWTP systems since antibiotic-resistant strains were found from the raw influent to the final effluent discharged into the environment, denoting the need for surveillance and containment measures.","PeriodicalId":502845,"journal":{"name":"Applied Microbiology","volume":"29 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139784144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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