Applied and Environmental Microbiology最新文献

{"title":"Articles of Significant Interest in This Issue.","authors":"","doi":"10.1128/aem.00543-25","DOIUrl":"10.1128/aem.00543-25","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":"91 3","pages":"e0054325"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11925004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655589","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":"Complex of intratumoral mycobiome and bacteriome predicts the recurrence of laryngeal squamous cell carcinoma.","authors":"Xinhui Mao, Huiying Huang, Limin Zhao, Feiran Li, Zhenwei Wang, Xiaohui Yuan, Hui-Ching Lau, Chi-Yao Hsueh, Ming Zhang","doi":"10.1128/aem.01954-24","DOIUrl":"10.1128/aem.01954-24","url":null,"abstract":"<p><p>Dysbiosis of intratumoral fungal and bacterial communities is associated with poor prognosis in various cancers. However, the mycobiome characteristics in laryngeal squamous cell carcinoma (LSCC) and its correlation with recurrence have not yet been investigated. The mycobiome in 80 LSCC samples was characterized using internal transcribed spacer sequencing, encompassing both tumor tissues and their matched para-cancerous tissues. The intratumoral bacteriome was further identified using 16S rRNA sequencing. These two microbial communities were analyzed using bioinformatics and statistical methods to determine its potential correlation with LSCC recurrence. The fungal alpha diversity in tumors was higher compared with that in para-cancerous tissues (<i>P</i> < 0.001). A significant difference in the overall fungal community patterns between tumor tissues and para-cancerous tissues was observed based on Bray-Curtis dissimilarity (<i>P</i> < 0.001). The presence of <i>Alloprevotella</i>, <i>Porphyromonas</i>, <i>Candida</i>, and <i>Fusarium</i> in tumors exhibited a correlation with alcohol consumption. The relative abundance of <i>Penicillium</i>, <i>Exophiala</i>, and <i>Aspergillus</i> in the mycobiome, as well as that of <i>Alloprevotella</i>, <i>Porphyromonas</i>, and <i>Peptostreptococcus</i> in the bacteriome significantly increased the risk of LSCC recurrence (<i>P</i> < 0.05). These six microorganisms can combine to form a <i>microbial complex</i>, which may independently contribute to recurrence risk in patients with LSCC when enriched within the tumor (hazard ratio = 6.844, <i>P</i> < 0.01). Intratumoral fungi and bacteria can be valuable indicators for assessing recurrence in patients with LSCC, indicating their potential as valuable targets for therapeutic intervention.</p><p><strong>Importance: </strong>Our results revealed that dysbiosis of intratumoral microbiota, including increased fungal community diversity and overgrowth of several fungal or bacterial organisms, is substantially linked to the recurrence of LSCC. Drinking habits might alter the laryngeal microbiota to influence the recurrence of LSCC. We also explored a method to potentially predict the recurrence of LSCC from a novel perspective. These findings could offer insights into the etiology of LSCC and pave way to prevent and treat LSCC.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0195424"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466701","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":"Phenanthrene degradation by a flavoprotein monooxygenase from <i>Phanerodontia chrysosporium</i>.","authors":"Mika Hayasaka, Link Hamajima, Yuki Yoshida, Reini Mori, Hiroyuki Kato, Hiromitsu Suzuki, Ryoga Tsurigami, Takaaki Kojima, Masashi Kato, Motoyuki Shimizu","doi":"10.1128/aem.01574-24","DOIUrl":"10.1128/aem.01574-24","url":null,"abstract":"<p><p>Phenanthrene (PHEN), a polycyclic aromatic hydrocarbon (PAH), is degraded by white-rot fungi like <i>Phanerochaete chrysosporium</i> (the fungus has been renamed as <i>Phanerodontia chrysosporium</i>). PHEN is metabolized by <i>P. chrysosporium</i> and transformed into various monohydroxylated and dihydroxylated products. These intermediates are further degraded by cleavage of the aromatic ring. However, the enzymes involved in PHEN conversion in <i>P. chrysosporium</i> remain largely unidentified. We aimed to identify and characterize the <i>P. chrysosporium</i> enzymes involved in the degradation of PHEN and its intermediates. Recombinant <i>P. chrysosporium</i> flavoprotein monooxygenase 11 (FPMO11), a homolog of the salicylate 1-monooxygenase from the naphthalene-degrading bacterium <i>Pseudomonas putida</i> G7, was overexpressed in <i>Escherichia coli</i>. FPMO11 catalyzes the oxidative decarboxylation of 1-hydroxy-2-naphthoate (1H2N) and 2-hydroxy-1-naphthoate (2H1N) to 1,2-dihydroxynaphthalene (1,2DHN). To the best of our knowledge, this is the first study to identify and characterize enzymes with 1H2N and 2H1N monooxygenase activities in members of the FPMO superfamily. Additionally, our search for a dioxygenase with the ability to catalyze the aromatic ring cleavage of 1,2DHN led to the identification of intradiol dioxygenase (IDD) 1 and IDD2 from <i>P. chrysosporium</i>, which catalyzes the ring cleavage of 1,2DHN. Thus, this study also identified, for the first time, intradiol 1,2DHN dioxygenase activity in members of the IDD superfamily. The findings highlight the unique substrate spectra of FPMO11 and IDDs, rendering them attractive candidates for biotechnological applications, especially mitigation of environmental and health risks associated with PAH pollution.IMPORTANCEPhenanthrene (PHEN), a polycyclic aromatic hydrocarbon (PAH), is a widely studied pollutant in environmental science and toxicology due to its presence in fossil fuels, tobacco smoke, and as a byproduct of incomplete combustion processes. White-rot fungi like <i>P. chrysosporium</i> can degrade PHEN through the production of extracellular oxidative enzymes. We investigated the properties of PHEN-degrading enzymes in <i>P. chrysosporium</i>, specifically one flavoprotein monooxygenase (FPMO11) and two intradiol dioxygenases (IDD1 and IDD2). Our findings indicate that the enzymes catalyze the aromatic ring cleavage of PHEN, using the intermediates as substrates, transforming them into less harmful and more biodegradable compounds. This could help reduce environmental pollution and mitigate health risks associated with PAH exposure. The potential of these enzymes for biotechnological applications is also highlighted, emphasizing their critical role in understanding PAH degradation by white-rot fungi.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0157424"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078474","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":"Gelling and reducing agents are potential carbon and energy sources in culturing of anaerobic microorganisms.","authors":"Yi-Fan Liu, Liu Yang, Qing-Ping He, Yi-Lin Xu, Yu-Tong Zhu, Yan-Le Mi, Lei Zhou, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu","doi":"10.1128/aem.02276-24","DOIUrl":"10.1128/aem.02276-24","url":null,"abstract":"<p><p>The majority of microorganisms in the environment have yet to be isolated in pure cultures, and the reasons behind this phenomenon remain elusive. In this study, we investigated the possibility of the commonly used gelling agent including agar and gellan gum as a source of carbon and energy in anaerobic roll-tube cultivation from one mangrove sediment sample and two high-temperature oilfield samples. Based on growth tests and genomic evidence, anaerobic gellan degraders were retrieved from genera of <i>Clostridium</i>, <i>Lacrimispora</i>, and lineages from the rarely cultivated phylum Atribacterota. Anaerobic agarolytic microorganisms were found to be members of <i>Bacillus</i> and <i>Clostridium</i>. We also proved the role of carbon and energy sources of L-cysteine, a routine agent used to make culture media anoxic/anaerobic in both enrichment cultures and isolated strains representing <i>Acetomicrobium</i>, <i>Thermodesulfovibrio</i>, <i>Lacrimispora</i>, <i>Clostridium</i>, <i>Bacillus</i>, <i>Coprothermobacter</i>, <i>Citrobacter</i>, and <i>Enterobacter</i>. Furthermore, the isolates and enriched microbial communities utilizing L-cysteine under anaerobic conditions were mainly through L-cysteine desulfuration to pyruvate, ammonia, and sulfide. This study demonstrates that the widely used gelling and reducing agents in the basal medium can serve as carbon and energy sources for anaerobic microorganisms and thus may bias the enrichment and isolation.</p><p><strong>Importance: </strong>Most microbial species inhabiting natural environments have not been isolated in pure cultures using conventional media and laboratory conditions, but the reason behind this is unclear. Here, we provided a new explanation for the phenomenon, in that both the gelling agents, like agar and gellan gum, and reducing agent L-cysteine-HCl in the media provide extra carbon and energy sources to microorganisms and therefore decrease the chance in isolation specifically for the supplemented substrate which is supposed to be the sole source of carbon and energy. This result demonstrated that further improvement in the effectiveness of isolation of targeted microorganisms will be facilitated by subtracting the overlooked organic ingredients in the medium and more innovations.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0227624"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397772","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":"Arginine accumulation suppresses heat production during fermentation of the biocontrol fungus <i>Beauveria bassiana</i>.","authors":"Tong Wu, Fangfang Zhan, Liqiong Zeng, Yanli Sun, Shihui Fu, Yu Fang, Xiaochun Lin, Haoyu Lin, Jun Su, Shouping Cai","doi":"10.1128/aem.02134-24","DOIUrl":"10.1128/aem.02134-24","url":null,"abstract":"<p><p><i>Beauveria bassiana</i> (<i>Bb</i>) is one of the most widely used biocontrol agents, and its products constitute more than one-third of the global market share of fungal insecticides. Solid-state fermentation (SSF) is widely used in the production of <i>Beauveria bassiana</i> (<i>Bb</i>) because of its economic practicality and high production efficiency. However, the heat generated during fermentation can sharply reduce both the yield and quality of <i>Bb</i>, and current industrial methods to mitigate high temperatures during fermentation are inadequate, leading to increased production costs. Thus, exploring the underlying mechanism of how heat is produced by <i>Bb</i> is crucial for improving the SSF procedure and yield. This study employed multiomics data analysis of <i>Bb</i> during SSF to explore the relationships between fungal fermentation and environmental factors. We found that the heat production period for SSF was 12 hours to 48 hours post-inoculation. To further explore the underlying mechanism during this heating period, we identified 454 temperature-correlated metabolites (TCMs) and 1,994 temperature-correlated genes (TCGs). Annotations of the above TCMs and TCGs revealed significant enrichment in the arginine biosynthesis pathway; specifically, the expression level of glutamine synthetase, a TCG, decreased with fermentation time, whereas the expression levels of the TCGs L-arginine and L-glutamine increased with fermentation time, and glutamine synthetase and L-glutamine in the arginine biosynthesis pathway cycle produced the end product L-arginine. Furthermore, when the substrates of the SSF were treated with exogenous arginine, the temperature peak of the SSF significantly decreased with increasing concentration of exogenously added arginine.IMPORTANCEA large amount of experimental evidence from the field has shown that <i>Bb</i> is an irreplaceable mature product that protects the health of our agriculture and ecosystem. In addition to high efficiency and host extensiveness, low cost is a critical merit that makes <i>Bb</i> products frequently used in the field. However, the growing cost of power and labor in the <i>Bb</i> industry, especially the SSF procedure, has significantly increased the price of its products, thus restricting the use of <i>Bb</i> in the field. This study not only fills the theoretical knowledge gaps concerning the molecular basis of the interrelationship between <i>Bb</i> and the fermentation environment during SSF but also provides an economical and applicable strategy (the addition of arginine to the fermentation media) to further lower the cost and increase the yield of <i>Bb</i> during SSF at the industrial level.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0213424"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188106","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":"Effect of fecal microbiota transplantation on diabetic wound healing through the IL-17A-mTOR-HIF1α signaling axis.","authors":"Chenmei Peng, Pan Lei, Hongying Qi, Qianjun Zhu, Chushun Huang, Ju Fu, Chengyu Zhao","doi":"10.1128/aem.02019-24","DOIUrl":"10.1128/aem.02019-24","url":null,"abstract":"<p><p>Diabetes is the third most common chronic disorder worldwide. Diabetic wounds are a severe complication that is costly and often results in non-traumatic lower limb amputation. Recent investigations have demonstrated that the gut microbiota as a \"virtual organ\" can regulate metabolic diseases like diabetes. Fecal microbiota transplantation (FMT) is an innovative therapeutic approach for promoting wound healing, but its function remains incompletely defined. A diabetes model was established by supplying mice with a high-fat diet and performing an intraperitoneal injection of streptozotocin. Diabetic wounds were then created, followed by bacterial transplantation. The relevant indexes of wound healing were evaluated to verify the promoting effect of FMT on the diabetic wounds. Human skin keratinocytes were also cultured, and cell scratch experiments were conducted to further investigate the underlying mechanism. The FMT regulated the levels of specific bacteria in the diabetic mice and helped restore the balance of intestinal microbes. This transplantation also enhanced wound healing in the diabetic mice by augmenting the closure rate, accelerating re-epithelialization, and boosting collagen deposition in skin wounds. Furthermore, FMT promoted the production of IL-17A, which significantly enhanced the growth and movement of human keratinocytes. Inhibiting molecules related to the IL-17A-mTOR-HIF1α signaling axis were shown to hinder wound re-epithelialization.This study clarifies the function of the IL-17A-mTOR-HIF1α signaling axis in the utilization of FMT in diabetic wound healing, providing a new therapeutic method and target for promoting the healing of diabetic wounds.</p><p><strong>Importance: </strong>The Intestinal microbiota, as the organ with the largest number of microorganisms in the body, plays a crucial role in the physiological functions of the human body. Normal microbiota can be involved in various functions such as energy absorption, metabolism, and immunity of the body, and microbiota imbalance is related to many diseases such as obesity and diabetes. Diabetes, as one of the world's three major chronic diseases, is a significant health issue that troubles more than a billion people globally. Diabetic wounds are a problem that all diabetic patients must confront when undergoing surgery, and it is an important cause of non-traumatic amputations. Exploring the role of intestinal microorganisms in the wound-healing process of diabetic mice can offer the possibility of using microorganisms as a therapeutic means to intervene in clinically related diseases.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0201924"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522519","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":"Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages.","authors":"Shujian Yuan, Yunling Wu, Jose Luis Balcazar, Danrui Wang, Dong Zhu, Mao Ye, Mingming Sun, Feng Hu","doi":"10.1128/aem.00296-25","DOIUrl":"https://doi.org/10.1128/aem.00296-25","url":null,"abstract":"<p><p>The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs (<i>aceF</i>, <i>GT</i>11, and <i>GT</i>6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration.IMPORTANCEThe phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0029625"},"PeriodicalIF":3.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative proteogenomics reveals ecological and evolutionary insights into the organohalide-respiring <i>Dehalobacter restrictus</i> strain T.","authors":"Xiaocui Li, Xiuying Li, Huijuan Jin, Jingjing Wang, Lian Yu, Jun Yan, Yi Yang","doi":"10.1128/aem.01719-24","DOIUrl":"https://doi.org/10.1128/aem.01719-24","url":null,"abstract":"<p><p>1,1,1-Trichloroethane (1,1,1-TCA) and chloroform (CF) are persistent groundwater contaminants because of their widespread industrial use as organic solvents and improper disposal in the past. Obligate organohalide-respiring bacteria (OHRB), such as <i>Dehalobacter</i> (<i>Dhb</i>), play crucial roles in biotransforming and detoxifying natural or anthropogenic halogenated organics including 1,1,1-TCA and CF through reductive dechlorination. Despite their significance, only five <i>Dhb</i> strains have been associated with the reductive dechlorination of 1,1,1-TCA or CF. Therefore, cultivating and characterizing novel <i>Dhb</i> strains from various environments of different origins worldwide is crucial for understanding the ecology and evolution of <i>Dhb</i> and the associated reductive dehalogenase (RDase) genes. This study reports the enrichment and investigation of a novel <i>Dhb</i> population capable of reducing 1,1,1-TCA to 1,1-dichloroethane, CF to dichloromethane, 1,1,2-TCA to vinyl chloride/1,2-dichloroethane, and 1,2,4-trichlorobenzene to 1,2-dichlorobenzene. The capability for dechlorinating both aliphatic and aromatic compounds was observed for the first time in the sediment sourced from the Xi River situated in the North China Plain. Comparative genomic analysis of <i>Dhb</i> strains revealed genome contraction might have resulted in the loss of various gene family members, contributing to the syntrophy interactions (e.g., cobalamin, hydrogen, and acetate) of <i>Dhb</i> with other anaerobes (e.g., fermenters and acetogens). Proteogenomic and phylogenetic analysis confirmed the highly expressed 1,1,1-TCA/CF-dechlorinating RDase, designated as TcaA, shared 94.7-96.7% amino acid sequence similarities with RDases, such as ThmA, CfrA, and TmrA. This study expands knowledge on <i>Dhb</i> biogeography and evolution while providing insights into potential syntrophy interactions supporting organohalide respiration by <i>Dhb</i>. The findings have implications for developing the novel biotechnologies for the remediation of halogenated alkane-contaminated sites.IMPORTANCEOrganohalide-respiring bacteria (OHRB) are essential for breaking down harmful pollutants in the environment. This study investigates a newly discovered OHRB capable of degrading multiple contaminants, including persistent 1,1,1-trichloroethane and chloroform. By understanding its unique abilities and interactions with other microbes, we gain valuable insights into how these bacteria evolve and function, enabling the development of improved bioremediation strategies to clean up polluted sites.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0171924"},"PeriodicalIF":3.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The insertion of the inverted repeat of an insertion sequence (IS) element from <i>Lacticaseibacillus rhamnosus</i> changes the host range and stability of pGK12, a shuttle vector for lactic acid bacteria.","authors":"Zifan Xie, Yong-Su Jin, Todd R Klaenhammer, Michael J Miller","doi":"10.1128/aem.01908-24","DOIUrl":"https://doi.org/10.1128/aem.01908-24","url":null,"abstract":"<p><p>Insertion sequences (ISs) are key components of most bacterial genomes and play a crucial role in bacterial mutagenesis. In this study, we observed the insertion of an IS element, ISLrh, from the <i>Lacticaseibacillus rhamnosus</i> M1 genome into plasmid pGK12, resulting in the generation of a new plasmid, pTRK829. This insertion enabled pTRK829 to replicate in hosts previously incompatible with pGK12, including <i>L. rhamnosus</i> M1, <i>L. rhamnosus</i> GG (LGG), <i>Lacticaseibacillus casei</i> ATCC 393, and <i>Lacticaseibacillus paracasei</i> ATCC 25598. However, the ISLrh-inserted plasmid, pTRK829, was unstable and underwent a spontaneous deletion, resulting in a smaller and more stable variant, pTRK830, which retained ISLrh. Characterization of pTRK829 and pTRK830 across several host strains showed that ISLrh insertion led to a dramatic alteration in host range and impacted plasmid stability and copy number. Sequence and functional analysis of pTRK830 revealed that the terminal inverted repeats (IRs) of the inserted ISLrh and its insertion location were essential for plasmid replication in LGG. Finally, pTRK830 was successfully used as an expression vector for heterologous β-glucuronidase expression in LGG, <i>L. casei</i> ATCC 393, and <i>L. paracasei</i> ATCC 25598. In conclusion, this study demonstrated that the insertion of the IRs from ISLrh at a specific location can directly change the host range and stability of pGK12. Furthermore, we also demonstrated the potential of pTRK830 as a new cloning and expression vector for genetically intractable lactobacilli.</p><p><strong>Importance: </strong>This study highlights the significant impact of insertion sequence (IS) elements on plasmid replication in lactobacilli. The spontaneous integration of an IS element from the <i>Laticaseibacillus rhamnosus</i> genome into plasmid pGK12 not only expands its host range in previously incompatible strains but also changes plasmid stability and copy number. This expansion of the plasmid's host range is crucial for developing versatile genetic tools across diverse lactobacilli species. Additionally, the stable plasmid variant of pGK12 with the IS element insertion offers a valuable tool for cloning and gene expression in lactobacilli. These findings enhance our understanding of plasmid-IS element interactions and may provide insight into a new method to expand the host range of existing plasmids.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0190824"},"PeriodicalIF":3.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel anaerobic selenium oxyanion reducers native to FGD wastewater for enhanced selenium removal.","authors":"Preom Sarkar, Meghan Beebe, Gita Bhandari, Jonas Wielinski, Gregory V Lowry, Djuna Gulliver","doi":"10.1128/aem.01222-24","DOIUrl":"https://doi.org/10.1128/aem.01222-24","url":null,"abstract":"<p><p>Biological treatment is a recognized approach for removing selenate and selenite oxyanions present in flue gas desulfurization (FGD) wastewater. However, the knowledge of the specific microbial species or communities responsible for reducing water-soluble selenium oxyanions to insoluble elemental selenium remains limited. In addition, the selenium oxyanion reduction genes and pathways have yet to be understood in these wastewaters. This study characterizes selenium oxyanion-reducing bacteria (SeRB) native to FGD wastewater, and the resulting elemental selenium particles formed. By selecting native SeRB microbes in a defined media, a novel resolution of these organisms has been achieved. This research identifies previously unrecognized selenium oxyanion-reducing capabilities in <i>Anaerosolibacter</i>, alongside predominant SeRB from <i>Mesobacillus</i> and <i>Tepidibacillus</i> genera. This work encompasses both 16S and metagenomic techniques to recover novel metagenome-assembled genomes, distinct to this environment. The biogenic selenium produced by these organisms was predominantly of elemental selenium, either amorphous or with a hexagonal structure. This study identifies the SeRB present in FGD wastewater and characterizes their selenium products, offering crucial insights to enhance the efficiency of biological treatment strategies and the potential of selenium recovery from this industrial waste.IMPORTANCEThis is the first report on the culturability and recovery of taxonomic and metabolic information of the anaerobic selenium oxyanion-reducing bacteria (SeRB) in flue gas desulfurization (FGD) wastewater. Selenium is a regulated contaminant in FGD wastewater found on average to be 3,130 µg/L that must be removed to meet EPA discharge limits of 16 µg/L (D. B. Gingerich, E. Grol, and M. S. Mauter, Environ Sci Water Res Technol 4:909-925, 2018, https://doi.org/10.1039/C8EW00264A; also see U.S. EPA EPA-821-R-20-001, 2020). Better understanding of anaerobic SeRB and the microbial community in FGD wastewater is needed to harness their full potential for the bioremediation and recovery of selenium from FGD wastewater. Optimizing the biotreatment strategies for these wastewaters promises to yield cleaner and healthier waterways and ecosystems, even as the United States undergoes a shift in its energy landscape.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0122224"},"PeriodicalIF":3.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}