Applied and Environmental Microbiology最新文献

{"title":"Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes.","authors":"Yana Beizman-Magen, Tomer Orevi, Nadav Kashtan","doi":"10.1128/aem.02004-24","DOIUrl":"https://doi.org/10.1128/aem.02004-24","url":null,"abstract":"<p><p>Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing <i>Bacillus velezensis</i> FZB42 and two bacterial strains susceptible to its antibiotics: <i>Xanthomonas euvesicatoria</i> 85-10 and <i>Pseudomonas syringae</i> DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably<i>, X. euvesicatoria</i> shows increased protection against both the cells and supernatants of <i>B. velezensis</i> under wet-dry cycles, while <i>P. syringae</i> cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between <i>P. syringae</i> and <i>B. velezensis</i>, where <i>P. syringae</i> inhibits <i>B. velezensis</i> under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.IMPORTANCEOur study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by <i>Bacillus velezensis</i> against two susceptible bacterial species: <i>Xanthomonas</i> and <i>Pseudomonas</i> varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0200424"},"PeriodicalIF":3.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875972","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":"Positive regulation of a LuxR family protein, MilO, in mildiomycin biosynthesis.","authors":"Zhiyu Li, Yuli Wang, Chen Lin, Yu Wen, Zixin Deng, Ming Jiang, Xinyi He","doi":"10.1128/aem.01654-24","DOIUrl":"https://doi.org/10.1128/aem.01654-24","url":null,"abstract":"<p><p>Mildiomycin is a representative peptidyl nucleoside antibiotic and was first isolated from <i>Streptoverticillium rimofaciens</i>, which has been used as an important biological agent to control powdery mildew in plants. Despite its importance, the biosynthetic pathways and regulatory mechanisms remain to be fully elucidated. In this study, we identified MilO as a positive pathway-specific regulator of mildiomycin biosynthesis in the heterologous host <i>Streptomyces avermitilis</i>. Gene disruption of <i>milO</i> resulted in almost loss of mildiomycin production, and it was restored to the level comparable to that in the wild-type strain in complemented strain. Overexpression of <i>milO</i> using host native promoter <i>rpsJ</i>p, engineered promotor <i>SP44,</i> and <i>kasO</i>p* led to a 50%, 6.5-fold, and 9.2-fold increase in mildiomycin production compared with the wild-type strain, respectively. Quantitative real-time PCR and electrophoretic mobility shift assay (EMSA) experiments revealed that MilO directly enhances the transcription of the <i>milA</i> gene by 20 folds after 48 h fermentation and indirectly regulates the transcription levels of other genes from <i>milB</i> to <i>milM</i>. Using DNase I footprinting assays, <i>milO</i> was revealed to bind to a 44 bp DNA sequence of the <i>milA</i> promoter region. The binding region consists of three imperfect direct repeats of TGTC(N)₃CGGT separated by two-nucleotide spacers and each repeat is important to efficient binding to MilO. In addition, we identified two related compounds by overexpressing <i>milO</i> in a structural gene <i>milN</i>-deficient mutant. Taken together, this study indicates that pathway-specific regulator MilO is essential for mildiomycin biosynthesis and provides an effective strategy to improve the production of mildiomycin and its intermediates.IMPORTANCEAs an important biological agent to control powdery mildew on plants, mildiomycin has been commercialized and used in various plants. However, its regulatory mechanisms and biosynthetic pathways remain unknown. This study provides new insights into the regulation of mildiomycin biosynthesis through MilO, a LuxR family protein that modulates mildiomycin production by directly enhancing the transcription of <i>milA</i>. The yield of mildiomycin was significantly improved by overexpressing <i>milO</i> in a heterologous host. In addition, the positive regulatory effect of <i>milO</i> helped to discover two related compounds, which provide important clues for the timing of uploading of two amino acid side chains during mildiomycin biosynthesis for the first time. In brief, our findings on transcriptional regulation of mildiomycin biosynthesis by <i>milO</i> will be valuable to further increase the yield of mildiomycin and explore its biosynthetic pathways.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0165424"},"PeriodicalIF":3.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876000","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":"Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation.","authors":"Frazer Midot, Kian Mau Goh, Kok Jun Liew, Sharon Yu Ling Lau, Mikk Espenberg, Ülo Mander, Lulie Melling","doi":"10.1128/aem.01986-24","DOIUrl":"https://doi.org/10.1128/aem.01986-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH&lt;sub&gt;4&lt;/sub&gt;), and nitrous oxide (N&lt;sub&gt;2&lt;/sub&gt;O) fluxes. Soil CO&lt;sub&gt;2&lt;/sub&gt; emission increased (doubling from approximately 200 mg C m&lt;sup&gt;-2&lt;/sup&gt; h&lt;sup&gt;-1&lt;/sup&gt;), while CH&lt;sub&gt;4&lt;/sub&gt; emissions decreased (from 200 µg C m&lt;sup&gt;-2&lt;/sup&gt; h&lt;sup&gt;-1&lt;/sup&gt; to slightly negative) following land use changes. The N&lt;sub&gt;2&lt;/sub&gt;O emissions in the oil palm plantation reached approximately 1,510 µg N m&lt;sup&gt;-2&lt;/sup&gt; h&lt;sup&gt;-1&lt;/sup&gt;, significantly higher than previous land uses. The CH&lt;sub&gt;4&lt;/sub&gt; fluxes were driven by groundwater table, humification levels, and C:N ratio, with &lt;i&gt;Methanomicrobia&lt;/i&gt; populations dominating methanogenesis and &lt;i&gt;Methylocystis&lt;/i&gt; as the main CH&lt;sub&gt;4&lt;/sub&gt; oxidizer. The N&lt;sub&gt;2&lt;/sub&gt;O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant &lt;i&gt;nirK&lt;/i&gt;-type denitrifiers (13-fold &lt;i&gt;nir&lt;/i&gt; to &lt;i&gt;nosZ&lt;/i&gt;) and a minor role by nitrification (a threefold increase in &lt;i&gt;amoA&lt;/i&gt;) in the plantation. &lt;i&gt;Proteobacteria&lt;/i&gt; and &lt;i&gt;Acidobacteria&lt;/i&gt; encoding incomplete denitrification genes potentially impact N&lt;sub&gt;2&lt;/sub&gt;O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.IMPORTANCETropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation ef","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0198624"},"PeriodicalIF":3.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876004","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":"A microaerobically induced small heat shock protein contributes to <i>Rhizobium leguminosarum</i>/<i>Pisum sativum</i> symbiosis and interacts with a wide range of bacteroid proteins.","authors":"Lucía Domingo-Serrano, Claudia Sanchis-López, Carla Alejandre, Joanna Soldek, José Manuel Palacios, Marta Albareda","doi":"10.1128/aem.01385-24","DOIUrl":"https://doi.org/10.1128/aem.01385-24","url":null,"abstract":"<p><p>During the establishment of the symbiosis with legume plants, rhizobia are exposed to hostile physical and chemical microenvironments to which adaptations are required. Stress response proteins including small heat shock proteins (sHSPs) were previously shown to be differentially regulated in bacteroids induced by <i>Rhizobium leguminosarum</i> bv. viciae UPM791 in different hosts. In this work, we undertook a functional analysis of the host-dependent sHSP RLV_1399. A <i>rlv_1399-</i>deleted mutant strain was impaired in the symbiotic performance with peas but not with lentil plants. Expression of <i>rlv_1399</i> gene was induced under microaerobic conditions in a FnrN-dependent manner consistent with the presence of an anaerobox in its regulatory region. Overexpression of this sHSP improves the viability of bacterial cultures following exposure to hydrogen peroxide and to cationic nodule-specific cysteine-rich (NCR) antimicrobial peptides. Co-purification experiments have identified proteins related to nitrogenase synthesis, stress response, carbon and nitrogen metabolism, and to other relevant cellular functions as potential substrates for RLV_1399 in pea bacteroids. These results, along with the presence of unusually high number of copies of <i>shsp</i> genes in rhizobial genomes, indicate that sHSPs might play a relevant role in the adaptation of the bacteria against stress conditions inside their host.IMPORTANCEThe identification and analysis of the mechanisms involved in host-dependent bacterial stress response is important to develop optimal <i>Rhizobium</i>/legume combinations to maximize nitrogen fixation for inoculant development and might have also applications to extend nitrogen fixation to other crops. The data presented in this work indicate that sHSP RLV_1399 is part of the bacterial stress response to face specific stress conditions offered by each legume host. The identification of a wide diversity of sHSP potential targets reveals the potential of this protein to protect essential bacteroid functions. The finding that nitrogenase is the most abundant RLV_1399 substrate suggests that this protein is required to obtain an optimal nitrogen-fixing symbiosis.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0138524"},"PeriodicalIF":3.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875968","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":"Patterns of spontaneous and induced genomic alterations in <i>Yarrowia lipolytica</i>.","authors":"Yuan-Ru Xiong, Yuan-Chun Fang, Min He, Ke-Jing Li, Lei Qi, Yang Sui, Ke Zhang, Xue-Chang Wu, Liang Meng, Ou Li, Dao-Qiong Zheng","doi":"10.1128/aem.01678-24","DOIUrl":"https://doi.org/10.1128/aem.01678-24","url":null,"abstract":"<p><p>This study explored the genomic alterations in <i>Yarrowia lipolytica</i>, a key yeast in industrial biotechnology, under both spontaneous and mutagen-induced conditions. Our findings reveal that spontaneous mutations occur at a rate of approximately 4 × 10^-10 events per base pair per cell division, primarily manifesting as single-nucleotide variations (SNVs) and small insertions and deletions (InDels). Notably, C-to-T/G-to-A transitions and C-to-A/G-to-T transversions dominate the spontaneous SNVs, while 1 bp deletions, likely resulting from template slippage, are the most frequent InDels. Furthermore, chromosomal aneuploidy and rearrangements occur, albeit at a lower frequency. Exposure to ultraviolet (UV) light, methylmethane sulfonate (MMS), and Zeocin significantly enhances the rates of SNVs and alters their mutational spectra in distinct patterns. Notably, Zeocin-induced SNVs are predominantly T-to-A and T-to-G substitutions, often occurring within the 5'-TGT^*-3' motif (^* denotes the mutated base). Additionally, Zeocin exhibits a higher potency in stimulating InDels compared to UV and MMS. Translesion DNA synthesis is implicated as the primary mechanism behind most Zeocin-induced SNVs and some InDels, whereas non-homologous end joining serves as the main pathway for Zeocin-mediated InDels. Intriguingly, the study identifies the gene <i>YALI1_E21053g</i>, encoding a protein kinase, as negatively associated with Zeocin resistance. Overall, our results not only deepened our knowledge about the genome evolution in <i>Y. lipolytica</i> but also provided reference to develop innovative strategies to harness its genetic potential.IMPORTANCE<i>Yarrowia lipolytica</i> exhibits high environmental stress tolerance and lipid metabolism capabilities, making it a microorganism with significant industrial application potential. In this study, we investigated the genomic variation and evolutionary patterns of this yeast under both spontaneous and induced mutation conditions. Our results reveal distinctive mutation spectra induced by different mutagenic conditions and elucidate the underlying genetic mechanisms. We further highlight the roles of non-homologous end joining and translesion synthesis pathways in Zeocin-induced mutations, demonstrating that such treatments can rapidly confer drug resistance to the cells. Overall, our research enhances the understanding of how yeast genomes evolve under various conditions and provides guidance for developing more effective mutagenesis and breeding techniques.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0167824"},"PeriodicalIF":3.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875996","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":"Identification of an antibiotic from an HTS targeting EF-Tu:tRNA interaction: a prospective topical treatment for MRSA skin infections.","authors":"Wlodek Mandecki, Maxim Chudaev, Wenjuan Ye, Amy Q Wang, Kenneth J Wilson, Xin Xu, Jisun Kim, Dane Parker, David Alland, Pradeep Kumar, Barry Li, Jason H Yang, Barry Kreiswirth, Jose R Mediavilla, Juan J Marugan, Mark J Henderson, Emanuel Goldman","doi":"10.1128/aem.02046-24","DOIUrl":"https://doi.org/10.1128/aem.02046-24","url":null,"abstract":"<p><p>Because of the urgent need for new antibiotics to treat drug-resistant bacterial pathogens, we employed an assay that rapidly screens large quantities of compounds for their ability to interfere with bacterial protein synthesis, in particular, the delivery of amino acids to the ribosome via tRNA and elongation factor Tu (EF-Tu). We have identified a drug lead, named MGC-10, which kills Gram-positive bacteria, including methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), with a MIC of 6 µM, while being harmless to mammalian cells <i>in vitro</i> in that concentration range. The antibacterial activity of MGC-10 was broad against over 50 strains of antibiotic-resistant samples obtained from hospital infections, where MGC-10 inhibited all tested strains of MRSA. Extensive selection and screening with MGC-10 did not yield any resistant strains, indicating it may have universal antibacterial activity against <i>S. aureus</i>. Pharmacokinetics performed in mice suggested that MGC-10 was too toxic for systemic use; however, it appears to have potential as a topical treatment for difficult-to-treat wounds or skin infections by Gram-positive pathogens such as MRSA. In a mouse skin-infection model with MRSA, MGC-10 performed as well or better than the present topical drug of choice, mupirocin. MGC-10 showed little, if any, accumulation in the livers of topically treated mice. These results bode well for the future use of MGC-10 in clinical application as it could be used to treat a broad range of <i>S. aureus</i> skin infections that are resistant to known antibiotics.IMPORTANCEThere is a critical need for new antibiotics to treat bacterial infections caused by pathogens resistant to many if not all currently available antibiotics. We describe here the identification of a prospective new antibiotic from high-throughput screening of a chemical library. The screening was designed to detect the inhibition of formation of a complex required for bacterial protein synthesis in all bacteria, the \"ternary complex,\" comprised of elongation factor Tu (EF-Tu), aminoacyl-tRNA, and GTP. The inhibitory compound, renamed MGC-10, was effective against all Gram-positive bacteria, including a wide variety of methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) strains. Although apparently too toxic for systemic use, the compound was safe and effective for topical use for treating skin infections in a mouse model. No resistance to the compound has been detected thus far, suggesting the potential to develop this compound for topical use to treat infections, especially those caused by pathogens resistant to existing antibiotics.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0204624"},"PeriodicalIF":3.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875975","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":"Mitigating genetic instability caused by the excision activity of the <i>phi</i>C31 integrase in <i>Streptomyces</i>.","authors":"Yadan Duan, Zhangliang Liu, Xiaofang Huang, Lu Xu, Xianxue Wang, Hao Liu, Zhoujie Xie","doi":"10.1128/aem.01812-24","DOIUrl":"https://doi.org/10.1128/aem.01812-24","url":null,"abstract":"<p><p>Over the past three decades, the integrase (Int) from <i>Streptomyces</i> phage <i>phi</i>C31 has become a valuable genome engineering tool across various species. <i>phi</i>C31 Int was thought to mediate unidirectional site-specific integration (<i>attP</i> × <i>attB</i> to <i>attL</i> and <i>attR</i>) in the absence of the phage-encoded recombination directionality factor (RDF). However, we have shown in this study that Int can also catalyze reverse excision (<i>attL</i> × <i>attR</i> to <i>attP</i> and <i>attB</i>) at low frequencies in <i>Streptomyces lividans</i> and <i>Escherichia coli</i>, causing genetic instability in engineered strains. To address this issue, we developed a two-plasmid co-conjugation (TPC) system. This system consists of an <i>attP</i>-containing integration vector and an Int expression suicide plasmid, both carrying <i>oriT</i> to facilitate efficient conjugation transfer from <i>E. coli</i> to <i>Streptomyces</i>. Using the TPC system, genetically stable integrants free of Int can be generated quickly and easily. The indigoidine-producing strains generated by the TPC system exhibited higher genetic stability and production efficiency compared to the indigoidine-producing strain generated by the conventional integration system, further demonstrating the utility of the TPC system in the field of biotechnology. We anticipate that the strategies presented here will be widely adopted for stable genetic engineering of industrial microbes using phage integrase-based integration systems.IMPORTANCELarge serine recombinases (LSRs), including the bacteriophage <i>phi</i>C31 integrase, were previously thought to allow only unidirectional site-specific integration (<i>attP</i> × <i>attB</i> to <i>attL</i> and attR). Our study is the first to show that the <i>phi</i>C31 integrase can also catalyze a low-efficiency reverse excision reaction in <i>Streptomyces</i> and <i>E. coli</i> without the involvement of the phage-encoded recombination directionality factor (RDF). The genetic instability caused by the low <i>in vivo</i> excisionase activity of the <i>phi</i>C31 integrase is a major challenge for biotechnological applications. Our study addresses this issue by developing a two-plasmid co-conjugation (TPC) system that facilitates the construction of Int-deficient genomic engineering strains. The Int-deficient integrants produced by this TPC system exhibit strong genetic stability for introduced genes and maintain stable production traits even in the absence of selection pressure, making them highly valuable for industrial applications.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0181224"},"PeriodicalIF":3.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863172","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":"Microbiome composition and turnover in the face of complex lifecycles and bottlenecks: insights through the study of dung beetles.","authors":"Joshua A Jones, Irene Garcia Newton, Armin P Moczek","doi":"10.1128/aem.01278-24","DOIUrl":"https://doi.org/10.1128/aem.01278-24","url":null,"abstract":"<p><p>Microbiome composition and function often change throughout a host's life cycle, reflecting shifts in the ecological niche of the host. The mechanisms that establish these relationships are therefore important dimensions of host ecology and evolution; yet, their nature remains poorly understood. Here, we sought to investigate the microbial communities associated with the complex life cycle of the dung beetle <i>Onthophagus taurus</i> and the relative contributions of host life stage, sex, and environment in determining microbiome assembly. We find that <i>O. taurus</i> plays host to a diverse microbiota that undergo drastic community shifts throughout host development, influenced by host life stage, environmental microbiota, and, to a lesser degree, sex. Contrary to predictions, we found that egg and pupal stages-despite the absence of a digestive tract or defined microbe-storing organs-do not constrain microbial maintenance, while host-constructed environments, such as a maternally derived fecal pellet or the pupal chamber constructed by late larvae, may still serve as complementary microbial refugia for select taxa. Lastly, we identify a small community of putative core microbiota likely to shape host development and fitness. Our results provide important insights into mechanisms employed by solitary organisms to assemble, maintain, and adjust beneficial microbiota to confront life-stage-specific needs and challenges.</p><p><strong>Importance: </strong>As the influence of symbionts on host ecology, evolution, and development has become more apparent so has the importance of understanding how hosts facilitate the reliable maintenance of their interactions with these symbionts. A growing body of work has thus begun to identify diverse behaviors and physiological mechanisms underpinning the selective colonization of beneficial symbionts across a range of host taxa. Yet, how organisms with complex life cycles, such as holometabolous insects, establish and maintain key symbionts remains poorly understood. This is particularly interesting considering the drastic transformations of both internal and external host morphology, and the ecological niche shifts in diet and environment, that are the hallmark of metamorphosis. This work investigates the dynamic changes of the microbiota associated with the complex life cycle and host-constructed environments of the bull-headed dung beetle, <i>Onthophagus taurus</i>, a useful model for understanding how organisms may maintain and modulate their microbiota across development.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0127824"},"PeriodicalIF":3.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863170","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":"Chlorine disinfectant significantly changed microfauna habitat, community structure, and colonization mode in wastewater treatment plants.","authors":"Yuening Zhong, Yibo Zhang, Qiyue Meng, Haoyu Zhang, Zhenbing Wu, Chenyuan Dang, Jie Fu","doi":"10.1128/aem.01517-24","DOIUrl":"https://doi.org/10.1128/aem.01517-24","url":null,"abstract":"<p><p>During the coronavirus disease 2019 epidemic, excessive chlorine disinfectants have been used to block the spread of severe acute respiratory syndrome-coronavirus 2, resulting in large amounts of residual disinfectants entering wastewater treatment plants (WWTPs) through sewage systems. So far, no relevant research has been conducted on the impact of chlorine disinfectants on microfauna, an important microbial component in activated sludge treatment systems. This study comprehensively investigated the changes in microfauna habitat, community structure, and colonization mode under the chlorine stress by combining the full-scale WWTP survey and laboratory-scale sequencing batch reactor experiments. The results showed that chlorine disinfectants significantly changed the community structure of microfauna, including decrease in sedentary ciliates and increase in free-living ciliates, amoebas, and flagellates. Besides the disinfection effect of chlorine disinfectants, the microfauna community was also influenced by changes in habitat and bacterial community. The loose structure and excessive extracellular polymeric substance (EPS) of activated sludge caused by chlorination would impact the colonization of sedentary ciliates, while it was conducive to the survival of free-living ciliates due to their predation on EPS as the nutrients. Bacteria in the activated sludge had strong interactions with protozoa, and their changes under chlorine stress directly affected the protozoan community and even indirectly affected the micro-metazoa community through the food chain.</p><p><strong>Importance: </strong>This study revealed that chlorine disinfectant significantly changed microfauna habitat, community structure, and colonization mode in wastewater treatment plants during the coronavirus disease 2019 pandemic. Chlorine disinfectant could destroy the structure and stability of sludge flocs, reduce the abundance of beneficial microfauna in activated sludge, and even affect the colonization of sedentary ciliates on sludge. In addition, chlorine disinfectants might induce environmental and ecological risks related to microfauna, such as elevated suspended solids and release of bacteria and microfauna in the effluents.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0151724"},"PeriodicalIF":3.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863169","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":"Development and application of a quadruple RT-qPCR assay for the simultaneous detection of NoV GI, NoV GII, and HAV in bivalve shellfish.","authors":"Yan Wang, Jinfeng Wang, Maolin Wei, Libing Liu, Jianchang Wang, Xiangdong Xu","doi":"10.1128/aem.01839-24","DOIUrl":"https://doi.org/10.1128/aem.01839-24","url":null,"abstract":"<p><p>To achieve rapid and simultaneous detection of NoV GI, NoV GII, and HAV, a quadruple real-time fluorescence quantitative PCR (RT-qPCR) assay was developed using MS2 bacteriophage as a process control virus. The quadruple RT-qPCR assay effectively detected NoV GI, NoV GII, HAV, and MS2 RNA with detection limits of 10² copies/μL, 10³ copies/μL, 10² copies/μL, and 10³ copies/μL, respectively, within 1 hour 50 minutes. The quadruple RT-qPCR assay could specifically detect NoV GI, NoV GII, HAV, and MS2 without cross-reactions with other common pathogens, demonstrating good reproducibility with intra-assay and inter-assay coefficients of variation all below 2.11%. In this study, 337 bivalve shellfish samples collected from various regions of Hebei Province were pretreated using the proteinase K-PEG 8000 precipitation-chloroform method, and viral nucleic acids were enriched and extracted from a volume of viral solution that was doubled. The developed quadruple RT-qPCR assay was used to detect NoV GI, NoV GII, and HAV in bivalve shellfish samples, and the positive rates were 19.88% (67/337), 20.47% (69/337), and 4.75% (16/337), respectively. In addition, mixed infections of NoV GI and NoV GII (10.68%, 36/337) and NoV GI and HAV (0.89%, 3/337) were observed. In all, 200 bivalve shellfish samples were randomly selected for the assay, and it was found that the total, positive, negative coincidence rates, and Kappa values of the quadruple RT-qPCR assay were 98.3%, 99.1%, 98.2%, and 0.945, respectively, compared with the single RT-qPCR assay. These results show that the developed quadruple RT-qPCR assay has comparable performance to the single RT-qPCR assay.IMPORTANCEFood-borne diseases caused by viral contamination have become a growing concern, and bivalve shellfish is a crucial source of infection, with many outbreaks of non-bacterial acute gastroenteritis associated with raw food or the use of undercooked shellfish such as oysters. As food contamination problems caused by NoV and HAV become more severe, it is important to study and establish a sensitive and efficient assay to simultaneously detect NoV and HAV by applying the MS2 process control virus for the protection of bivalve shellfish food safety and the monitoring of the above food-borne viral contamination. In addition, bivalve shellfish samples contain a large number of PCR inhibitors such as polysaccharides, lipids, and proteins, so optimization of the virus enrichment and extraction method is essential and is expected to provide a research basis for subsequent related experiments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0183924"},"PeriodicalIF":3.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142851705","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}