Applied and Environmental Microbiology最新文献

{"title":"Comparative analysis of environmental persistence of SARS-CoV-2 variants and seasonal coronaviruses.","authors":"Geun Woo Park, Boris Reija, Azaibi Tamin, Heather Hicks, Matthew Hayden Flanders, John M Metz, Shufang Fan, Jennifer L Harcourt, Jennifer M Folster, Natalie Thornburg, Jan Vinjé","doi":"10.1128/aem.01688-24","DOIUrl":"10.1128/aem.01688-24","url":null,"abstract":"<p><p>Conducting persistence studies of infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on environmental surfaces may require a biosafety level 3 (BSL-3) laboratory. We aimed to compare the environmental persistence of BSL-2 level human coronaviruses (229E, NL63, and OC43) and bovine coronavirus (BoCoV) with three SARS-CoV-2 variants (WA-1, Delta, and Omicron). OC43 (1.8 TCID₅₀/mL) and BoCoV (1.0 TCID₅₀/mL) had lower detection thresholds in cell culture assays compared to 229E (150 TCID₅₀/mL) and NL63 (2,670 TCID₅₀/mL) and were used for persistence tests at room temperature. Viable OC43 became undetectable (>5.2log₁₀) after 48 hours on stainless steel and plastic coupons but exhibited extended persistence up to 72 hours on touchscreen glass coupons. In contrast, BoCoV remained viable for up to 120 hours with <1.8 log₁₀ infectivity loss. Both OC43 and BoCoV showed a reduction of >5 log₁₀ on vinyl coupons after 48 hours. On stainless steel coupons, the viability of all three SARS-CoV-2 variants became undetectable (>2.3 log₁₀ reduction) after 48 hours, with minor differences in reduction levels at 24 hours, whereas on touchscreen glass coupons, the viable virus could be detected for up to 48 hours for WA-1 and Omicron and 72 hours for the Delta variant. Regardless of coupon or virus type, viral RNA titers increased <4.5 Ct values after 120 hours. Our data demonstrate distinct persistence characteristics between BoCoV and OC43, with neither fully mimicking SARS-CoV-2 variants. This variability along with the impact of surface types on viral persistence underscores the need for caution when using these viruses as surrogates for SARS-CoV-2.IMPORTANCEIn this study, we evaluated three human seasonal coronaviruses (OC43, NL63, and 229E) and one bovine coronavirus (BoCoV) as potential surrogate viruses for SARS-CoV-2. Our data suggest that among the four surrogate viruses tested, OC43 and BoCoV were the most promising candidates due to their assay sensitivity, ease of handling, and high genetic similarity to SARS-CoV-2. However, neither BoCoV nor OC43 fully mimicked the environmental persistence characteristics of SARS-CoV-2 variants highlighting the potential limitations of using surrogate viruses.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0168824"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016524/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565838","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":"Synergistic effect of transporter and pathway engineering on the key performance indicators of erythritol synthesis by the yeast <i>Yarrowia lipolytica</i>.","authors":"Shuo Xu, Qian Li, Ye Li, Yue Zhang, Qing Li, Liyun Ji, Hairong Cheng","doi":"10.1128/aem.00061-25","DOIUrl":"10.1128/aem.00061-25","url":null,"abstract":"<p><p>Erythritol, a food additive, is produced on an industrial scale using the yeast <i>Yarrowia lipolytica</i>. Nevertheless, the key performance indicators (KPIs) have been found to be unsatisfactory, resulting in elevated erythritol production cost. This study demonstrated that the KPIs (titer, productivity, and yield) of erythritol can be improved by the synergistic application of transporter and pathway engineering strategies in the producing strain. The engineered <i>Y. lipolytica</i> strain Ylxs48 exhibits a glucose consumption rate of 310 g/L of glucose within 46 h during batch culture in 3, 100, and 200 L bioreactors as compared to above 72 h for the parental strain Ylxs01. The erythritol yield achieved ranges from 0.69 to 0.74 g/g depending on the culture conditions as compared to 0.55-0.57 g/g for the parental strain Ylxs01. The productivity surpasses 4.60 g/(L·h), representing a 1.91-fold improvement over the parental strain Ylxs01 in 3, 100, or 200 L bioreactors. Under fed-batch conditions in a 200 L bioreactor, an erythritol titer of 355.81 g/L was achieved, marking the highest titer ever reported. This increased erythritol titer enabled crystallization at 4°C directly from the clear supernatant, eliminating the requirement for evaporation or concentration steps. A comprehensive techno-economic analysis of the entire process conclusively demonstrated that implementing the industrial process based on the engineered strain Ylxs48 led to a significant 23% reduction in production cost. This approach holds the potential to substantially reduce erythritol costs and provides novel insights for engineering other industrial strains.</p><p><strong>Importance: </strong>The expansion of the erythritol market attracted excessive capital injection, resulting in overcapacity, operational difficulties, and even bankruptcy of erythritol manufacturers. Technology upgrades in the industry are imminent. However, the production technology of existing enterprises is seriously homogenized, and there is a lack of competitive core-producing strains. In this study, the industrial erythritol-producing strain <i>Y. lipolytica</i> CGMCC7326 was genetically modified by integrating substrate transport and pathway modification, which improved the conversion of glucose and significantly improved KPIs, thereby reducing the erythritol production cost.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0006125"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707894","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":"Lipid hydrogen isotope compositions primarily reflect growth water in the model archaeon <i>Sulfolobus acidocaldarius</i>.","authors":"Carolynn M Harris, Sebastian Kopf, Jeemin H Rhim, Alec Cobban, Felix J Elling, Xiahong Feng, Jamie McFarlin, Yuki Weber, Yujiao Zhang, Alice Zhou, Harpreet Batther, Ann Pearson, William D Leavitt","doi":"10.1128/aem.01983-24","DOIUrl":"10.1128/aem.01983-24","url":null,"abstract":"<p><p>The stable hydrogen isotope composition (δ²H) of lipid biomarkers can track environmental processes and remain stable over geologically relevant time scales, enabling studies of past climate, hydrology, and ecology. Most research has focused on lipids from the domain Eukarya (e.g., plant waxes, long-chain alkanes), and the potential of prokaryotic lipid biomarkers from the domain Archaea to offer unique insights into environments not captured by eukaryotic lipids remains unclear. Here, we investigate the H-isotope composition of biphytanes in <i>Sulfolobus acidocaldarius</i>, a model thermoacidophile and obligate heterotroph. We conducted a series of experiments that varied temperature, pH, shaking rate, electron acceptor availability, or electron donor flux. From these experiments, we quantified the lipid/water H-isotope fractionation (²ε_L/W) values for core biphytane chains derived from tetraether lipids. The ²ε_L/W values are consistently negative (-230‰ to -180‰) and are relatively invariant across all experiments despite a 20-fold change in doubling times and a twofold change in lipid cyclization. The magnitude and relative invariance of ²ε_L/W values are consistent with studies on other heterotrophic archaea and suggest archaeal lipids may be faithful recorders of the δ²H composition of growth water. Our study highlights the potential of archaeal lipid δ²H values as a hydrological proxy, offering new insights into environments where traditional proxies, such as plant-derived lipids, are not available, including extreme environments and extraterrestrial settings.IMPORTANCEReconstructing past climates is crucial for understanding Earth's environmental history and its responses to changing conditions. This study examines <i>Sulfolobus acidocaldarius</i>, a thermoacidophilic archaeon that thrives in extreme environments like hot springs. These microorganisms incorporate hydrogen water in the growth environment into membrane lipids, creating hydrogen isotope signatures that can reflect hydroclimate conditions. Our findings show that these hydrogen isotope ratios remain consistent even under varying temperatures, pH, oxygen levels, and electron donor fluxes, indicating a stable fractionation between lipids and water. This invariance suggests that <i>S. acidocaldarius</i> lipids could serve as a robust proxy for reconstructing ancient water H-isotope values, especially in extreme environments where traditional proxies, such as plant waxes, are absent. This research has broader implications for planetary-scale reconstructions, including potential applications in studying past climates on other planets, such as Mars, where similar microorganisms may have existed in hydrothermal conditions.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0198324"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699458","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":"Mycoidesin, a novel lantibiotic, exhibits potent bacteriostatic activity against <i>Listeria monocytogenes</i> and effectively controls its growth in beef.","authors":"Fei Zhang, Jiajia Ding, Shu Liu, Guoqiang Huang, Shulin Deng, Mengyu Gao, Hualin Liu, Wanjing Lv, Xin Zeng, Bingyue Xin, Congcong Xu","doi":"10.1128/aem.00067-25","DOIUrl":"10.1128/aem.00067-25","url":null,"abstract":"<p><p><i>Listeria monocytogenes</i> can cause severe listeriosis, with the consumption of contaminated food being an important route of its transmission. Biopreservatives can be used for the prevention and control of <i>L. monocytogenes</i> in food. In this study, we identified a novel lantibiotic, mycoidesin, with potent bacteriostatic activity against <i>L. monocytogenes</i>. It exhibited 4- to 16-fold higher bacteriostatic activity against the <i>L. monocytogenes</i> strains than nisin A. Analysis of the mode of action of mycoidesin revealed that it exerted bacteriostatic activity against <i>L. monocytogenes</i> ATCC 19111 at low and high concentrations (1×-32× MIC, 0.39-12.5 µM). It blocked cell wall synthesis by binding to Lipid II and inhibiting the growth of <i>L. monocytogenes</i>. For other sensitive strains, such as <i>Bacillus cereus</i> CMCC 63301, mycoidesin exerted a bacteriostatic effect at a low concentration (1× MIC, 1.56 µM) via the same mechanism, whereas it exerted a bactericidal effect at high concentrations (2×-8× MIC, 3.13-12.5 µM), which can damage the cell membrane and cause cell death. The stability test showed that mycoidesin had increased stability compared to nisin A. Additionally, mycoidesin showed low cytotoxic and hemolytic activity. Furthermore, mycoidesin effectively inhibited the growth of <i>L. monocytogenes</i> in beef and delayed the decline in beef quality. Our study demonstrates the potential of mycoidesin as a biopreservative to prevent <i>L. monocytogenes</i> contamination and improve the safety of meat and meat products in the food industry.</p><p><strong>Importance: </strong>This study aimed to identify highly effective, stable, and safe natural bacteriocin preservatives with anti-<i>Listeria monocytogenes</i> activity. We isolated a novel class II lantibiotic, mycoidesin, which exhibited more efficient bacteriostatic activity against <i>L. monocytogenes</i> and increased stability compared to the applied bacteriocin food preservative, nisin A. Mycoidesin also showed favorable biosafety. Moreover, mycoidesin could be effectively used for controlling <i>L. monocytogenes</i> in beef, demonstrating its potential as a biopreservative to prevent <i>L. monocytogenes</i>-related contamination and improve the safety of meat and meat products in the agricultural and food industries.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0006725"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699462","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":"Fresh pork microbiota is temporally dynamic and compositionally diverse across meat, contact surfaces, and processing lines in a pork processing facility.","authors":"A E Asmus, T N Gaire, K M Heimer, K E Belk, R S Singer, T J Johnson, N R Noyes","doi":"10.1128/aem.00044-25","DOIUrl":"10.1128/aem.00044-25","url":null,"abstract":"<p><p>The goal of this study was to analyze the microbial profiles of meat and contact surfaces from two different processing lines in a pork processing plant, using a 16S rRNA gene amplicon sequencing workflow specifically designed to investigate fresh meat and environmental samples throughout a commercial production schedule. Results indicated that the microbiota differed between the meat and contact surface, both across the two processing lines and within each individual processing line. Differences in the microbiota composition were also strongly associated with both the specific processing dates and the time of day during processing. Much of this variation was associated with distinct amplicon sequence variants unique to each processing date and each processing line throughout the day. The abundance of key taxa associated with food safety and spoilage was also temporally dynamic across a production shift and was different between the meat and contact surface. Overall, the results of this study indicate significant differences in the microbial profiles of the meat and contact surfaces between two processing lines within the same plant. These differences are likely influenced by daily variation in processing and sanitation procedures, as well as differences in the design of the processing lines, which appear to affect the microbiotas of both the meat and contact surfaces.IMPORTANCEThis study provides critical knowledge that can be used as a foundation for tailored processes to improve fresh pork safety and quality, potentially customized to individual processing lines, time points within a shift, and/or production days. Additionally, this study provides a list of potential biological markers associated with food safety and quality that could be used by processors to develop and validate intervention strategies specific to different processing lines.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0004425"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A <i>Rhodopseudomonas</i> strain with a substantially smaller genome retains the core metabolic versatility of its genus.","authors":"Yasuhiro Oda, William C Nelson, William G Alexander, Stella Nguyen, Robert G Egbert, Caroline S Harwood","doi":"10.1128/aem.02056-24","DOIUrl":"10.1128/aem.02056-24","url":null,"abstract":"<p><p><i>Rhodopseudomonas</i> are a group of phototrophic microbes with a marked metabolic versatility and flexibility that underpins their potential use in the production of value-added products, bioremediation, and plant growth promotion. Members of this group have an average genome size of about 5.5 Mb, but two closely related strains have genome sizes of about 4.0 Mb. To identify the types of genes missing in a reduced genome strain, we compared strain DSM127 with other <i>Rhodopseudomonas</i> isolates at the genomic and phenotypic levels. We found that DSM127 can grow as well as other members of the <i>Rhodopseudomonas</i> genus and retains most of their metabolic versatility, but it has many fewer genes associated with high-affinity transport of nutrients, iron uptake, nitrogen metabolism, and biodegradation of aromatic compounds. This analysis indicates genes that can be deleted in genome reduction campaigns and suggests that DSM127 could be a favorable choice for biotechnology applications using <i>Rhodopseudomonas</i> or as a strain that can be engineered further to reside in a specialized natural environment.IMPORTANCE<i>Rhodopseudomonas</i> are a cohort of phototrophic bacteria with broad metabolic versatility. Members of this group are present in diverse soil and water environments, and some strains are found associated with plants and have plant growth-promoting activity. Motivated by the idea that it may be possible to design bacteria with reduced genomes that can survive well only in a specific environment or that may be more metabolically efficient, we compared <i>Rhodopseudomonas</i> strains with typical genome sizes of about 5.5 Mb to a strain with a reduced genome size of 4.0 Mb. From this, we concluded that metabolic versatility is part of the identity of the <i>Rhodopseudomonas</i> group, but high-affinity transport genes and genes of apparent redundant function can be dispensed with.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0205624"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584406","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":"Efficient genetic manipulation of <i>Shewanella</i> through targeting defense islands.","authors":"Yilong Ruan, Huan Tang, Tongxuan Cai, Xiaofei Du, Tianlang Liu, Xiaoxue Wang, Pengxia Wang","doi":"10.1128/aem.02499-24","DOIUrl":"10.1128/aem.02499-24","url":null,"abstract":"<p><p>The <i>Shewanella</i> genus is widely recognized for its remarkable respiratory adaptability in anaerobic environments, exhibiting potential for bioremediation and microbial fuel cell applications. However, the genetic manipulation of certain <i>Shewanella</i> strains is hindered by defense systems that limit their genetic modification in biotechnology processes. In this study, we present a systematic method for predicting, mapping, and functionally analyzing defense islands within bacterial genomes. We investigated the genetically recalcitrant strain <i>Shewanella putrefaciens</i> CN32 and identified several defense systems located on two genomic islands integrated within the conserved chromosomal genes <i>trmA</i> and <i>trmE</i>. Our experimental assays demonstrated that overexpression of excisionases facilitated the excision of these islands from the chromosome, and their removal significantly enhanced the genetic manipulation efficiency of <i>S. putrefaciens</i> CN32. Further analysis revealed that these defense islands are widespread across various <i>Shewanella</i> strains and other gram-negative bacteria. This study presents an effective strategy to circumvent genetic barriers and fully exploit the potential of <i>Shewanella</i> for environmental and microbial engineering applications.</p><p><strong>Importance: </strong>Efficiently modifying bacterial genomes is critical for advancing their industrial applications. However, bacteria in complex environments naturally develop defense mechanisms in response to bacteriophages and exogenous DNA, which pose significant challenges to their genetic modification. Several methods have emerged to tackle these challenges, including <i>in vitro</i> methylation of plasmid DNA and targeting specific restriction-modification (R-M) and CRISPR loci. Nevertheless, many bacteria harbor multiple, often uncharacterized defense mechanisms, limiting these strategies. Our study differs from previous approaches by specifically targeting defense islands-clusters of defense systems located within mobile genetic elements. Here, we investigated <i>Shewanella putrefaciens</i> CN32 and identified two key defense islands responsible for these protective functions. By selectively deleting these defense islands, we significantly enhanced the efficiency of genetic manipulation in <i>S. putrefaciens</i>. Our findings not only demonstrate a promising strategy for improving genetic engineering in <i>Shewanella</i> but also suggest broader applicability across other bacterial species. This work opens new opportunities for optimizing microbial processes in biotechnology, highlighting the potential of defense island-targeted genetic modification.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0249924"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673193","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":"SGBP-B-like bimodular cellulose-binding protein CHU_1279 is essential for cellulose utilization by <i>Cytophaga hutchinsonii</i>.","authors":"Weixin Zhang, Lizhu Li, Tengxin Li, Xin Li, Xia Wang, Qiang Yao, Xuemei Lu, Guanjun Chen, Weifeng Liu","doi":"10.1128/aem.02471-24","DOIUrl":"10.1128/aem.02471-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The widespread cellulolytic specialist &lt;i&gt;Cytophaga hutchinsonii&lt;/i&gt; belonging to the phylum Bacteroidetes adopted a unique cellulose utilization strategy that did not conform to the known cellulose-degrading paradigms involving free cellulases or cellulosomes. The strategy used by &lt;i&gt;C. hutchinsonii&lt;/i&gt; still remains largely unclear. In this study, we showed that &lt;i&gt;chu_1279&lt;/i&gt; within the &lt;i&gt;chu_1276-chu_1280&lt;/i&gt; gene cluster, which has been previously shown to be important for cellulose utilization by &lt;i&gt;C. hutchinsonii&lt;/i&gt;, encodes an outer membrane protein, and its elimination prohibited bacterial growth on cellulose. Structural prediction revealed that CHU_1279 is a surface glycan-binding protein B (SGBP-B)-like protein comprising two putative carbohydrate-binding module (CBM)-like domains. Further analyses verified that recombinant CHU_1279 displayed significant cellulose-binding protein, and its C-terminal domain is predominantly responsible for cellulose binding. Expression of the C-terminal domain but not the N-terminal domain restored cellulose utilization of ∆&lt;i&gt;chu_1279&lt;/i&gt;. Moreover, site-directed mutagenesis analyses identified three aromatic residues important for cellulose binding of the recombinant CHU_1279 protein. The defective cellulose utilization of ∆&lt;i&gt;chu_1279&lt;/i&gt; cells otherwise could be recovered by CHU_1279 variants with significantly damaged cellulose-binding capability. Sequence analyses revealed that orthologs of CHU_1279 as well as the atypical polysaccharide utilization loci (PUL) constituted by the gene cluster &lt;i&gt;chu_1276-chu_1280&lt;/i&gt; are also present in two other cellulolytic Bacteroidetes bacteria, &lt;i&gt;Cytophaga aurantiaca&lt;/i&gt; and &lt;i&gt;Sporocytophaga myxococcoides&lt;/i&gt;, which are closely related to &lt;i&gt;C. hutchinsonii&lt;/i&gt;. Our results contribute to unveiling the unique mechanism underlying the efficient cellulose utilization by &lt;i&gt;C. hutchinsonii&lt;/i&gt; and similar cellulolytic bacteria.IMPORTANCEMost members of the phylum Bacteroidetes are highly competitive and efficient degraders of complex polysaccharides largely ascribed to their employment of a SusC-like system encoded by a polysaccharide utilization locus (PUL). However, characterization of PULs is limited to those responsible for utilization of (semi)soluble glycans. PULs involved in the utilization of cellulose, the most abundant renewable polymer, have not been identified and functionally characterized yet. We demonstrated that &lt;i&gt;chu_1279&lt;/i&gt; in the cellulolytic specialist &lt;i&gt;C. hutchinsonii&lt;/i&gt; encodes an SGBP-B-like protein that is required for cellulose utilization, supporting that the gene cluster &lt;i&gt;chu_1276-chu_1280&lt;/i&gt; in &lt;i&gt;C. hutchinsonii&lt;/i&gt; encodes an atypical PUL system dedicated to cellulose assimilation. Further analyses showed that this atypical PUL system is also present in two other cellulolytic Bacteroidetes bacteria. This study not only contributes to unveiling the unusual cellulose utilization strategy adopted by &lt;i&gt;C. hutchinsonii","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0247124"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A suite of ddPCR assays targeting microbial pathogens for improved management of shellfish aquaculture.","authors":"Mark Ciesielski, Thomas Clerkin, Nicholas Funnell, Tal Ben-Horin, Rachel T Noble","doi":"10.1128/aem.02149-24","DOIUrl":"10.1128/aem.02149-24","url":null,"abstract":"<p><p>The shellfish aquaculture industry is one of the fastest-growing sectors of global food production, but it is currently facing major challenges stemming from microbial pathogens. This study presents an optimized and validated suite of droplet digital PCR (ddPCR) assays using water samples proximal to oyster farms in North Carolina to quantify pathogens relevant to the aquaculture industry. Two of the molecular assays enable the quantification of the pathogens, <i>Vibrio parahaemolyticus</i> and <i>Perkinsus marinus</i>, that threaten human health and oyster performance, respectively. This work also introduces two ddPCR assays that enable the simultaneous quantification of at least nine ecologically relevant <i>Vibrio spp</i>. using only two sets of primers and probes targeting the glycosyl hydrolase family 18 (GH18) domain of the <i>chiA</i> gene in <i>Vibrio</i> bacteria. The entire suite of assays was applied to single assessments at 12 sites, revealing heterogeneity in microbial pathogen concentrations across the coastal landscape and variability of abundances within individual estuarine river systems. Additionally, a longitudinal study conducted at a demonstration lease elucidated unique temporal trends for all microbial targets. Notably, when concentrations of <i>Vibrio spp</i>. quantified using the two assays targeting the <i>chiA</i> gene reached their maximum, the daily probability of mortality increased, suggesting a role for other ecologically pertinent <i>Vibrio spp</i>. in the progression of mortality that would otherwise be missed. This study highlights the utility of ddPCR for the advancement of shellfish management by offering insights into the spaciotemporal dynamics of microbial pathogens.</p><p><strong>Importance: </strong>Climate change is drastically altering the environment and changing the abundance and geographical distribution of marine pathogens. These microbial species put additional pressure on the aquaculture industry by acting as sources of disease for animals important to the food industry as well as for humans upon consumption of contaminated food. To address growing concerns, high-resolution monitoring of pathogens can offer insights for effective management in a critical industry. Validated in the field, the suite of molecular droplet digital PCR assays presented here improves upon current methods, enabling the simultaneous quantification of several targets. This technology makes it possible to track pathogens as they move through the environment and reveals changes in abundance that may inform adjustments to farming practices aimed at mitigating negative outcomes. Additionally, this work presents a unique approach to molecular assay design that unveils potential drivers of ecological shifts and emerging etiologies of disease more efficiently.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0214924"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762869","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":"First report of the agricultural biocontrol agent <i>Bacillus velezensis</i> and foodborne outbreak due to rope spoilage in cakes.","authors":"Donald E Brannen, Jere Marks, Richard Schairbaum, Rick Bokanyi","doi":"10.1128/aem.02570-24","DOIUrl":"10.1128/aem.02570-24","url":null,"abstract":"<p><p>This paper presents an outbreak involving retail bakery cakes and a celebration at a business with multiple sites. <i>Bacillus</i> spore-forming bacteria have been identified as the cause of \"ropey bread\" spoilage for over 100 years. Causative strains of rope spoilage include <i>B. subtilis</i> and other <i>Bacillus</i> species. Thirty-five employees identified as having been at a celebration event across 11 sites were questioned to characterize the amount of cake eaten, observations, and symptoms. No human specimens were obtained, but leftover cake was analyzed by the Ohio Department of Health Bureau of Public Health Laboratory. The odds that cake caused symptoms were 9.23 (1.02-83). The presence of odor decreased the amount eaten by 151 g (103-205 g), <i>P</i> = 0.001. Enteric symptoms developed 0.41-4.5 hours after exposure, with 5 of 12 cases having latent diarrhea. Cakes were positive for <i>Bacillus velezensis</i>. This appears to be the first mention of <i>B. velezensis</i> as a contributor to the re-emergence of rope spoilage in the bakery industry. Updates to the <i>Bacillus</i> taxonomy starting in 1973 may account for why <i>B. subtilis</i> and other <i>Bacillus</i> strains are historically listed without mention of <i>B. velezensis</i> as a cause of rope spoilage. Given the ability of <i>B. velezensis</i> to be an effective biocontrol agent and to grow at pH and water activity levels like many baked goods, there is a need to study issues along the entire food chain to balance the impact on biocontrol additives on food production and safety.IMPORTANCEThis appears to be the first mention of <i>Bacillus velezensis</i> as a contributor to the re-emergence of rope spoilage in the bakery industry. Given the ability of <i>B. velezensis</i> to be an effective biocontrol agent and to grow at pH and water activity levels like many baked goods, there is a need to study issues along the entire food chain to balance the impact on biocontrol additives on food production and safety.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0257024"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727489","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}