Applied and Environmental Microbiology最新文献

{"title":"Compositional shifts and co-occurrence patterns of topsoil bacteria and micro-eukaryotes across a permafrost thaw gradient in alpine meadows of the Qilian Mountains, China.","authors":"Zhu Wang, Yang Liu, Fang Wang","doi":"10.1128/aem.01955-24","DOIUrl":"10.1128/aem.01955-24","url":null,"abstract":"<p><p>Soil microorganisms play a pivotal role in the biogeochemical cycles of alpine meadow ecosystems, especially in the context of permafrost thaw. However, the mechanisms driving microbial community responses to environmental changes, such as variations in active layer thickness (ALT) of permafrost, remain poorly understood. This study utilized next-generation sequencing to explore the composition and co-occurrence patterns of soil microbial communities, focusing on bacteria and micro-eukaryotes along a permafrost thaw gradient. The results showed a decline in bacterial alpha diversity with increasing permafrost thaw, whereas micro-eukaryotic diversity exhibited an opposite trend. Although changes in microbial community composition were observed in permafrost and seasonally frozen soils, these shifts were not statistically significant. Bacterial communities exhibited a greater differentiation between frozen and seasonally frozen soils, a pattern not mirrored in eukaryotic communities. Linear discriminant analysis effect size analysis revealed a higher number of potential biomarkers in bacterial communities compared with micro-eukaryotes. Bacterial co-occurrence networks were more complex, with more nodes, edges, and positive linkages than those of micro-eukaryotes. Key factors such as soil texture, ALT, and bulk density significantly influenced bacterial community structures, particularly affecting the relative abundances of the Acidobacteria, Proteobacteria, and Actinobacteria phyla. In contrast, fungal communities (e.g., <i>Nucletmycea</i>, <i>Rhizaria</i>, <i>Chloroplastida</i>, and <i>Discosea</i> groups) were more affected by electrical conductivity, vegetation coverage, and ALT. This study highlights the distinct responses of soil bacteria and micro-eukaryotes to permafrost thaw, offering insights into microbial community stability under global climate change.IMPORTANCEThis study sheds light on how permafrost thaw affects microbial life in the soil, with broader implications for understanding climate change impacts. As permafrost degrades, it alters the types and numbers of microbes in the soil. These microbes play essential roles in environmental processes, such as nutrient cycling and greenhouse gas emissions. By observing shifts from bacteria-dominated to fungi-dominated communities as permafrost thaws, the study highlights potential changes in these processes. Importantly, this research suggests that the stability of microbial networks decreases with permafrost degradation, potentially disrupting the delicate balance of these ecosystems. The findings not only deepen our understanding of microbial responses to changing climates but also support the development of strategies to monitor and potentially mitigate the effects of climate change on fragile high-altitude ecosystems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0195524"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397771","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":"Persistence in time: the hunt for <i>Bacillus anthracis</i> at a historic tannery site in Austria reveals genetic diversity thought extinct.","authors":"Maximilian F Mayerhofer-Rochel, Florian Himmelbauer, Pierre Reinprecht, Sebastian Herndler, Hugo Weidinger, Hans-Jörg Hellinger, Michael P Szostak, Gregor Grass, Monika Ehling-Schulz","doi":"10.1128/aem.01732-24","DOIUrl":"10.1128/aem.01732-24","url":null,"abstract":"<p><p>Identifying and analyzing historic anthrax loci may provide a treasure trove to fill in the gaps of persistence in time and genetic diversity of <i>Bacillus anthracis</i>. In countries where anthrax has become a disease of the past, detailed knowledge of the exact location and stability of spores in soil reservoirs is limited. Reviewing archival records may provide valuable clues to unearthing such forgotten sites. Knowledge of anthrax diversity in Austria is scarce, as the only available isolates-originating from the last outbreak in Austria in 1988-cluster in the B.Br.004 (CNEVA) canonical single-nucleotide polymorphism (canSNP) group. Thus, we analyzed archival records on anthrax incidents in Austria to locate historic <i>B. anthracis</i> soil reservoirs. In parallel, we tested the performance of different soil processing protocols for the isolation of <i>B. anthracis</i> spores to establish a suitable workflow for screening historical anthrax loci. Using an optimized workflow, we were able to isolate viable <i>B. anthracis</i> spores 80 years after the last occurrence of anthrax at an abandoned tannery identified through our archival work. Genome analysis of the isolated strains allowed to improve the phylogeographic resolution within the hitherto poorly covered A.Br.064 (V770) canSNP group by linking historical records to genetic information. Furthermore, our results re-emphasize that <i>B. anthracis</i> can survive for decades at historic sites and may pose a health threat when such sites are eventually reactivated by climatic factors or human intervention.</p><p><strong>Importance: </strong><i>Bacillus anthracis</i> is a continuing threat from a One Health perspective since it leads to severe infections in animals and humans. Ongoing climate change or human activities can reactivate historical <i>B. anthracis</i> loci, previously considered inactive or forgotten. Therefore, knowledge of historic anthrax incidents at abandoned animal processing facilities, such as tanneries or farmyards, along with robust detection protocols, is of prime interest when monitoring this important zoonosis. As shown here, archival records of possible origins of anthrax-contaminated goods received at tanneries are valuable sources and support these efforts. Investigation for viable spores at such historical sites could not only provide new insights into the past genetic diversity and population structure of <i>B. anthracis</i> but also provide important information for taking appropriate measures to prevent future outbreaks originating from these sites.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0173224"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921346/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363609","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":"Diversity and abundance of filamentous and non-filamentous \"<i>Leptothrix\"</i> in global wastewater treatment plants.","authors":"Karina Seguel Suazo, Marta Nierychlo, Zivile Kondrotaite, Francesca Petriglieri, Miriam Peces, Caitlin Singleton, Jan Dries, Per H Nielsen","doi":"10.1128/aem.01485-24","DOIUrl":"10.1128/aem.01485-24","url":null,"abstract":"<p><p>Species belonging to the genus <i>Leptothrix</i> are widely distributed in the environment and in activated sludge (AS) wastewater treatment plants (WWTPs). They are commonly found in iron-rich environments and reported to cause filamentous bulking in WWTPs. In this study, the diversity, distribution, and metabolic potential of the most prevalent <i>Leptothrix</i> spp. found in AS worldwide were studied. Our 16S rRNA amplicon survey showed that <i>Leptothrix</i> belongs to the general core community of AS worldwide, comprising 32 species with four species being most commonly found. Their taxonomic classification was re-evaluated based on both 16S rRNA gene and genome-based phylogenetic analysis showing that three of the most abundant \"<i>Leptothrix\"</i> species represented species in three other genera, <i>Rubrivivax</i>, <i>Ideonella</i>, and the novel genus, <i>Ca</i>. Intricatilinea. New fluorescence <i>in situ</i> hybridization (FISH) probes revealed rod-shaped morphology for the novel <i>Ca</i>. Rubrivivax defluviihabitans and <i>Ca</i>. Ideonella esbjergensis<i>,</i> while filamentous morphology was found only for <i>Ca</i>. Intricatilinea gracilis. Analysis of high-quality metagenome-assembled genomes revealed metabolic potential for aerobic growth, fermentation, storage of intracellular polymers, partial denitrification, photosynthesis, and iron reduction. FISH in combination with Raman microspectroscopy confirmed the <i>in situ</i> presence of chlorophyll and carotenoids in <i>Ca</i>. Rubrivivax defluviihabitans and <i>Ca</i>. Intricatilinea gracilis. This study resolves the taxonomy of abundant but poorly classified \"<i>Leptothrix\"</i> species, providing important insights into their diversity, morphology, and function in global AS wastewater treatment systems.IMPORTANCEThe genus <i>Leptothrix</i> has been extensively studied and described since the 1880s, with six species currently described but with the majority uncultured and undescribed. Some species are assumed to have a filamentous morphology and can cause settling problems in wastewater treatment plants (WWTPs). Here, we revised the classification of the most abundant <i>Leptothrix</i> spp. present in WWTPs across the world, showing that most belong to other genera, such as <i>Rubrivivax</i> and <i>Ideonella</i>. Furthermore, most do not have a filamentous morphology and are not problematic in WWTPs as previously believed. Metabolic reconstruction, including some traits validated <i>in situ</i> by the application of new fluorescence <i>in situ</i> hybridization probes and Raman microspectroscopy, provided additional insights into their metabolism. The study has contributed to a better understanding of the diversity, morphology, and function of \"<i>Leptothrix</i>,\" which belong to the abundant core community across global activated sludge WWTPs.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0148524"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143413048","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":"Gut-binding peptides as potential tools to reduce virus binding to honey bee gut surface proteins.","authors":"Ya Guo, Lincoln N Taylor, Ruchir Mishra, Adam G Dolezal, Bryony C Bonning","doi":"10.1128/aem.02418-24","DOIUrl":"10.1128/aem.02418-24","url":null,"abstract":"<p><p>Colonies of the western honey bee, <i>Apis mellifera,</i> are severely impacted by a wide range of stressors, with <i>Varroa</i> mites and associated viruses being among the most serious threats to honey bee health. Viral load plays an important role in colony demise, with the iflavirus <i>Deformed wing virus</i> (DWV) and the dicistrovirus <i>Israeli acute paralysis virus</i> (IAPV) being of particular concern. By feeding adult honey bees on a phage display library to identify gut-binding peptides (R. Mishra, Y. Guo, P. Kumar, P. E. Cantón, C. S. Tavares, R. Banerjee, S. Kuwar, and B. C. Bonning, Curr Res Insect Sci, 1:100012, https://doi.org/10.1016/j.cris.2021.100012), we identified Bee midgut-Binding Peptide (BBP2.1), which shares 75% and 85% identity with regions on the DWV capsid protein and IAPV ORFx protein, respectively. These viral protein domains are likely to be instrumental in virus interaction with the honey bee gut. Pull-down assays with honey bee gut brush border membrane vesicles were used to confirm peptide-mCherry binding to the gut for BBP2.1 and the two similar virus-derived sequences, peptides BBP2.1^DWV and BBP2.1^IAPV. <i>In vitro</i> competition assays showed that all three peptides compete with both IAPV and DWV virions for binding to honey bee gut-derived brush border membrane vesicles, suggesting that the three peptides and the two viruses bind to the same proteins. Ingestion of BBP2.1 reduced the movement of DWV, but not IAPV from the honey bee gut into the body and did not rescue IAPV-associated mortality. These results are discussed in relation to the biological function of IAPV ORFx and the potential utility of virus-blocking peptides for suppression of virus infection to reduce virus load and virus-associated honey bee mortality.IMPORTANCEEach year, approximately 40% of managed honey bee hives in the United States are lost due to a variety of environmental stressors. Although increases in virus infection are among the most important factors resulting in colony loss, there are currently no effective tools for the management of virus infection in honey bees. In this study, we identified a peptide that binds to the gut of the honey bee and competes with two of the most important honey bee viruses, Israeli acute paralysis virus of bees (IAPV) and Deformed wing virus (DWV), for binding to gut proteins. <i>In vivo</i> competition between this peptide and DWV demonstrates the potential utility of gut-binding peptides for the protection of honey bees from virus infection for reduced virus-associated honey bee mortality.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0241824"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522146","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":"The production of esters by specific sourdough lactic acid bacteria species is limited by the precursor concentrations.","authors":"Inés Pradal, Stefan Weckx, Luc De Vuyst","doi":"10.1128/aem.02216-24","DOIUrl":"10.1128/aem.02216-24","url":null,"abstract":"<p><p>The production of fruity esters by sourdough lactic acid bacteria (LAB) and yeasts has not been explored in detail. Moreover, the biosynthesis of esters by LAB species under conditions similar to those occurring during sourdough production is still questionable. Concerning yeasts, a genome mining of 75 genomes revealed a strain dependency of the presence of seven specific ester biosynthesis genes. Accordingly, PCR assays to detect these acetate (<i>ATF1</i> and <i>ATF2</i>) and ethyl ester (<i>EHT1</i> and <i>EEB1</i>) biosynthesis genes were developed and used to screen 91 strains of yeast species. Concerning LAB, a genome mining of 401 genomes revealed a species dependency of the presence of three esterase-encoding genes (<i>estA</i>, <i>estB</i>, and <i>estC</i>). A phenotypic analysis carried out with a selection of 10 strains of the LAB species <i>Companilactobacillus crustorum</i>, <i>Companilactobacillus nantensis</i>, <i>Companilactobacillus paralimentarius, Fructilactobacillus sanfranciscensis</i>, <i>Lactiplantibacillus xiangfangensis</i>, <i>Levilactobacillus zymae</i>, and <i>Limosilactobacillus fermentum</i> in a wheat sourdough simulation medium (WSSM) supplemented with ester precursor molecules ([higher] alcohols and fatty acids) revealed that their ester biosynthesis capacity was limited by the precursor concentrations. Ethyl acetate and ethyl lactate were produced by all strains, except for those of <i>Frul. sanfranciscensis</i>. These results suggested that one of the esterase-encoding genes considered could be implicated in the ethyl acetate and/or ethyl lactate biosynthesis. Overall, the ester biosynthesis capacity by LAB is of great interest in view of fruity flavor formation during sourdough and sourdough bread productions.</p><p><strong>Importance: </strong>The present study gave insights into the production of esters, which impart fruity flavors to fermented foods, by not only sourdough yeasts but also lactic acid bacteria. It showed that some lactic acid bacteria species can synthesize the esters ethyl acetate (sweet notes) and ethyl lactate (creamy notes) under specific conditions. The information gathered during the present study will enable sourdough bakers and companies from the bakery sector to get more information on how to produce sourdoughs that can add fruity notes to the final products after a rational screening and selection of potential starter culture strains.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0221624"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514471","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":"Erratum for Zhang et al., \"Evaluating the stability of nursery-established arbuscular mycorrhizal fungal associations in apple rootstocks\".","authors":"Huiting Zhang, Wanyan Wang, Loren Honaas, Mark Mazzola, Tracey Somera","doi":"10.1128/aem.00198-25","DOIUrl":"10.1128/aem.00198-25","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0019825"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466705","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":"Comparative assessment of a restored and natural wetland using ¹³C-DNA SIP reveals a higher potential for methane production in the restored wetland.","authors":"Nora Hamovit, Taniya RoyChowdhury, Denise M Akob, Xuesong Zhang, Gregory McCarty, Stephanie Yarwood","doi":"10.1128/aem.02161-24","DOIUrl":"10.1128/aem.02161-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Wetlands are the largest natural source of methane (CH&lt;sub&gt;4&lt;/sub&gt;), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland's Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with &lt;sup&gt;13&lt;/sup&gt;C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus &lt;i&gt;Methanosarcina&lt;/i&gt; were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders &lt;i&gt;Firmicutes&lt;/i&gt; and &lt;i&gt;Bacteroidetes&lt;/i&gt;. In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla &lt;i&gt;Acidobacteria&lt;/i&gt;, &lt;i&gt;Actinobacteria&lt;/i&gt;, and class &lt;i&gt;Alphaproteobacteria&lt;/i&gt;. Iron-reducing bacteria, in the genus &lt;i&gt;Geobacter&lt;/i&gt;, were active across all redox conditions in both the restored and the natural cores, except the natural oxic-anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.IMPORTANCEMethane (CH&lt;sub&gt;4&lt;/sub&gt;) is a potent greenhouse gas with an atmospheric half-life of ~10 years. Wetlands are the largest natural emitters of CH&lt;sub&gt;4&lt;/sub&gt;, but CH&lt;sub&gt;4&lt;/sub&gt; dynamics are difficult to constrain due to high spatial and temporal variability. In the past, wetlands were drained for agriculture. Now, restoration is an important strategy to increase these ecosystems' potential for sequestering carbon. However, the consequences of wetland restoration on carbon biogeochemistry are under-evaluated, and a thorough assessment of the active microbial community as a driver of biogeochemical changes is needed. Particularly, the effects of seasonal flooding/drying cycles in geographically isolated wetlands might have implications for CH&lt;sub&gt;4&lt;/sub&gt; emissions in both natural and restored wetlands. Here, we found that active microbial communities in natural and restored wetlands responded differently to flooding and drying regimes, resulting in differences in CH&lt;sub&gt;4&lt;/sub&gt; production potentials. Restored wetlands had a higher potential for CH&lt;sub&gt;4&lt;/sub&gt; production compared to natural w","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0216124"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254334","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":"Retrospective analysis of antimicrobial resistance associated with bovine respiratory disease.","authors":"Daniel Kos, Murray Jelinski, Antonio Ruzzini","doi":"10.1128/aem.01909-24","DOIUrl":"10.1128/aem.01909-24","url":null,"abstract":"<p><p>The administration and utility of antibiotics to control and treat bovine respiratory disease (BRD) in beef cattle feedlots is a growing concern. Antimicrobial resistance (AMR) among BRD-associated bacterial pathogens has been the subject of cultivation-dependent and cultivation-independent surveillance. Bacterial genome sequencing and metagenomic approaches facilitate the characterization of AMR in the beef industry; however, the current collection of cattle-associated AMR research programs lack connections to each other. A more integrated view of how antimicrobial use (AMU) is related to resistance at a gene level is needed. We sought to establish a catalog of commonly observed AMR genes (ARGs) in opportunistic bacterial pathogens that contribute to BRD using publicly available data sets that were generated by the scientific community with and without AMU in mind. The presence of these clinically relevant ARGs appeared to differ by geography. Greater sampling in North America facilitated the generation of a list of ARGs often encoded by <i>Mannheimia haemolytica</i> and <i>Pasteurella multocida</i>. Detection of clinically relevant ARGs in shotgun metagenomes of cattle-associated and accessible feedlot samples such as water, soil, and feces was possible but limited by relative sequence read abundance. An exception was the tylosin esterase-encoding gene <i>estT</i>, which is among the most frequently observed ARGs in <i>M. haemolytica</i> and feedlot-related metagenomic data sets. Finally, by re-evaluating studies on the impact of AMU on AMR in beef production systems, we show that conventional practices, including in-feed antibiotic use, increase the relative abundance of ARGs in animal-derived samples.IMPORTANCEThis retrospective analysis delivers a list of ARGs found in opportunistic pathogens that contribute to BRD. The high incidence of BRD in North America is linked to the origin and implementation of metaphylaxis to mitigate detrimental animal losses at feedlots. Notably, ARGs commonly observed in these pathogens isolated in North America were not conserved across the globe, underscoring the relationship between regional AMU and AMR. A positive relationship was also observed between the relative abundance of ARGs in cattle-associated metagenomes with greater exposure to antibiotics. Overall, this analysis should help to guide future surveillance efforts and experimental designs to more directly evaluate the impacts of feedlot practices on AMR.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0190924"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363199","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":"Traits determine dispersal and colonization abilities of microbes.","authors":"Isidora Echenique-Subiabre, Sara L Jackrel, Jay McCarren, Chase C James, Elisabet Perez-Coronel, Cindy Tran, Madeline Perreault, Ugbad Farah, P Signe White, Henry K Baker, Christopher B Wall, Lindsay Sager, Scott Becker, Andrew D Barton, Jonathan B Shurin","doi":"10.1128/aem.02055-24","DOIUrl":"10.1128/aem.02055-24","url":null,"abstract":"<p><p>Many microbes disperse through the air, yet the phenotypic traits that enhance or constrain aerial dispersal or allow successful colonization of new habitats are poorly understood. We used a metabarcoding bacterial and eukaryotic data set to explore the trait structures of the aquatic, terrestrial, and airborne microbial communities near the Salton Sea, California, as well as those colonizing a series of experimental aquatic mesocosms. We assigned taxonomic identities to amplicon sequence variants (ASVs) and matched them to functional trait values through published papers and databases that infer phenotypic and/or metabolic traits information from taxonomy. We asked what traits distinguish successful microbial dispersers and/or colonizers from terrestrial and aquatic source communities. Our study found broad differences in taxonomic and trait composition between dispersers and colonizers compared to the source soil and water communities. Dispersers were characterized by larger cell diameters, colony formation, and fermentation abilities, while colonizers tended to be phototrophs that form mucilage and have siliceous coverings. Shorter population doubling times, spore-, and/or cyst-forming organisms were more abundant among the dispersers and colonizers than the sources. These results show that the capacity for aerial dispersal and colonization varies among microbial functional groups and taxa and is related to traits that affect other functions like resource acquisition, predator avoidance, and reproduction. The ability to disperse and colonize new habitats may therefore distinguish microbial guilds based on tradeoffs among alternate ecological strategies.IMPORTANCEMicrobes have long been thought to disperse rapidly across biogeographic barriers; however, whether dispersal or colonization vary among taxa or groups or is related to cellular traits remains unknown. We use a novel approach to understand how microorganisms disperse and establish themselves in different environments by looking at their traits (physiology, morphology, life history, and behavior characteristics). By collecting samples from habitats including water, soil, and the air and colonizing experimental tanks, we found dispersal and invasion vary among microorganisms. Some taxa and functional groups are found more often in the air or colonizing aquatic environments, while others that are commonly found in the soil or water rarely disperse or invade new habitat. Interestingly, the traits that help microorganisms survive and thrive also play a role in their ability to disperse and colonize. These findings have significant implications for understanding microorganisms' success and adaptation to new environments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0205524"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456815","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":"CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment.","authors":"Dirk Hackenberger, Hamna Imtiaz, Amogelang R Raphenya, Brian P Alcock, Hendrik N Poinar, Gerard D Wright, Andrew G McArthur","doi":"10.1128/aem.01876-24","DOIUrl":"10.1128/aem.01876-24","url":null,"abstract":"<p><p>Better interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here, we describe the Comprehensive Antibiotic Resistance Probe Design Machine (CARPDM), a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and tested two separate probe sets: allCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database's protein homolog models (<i>n</i> = 4,661), and clinicalCARD, which focuses on a clinically relevant subset of resistance genes (<i>n</i> = 323). We demonstrate that allCARD increases the number of reads mapping to resistance genes by up to 594-fold. clinicalCARD performs similarly when clinically relevant genes are present, increasing the number of resistance-gene mapping reads by up to 598-fold. In parallel with this development, we have established a protocol to synthesize any probe set in-house, saving up to 350 dollars per reaction. Together, these probe sets, their associated design program CARPDM, and the protocol for in-house synthesis will democratize metagenomic resistome analyses, allowing researchers access to a cost-effective and efficient means to explore the antibiotic resistome.IMPORTANCEAntimicrobial resistance threatens to undermine all modern medicine and is driven by the spread of antimicrobial resistance genes among pathogens, environments, patients, and animals. DNA sequencing of complex samples, such as wastewater, shows considerable promise for tracking these genes and making risk assessments. However, these methods suffer from high costs and low detection limits, plus a requirement for frequent redesign due to the constantly evolving diversity of resistance genes. Building upon our Comprehensive Antibiotic Resistance Database, our research provides software for on-demand renewal, based on the latest knowledge of resistance gene diversity, of our novel bait-capture hybridization platform that simultaneously reduces cost and increases detection levels for DNA sequencing of complex samples. The significance of our research is in the development of new software tools, reagent synthesis protocols, and hybridization enrichment protocols to provide affordable, high-resolution metagenomics DNA sequencing, which we test using environmental and wastewater samples.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0187624"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522518","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}