Applied and Environmental Microbiology最新文献

{"title":"Survival, growth, and potential of horizontal gene transfer of antibiotic resistance genes of bovine <i>Salmonella</i> on the cantaloupe surface.","authors":"Zaira L Castro-Delgado, Norma Heredia, Jose Angel Merino-Mascorro, Eduardo Franco-Frías, Jorge E Dávila-Aviña, Santos García","doi":"10.1128/aem.01076-26","DOIUrl":"https://doi.org/10.1128/aem.01076-26","url":null,"abstract":"<p><p><i>Salmonella</i> outbreaks are often linked to contaminated cantaloupes, and bacterial multiple antibiotic resistance is frequently observed. Research is needed to understand the growth and survival of <i>Salmonella</i> on cantaloupe surfaces, and the mechanisms of antibiotic resistance in that environment. This study investigated the growth, survival, and capacity for horizontal gene transfer of antibiotic resistance genes in <i>Salmonella</i> on the surface of cantaloupe. Bovine-derived <i>Salmonella</i> isolates were inoculated onto the surface of cantaloupe and incubated at 35°C under 65-75% humidity for 5 days. Each isolate was co-inoculated with donor <i>E. coli</i> CSH56 harboring helper plasmid RP4-8 and mobilizable plasmid pSC27, which carries kanamycin, neomycin, and ampicillin resistance genes. One hundred microliters of the <i>Salmonella</i> suspension (1 × 10⁸ CFU/mL) and 100 µL of the <i>E. coli</i> suspension (1 × 10⁷ CFU/mL) was applied to each cantaloupe (1:10 ratio). <i>Salmonella</i> survival and growth were monitored on Hektoen agar, transconjugants were enumerated on Hektoen agar with kanamycin, and donor <i>E. coli</i> were quantified on MacConkey agar. All <i>Salmonella</i> isolates survived and exhibited growth within the 5-day period, with increases ranging from 0.94 log₁₀ CFU/mL to 3.43 log₁₀ CFU/mL. Notably, all <i>Salmonella</i> isolates possess the capability to accept and integrate sequences derived from the pSC27 plasmid from <i>E. coli</i> into their chromosome, both <i>in vitro</i> and on cantaloupe. After conjugation, the count of <i>Salmonella</i> mutants carrying the plasmid was 2.79 log₁₀ CFU/mL <i>in vitro</i>. The survival, growth, and horizontal gene transfer of <i>Salmonella</i> on the surface of cantaloupe pose significant risks to public health.IMPORTANCE<i>Salmonella</i>, a leading cause of foodborne diseases, poses a global health threat, with multidrug resistance emerging as a severe problem. Cantaloupes have been implicated in salmonellosis outbreaks in multiple countries over the last three decades. We hypothesize that acquisition of antibiotic resistance genes from other bacteria may occur on the surface of the fruit. This study established that <i>Salmonella</i> can survive, proliferate, and acquire antibiotic resistance genes on cantaloupe surfaces. This observation underscores the potential risks on the growth and transfer of genes between pathogens such as <i>Salmonella</i> and <i>E. coli</i> in foods. This impact goes beyond disease production and contributes to the rapid escalation of antimicrobial resistance and transmission of virulence genes in foods and the environment, which is a significant threat to public health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0107626"},"PeriodicalIF":4.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102979","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":"Formulations containing co-biotic compounds mediate microbiome function and composition without increased gas production in an <i>ex vivo</i> gastrointestinal model.","authors":"Brooke A Napier, Bryan D Merrill, Madeline Krieger, Dirk Gevers, Gregor Reid","doi":"10.1128/aem.01311-26","DOIUrl":"https://doi.org/10.1128/aem.01311-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Dietary supplement formulations that contain co-biotics or compounds that modulate biological processes in both the host and microbiome to confer a health benefit are an emerging strategy to fine-tune both host physiology and gut microbiome function. Here, we evaluated three novel formulations containing co-biotic compounds (DM-02, a multivitamin; AM-02, formulated for energy and focus; and PM-02, formulated to promote sleep) for their effects on human gut microbiome composition and function. The three formulations and untreated control (Unt-Ctrl) were subjected to upper gastrointestinal digestion, after which the digesta were exposed to 24-h simulated colonic fermentation in the validated &lt;i&gt;ex vivo&lt;/i&gt; systemic intestinal fermentation research (SIFR) technology (&lt;i&gt;n&lt;/i&gt; = 6 healthy adults). Outcomes included pH, short-chain fatty acid (SCFA) and gas production, ultra-deep metagenomic profiling, and untargeted metabolomics of post-colonic supernatants, each compared to Unt-Ctrl. All three formulations significantly reduced pH (3%-4%) and increased total SCFAs (9%-11%) and acetate (9%-12%), with AM-02 and PM-02 also increasing butyrate by 20% and propionate by 7%-8%, without increasing gas production. Each formulation significantly enriched specific SCFA- and B-vitamin-producing taxa. AM-02 significantly increased the abundance of two pyruvate fermentation to acetate/lactate pathways. PM-02 significantly increased the abundance of two tryptophan biosynthesis pathways, accompanied by an increase in available tryptophan and the abundance of tryptophan-producing microbes. All three formulations increased the availability of microbiome-derived metabolites, indicating microbiome functional modulation by the treatments. These findings support clinical evaluation of these novel formulations as a strategy to enhance microbiome composition and function.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The gut microbiome produces metabolites, including short-chain fatty acids, B vitamins, and tryptophan derivatives, that are critical regulators of host physiology, from energy metabolism and gut barrier integrity to sleep and immune function. While probiotics introduce live microorganisms, and prebiotics selectively feed existing microbes, co-biotics represent a distinct category of compounds that simultaneously modulate host cell biology and microbiome activity. Despite growing interest in co-biotic supplementation, the impact of complete co-biotic-containing formulations on gut microbiome composition and functional output has not been evaluated. Using a validated &lt;i&gt;ex vivo&lt;/i&gt; gastrointestinal model inoculated with fecal microbiota from six healthy adults, we demonstrate that three supplement formulations containing co-biotic compounds consistently increased production of health-associated metabolites, selectively enriched beneficial microbial taxa, and modulated functional metabolic pathways, all without increasing gas production. These findings establish a me","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0131126"},"PeriodicalIF":4.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102915","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":"Regulation of central carbon metabolism and storage polymers by PTS^Ntr in <i>Rhizobium leguminosarum</i>.","authors":"Olivia Tjahjono, Jingkai Wang, Evan Turner, Jürgen Prell, Wei E Huang, Philip S Poole, Carmen Sánchez-Cañizares","doi":"10.1128/aem.01073-26","DOIUrl":"https://doi.org/10.1128/aem.01073-26","url":null,"abstract":"<p><p>The coordination of intracellular carbon and nitrogen levels is essential for optimal bacterial growth and, in rhizobia, for survival in the soil, root colonization, and symbiotic interactions with their host plants. Here, we show that the phosphotransferase system PTS^Ntr, a global regulator of carbon and nitrogen metabolism, modulates the tricarboxylic acid (TCA) cycle activity and the accumulation of three major carbon storage polymers: glycogen, polyhydroxybutyrate, and exopolysaccharide in <i>Rhizobium leguminosarum</i>. The unphosphorylated form of the effector protein ManX is sufficient for the full activation of the TCA cycle dehydrogenase enzymes. Accordingly, loss of <i>manX</i> reduced dehydrogenase activity and redirected overflow carbon into storage polymers, phenocopying wild-type cells grown under nitrogen starvation. We further demonstrate that carbon metabolism in <i>R. leguminosarum</i> is also tightly regulated by the HPr kinase (HprK) protein. In an <i>hprK</i> mutant, loss of NPr Ser48 phosphorylation favors phosphotransfer through the histidyl arm and is predicted to increase phosphorylation of downstream PTS^Ntr components. When grown on glucose, the <i>hprK</i> mutant accumulates elevated intracellular pyrimidine levels and exhibits increased malate dehydrogenase and TCA cycle activity, consistent with a misregulated shift toward gluconeogenesis. This mutant also overproduces exopolysaccharide, an effect potentially mediated by crosstalk between phosphorylated PtsN and the ChvI/ChvG two-component regulatory system. Together, these data suggest that HprK exerts pleiotropic control over processes regulated by PTS^Ntr, influencing central metabolism while repressing exopolysaccharide production, likely by promoting the unphosphorylated state of PtsN.IMPORTANCEBacteria must continuously balance growth, nutrient availability, and storage to ensure fitness and survival in fluctuating environments. However, how regulatory networks integrate central metabolism with carbon storage remains poorly understood. This study reinforces the role of the PTS^Ntr system as a central coordinator of carbon routing and polymer accumulation. By revealing how ManX and HprK-dependent phosphorylation influence central metabolism and the production of major carbon storage polymers in <i>Rhizobium leguminosarum</i>, we show that disruption of PTS^Ntr signaling reprograms carbon allocation, uncoupling growth from carbon storage and mimicking nitrogen starvation even under nitrogen-replete conditions. These findings highlight a regulatory link between carbon-nitrogen signaling and bacterial storage strategies, with implications for cellular survival and plant symbiosis. More broadly, our work illustrates how global metabolic regulators shape bacterial physiological states, providing new insights into mechanisms that support microbial adaptation in complex environments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0107326"},"PeriodicalIF":4.2,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079456","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":"Effects of RyhB on Fur regulation of cytochrome <i>c</i> synthesis in <i>Shewanella oneidensis</i>.","authors":"Kaiyue Jie, Xinyue Liu, Fuqian Zhang, Jim Yah, Lulu Liu, Haichun Gao","doi":"10.1128/aem.01500-26","DOIUrl":"https://doi.org/10.1128/aem.01500-26","url":null,"abstract":"<p><p><i>Shewanella oneidensis</i> is one of the most extensively studied electrochemically active bacteria because of its unparalleled respiratory versatility, which is largely built on diverse cytochromes (cyts) <i>c</i>. It has been firmly established that Fur, RyhB, and Hfq are critical for cyt <i>c</i> production through regulation of iron homeostasis, but how they interplay remains largely unknown. In this study, we show that <i>S. oneidensis</i> RyhB carries novel features, such as unusual length and functional exchangeability with its <i>Escherichia coli</i> counterpart but not its <i>Vibrio cholerae</i> counterpart. The RyhB loss suppresses the signature phenotypes caused by the Fur loss, including impaired growth and cyt <i>c</i> production in <i>S. oneidensis</i>. Despite this, neither the direct regulation of expression of most cyt <i>c</i> genes nor the suppression of disrupted iron homeostasis resulting from Fur loss appears to be a primary mechanism underlying RyhB's influence on cyt <i>c</i> content. Rather, this effect is achieved by modulating heme levels; RyhB mediates the expression of the key genes in heme biosynthesis and the entire heme uptake/degradation system. Overall, our work highlights the significance of RyhB-mediated post-transcriptional regulation in the physiology of <i>S. oneidensis</i>, unraveling unexpected mechanisms by which RyhB affects cyt <i>c</i> biosynthesis.</p><p><strong>Importance: </strong>In bacteria, RyhB has been implicated in the regulation of diverse biological processes post-translationally. In <i>Shewanella oneidensis</i>, both Fur and RyhB influence the cytochrome (cyt) <i>c</i> content, which are the cornerstones of bacterial respiratory versatility and potential application in bioenergy and bioremediation. Here, we show that while RyhB generally exhibits an antagonistic relationship with Fur, it carries novel sequence features and differentially regulates heme biosynthesis and degradation, leading to altered cyt <i>c</i> content. The data presented show that the biological processes in a given bacterium regulated by RyhB are highly complex, amounting to the required coordination of multiple regulators to allow cells to respond to environmental changes promptly.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0150026"},"PeriodicalIF":4.2,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079523","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":"Welcome to the house-warming party: social interactions and antagonism against <i>Listeria monocytogenes</i> in multi-species biofilms.","authors":"Yatong C Jiang, Ranine El-Jurdi, Yuen Ying Chan, Donghe M Deng, Zhaohui S Xu, Michael G Gänzle","doi":"10.1128/aem.01386-26","DOIUrl":"https://doi.org/10.1128/aem.01386-26","url":null,"abstract":"<p><p><i>Listeria monocytogenes</i> integrates into multi-species biofilms and persists in food processing facilities. Its persistence depends on the composition of the microbial communities, but those species that accommodate <i>L. monocytogenes</i>, or not, remain to be identified. Moreover, the decision-making on biofilm vs pellicle formation in microbial communities remains poorly understood. It was the aim of this study to identify communities that accommodate <i>Listeria</i>, or not, and to observe biofilm vs pellicle formation in multi-species biofilms. We quantified <i>L. monocytogenes</i> in six reconstituted communities, each consisting of 5-19 strains. A 15-member community was simplified into five species to quantify <i>L. monocytogenes</i> in all 31 combinations of these five strains. <i>Janthinobacterium tructae</i> favored pellicle formation, while <i>Pseudomonas shahriarae</i> convinced others to join a surface-attached biofilm. In the six microbial communities, cell counts of <i>L. monocytogenes</i> were lowest when <i>Carnobacterium maltaromaticum</i> was also present. The antagonistic effect of <i>C. maltaromaticum</i> was confirmed when analyzing all combinations of five strains. The presence of <i>C. maltaromaticum</i> reduced cell counts of <i>L. monocytogenes</i> by about 1 log CFU/cm². <i>Serratia liquefaciens</i> also antagonized <i>L. monocytogenes</i>, but this was observed (<i>P</i> < 0.05) only in the absence of <i>C. maltaromaticum</i>. Genome analyses of the community identified close to 100 different quorum-sensing systems, including peptides that are also bactericidal against <i>L. monocytogenes</i>. We conclude that the language used to describe human social interactions is also suited to describe microbial interactions in multi-species biofilm communities, but unraveling mechanisms of communication among biofilm-embedded bacteria remains subject to future studies.</p><p><strong>Importance: </strong>Microbial communication in relation to biofilm vs pellicle formation and on whether to accommodate <i>Listeria monocytogene</i>s or not partially converge with quorum-sensing systems as a key mechanism. Two organisms, <i>Carnobacterium maltaromaticum</i> and <i>Serratia liquefaciens</i>, antagonized <i>L. monocytogenes</i>. Microbial interactions are strongly dependent on the complexity of the microbial community, and different behaviors were observed in biofilms formed by 2, 5, or 15 strains. Results presented in this study document that the use of protective cultures may also reduce persistence of <i>Listeria</i> in food processing facilities but are far from providing an understanding of communication and social rules in complex bacterial communities. The novel perspective on microbial interactions may direct future experiments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0138626"},"PeriodicalIF":4.2,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079486","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":"Double-edged sword of FeS oxidation in estuarine and coastal sediments: accelerating elemental cycling yet enhancing antibiotic resistance enrichment.","authors":"Wei Qiu, Xiufeng Tang, Boshuang Wu, Haoran Huang, Xiangyang Zhao, Jun Yuan, Xiaofei Li","doi":"10.1128/aem.01525-26","DOIUrl":"https://doi.org/10.1128/aem.01525-26","url":null,"abstract":"<p><p>Biogeochemical cycles exert significant influences on the fate and behavior of antibiotics in estuarine and coastal environments; however, ferrous sulfide (FeS)-mediated enrichment and dissemination of antibiotic resistance genes (ARGs) remain poorly understood. Here, we conducted microcosm experiments and field investigations to examine the relationships of FeS amendment, microbial communities, functional potentials in relation to elemental cycling, and ARG abundance. The positive effects of FeS on ARG abundance were aerobic dependent, which were accompanied by a significant enrichment of Proteobacteria, as the crucial hosts of ARGs. Proteobacteria were associated with systematic metabolic pathways for carbon fixation (Calvin-Benson-Bassham [CBB] cycle), N₂ fixation, and FeS oxidation. In addition, field samples from China estuarine and coastal wetlands further showed that CBB cycle, N₂ fixation, and sulfur oxidation pathways were significantly correlated with the relative abundance of ARGs. These findings collectively indicate that FeS oxidation facilitates enrichment and dissemination of ARGs through selective enrichment of Proteobacteria and consequent enhancement of metabolic synergies between sulfur, iron, carbon, and nitrogen cycles. However, FeS-mediated oxidation may also degrade microbial DNA and suppress ARG proliferation, indicating that the net outcome of ARG enrichment depends on oxygen conditions and microbial community filtering. The cascade processes of environmental regulation-community restructuring-metabolic synergy are of great significance to enhance ARG enrichment and dissemination. Therefore, redox fluctuations can enhance elemental cycling and further promote significant enrichment and dissemination of ARGs. These findings highlight the importance of redox dynamics in ARG monitoring and risk assessment in estuarine and coastal wetlands.IMPORTANCEEstuarine and coastal wetlands are important ecosystems for antibiotic resistance gene (ARG) enrichments. This study investigated FeS oxidation-mediated biogeochemical cycling and ARG dissemination. FeS oxidation increased enrichment and dissemination of the ARGs in estuarine and coastal sediments. The FeS oxidation reshaped microbial community structure and selectively enriched the critical Proteobacteria, which played the crucial hosts of the ARGs. The enrichment and dissemination of ARGs in the presence of FeS oxidation were due mainly to the enhanced metabolic coupling of sulfur oxidation, nitrogen fixation, and carbon fixation. CBB cycle, N₂ fixation, and sulfur oxidation pathways were also significantly correlated with ARG abundance along the latitudinal gradient. Therefore, enhanced elemental metabolic pathways under FeS oxidation exacerbated enrichment and dissemination of ARGs, highlighting the coupling mechanisms of biogeochemical cycle and ARGs in estuarine and coastal wetlands.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0152526"},"PeriodicalIF":4.2,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079435","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":"Microfluidic-based high-throughput isolation enhances the recovery of novel strains and diversity from Arctic soil microbiome.","authors":"Li Liao, Tingyi Lai, Wanning Jiang, Zedong Duan, Peiyuan Sun, Yunpeng Zhao, Fang Peng, Qilong Qin, Mukan Ji, Siqi Zhang","doi":"10.1128/aem.01124-26","DOIUrl":"https://doi.org/10.1128/aem.01124-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Microbial cultivation remains essential for understanding the physiology, ecology, and biotechnological potential of environmental microbes, yet conventional plate-based methods (CPM) recover only a minute fraction of the environmental microbiome. Polar regions, particularly Arctic soils, represent unique reservoirs of \"microbial dark matter\" that remain challenging to cultivate, owing to oligotrophic conditions, low temperatures, and freeze-thaw cycles that impose severe physiological constraints on microbial growth. Here, we report the first systematic application of microfluidic droplet technology (MDT) to Arctic active-layer soil microbiota and benchmark its performance against CPM using identical starting cell numbers, R2A medium, and incubation at 15°C. MDT achieved 6.5- to 8.1-fold higher recovery rates than CPM and improved isolation throughput by &gt;180-fold. Near-full-length 16S rRNA gene sequencing (PacBio) revealed that MDT recovered significantly higher taxonomic richness across all taxonomic levels, with 256 genera detected in the high-cell-input group (DropAS_H) versus 211 in the corresponding plate group (PlateAS_H). Notably, MDT yielded a more even community distribution, significantly reducing the dominance of fast-growing copiotrophs, such as &lt;i&gt;Pseudomonas&lt;/i&gt; and &lt;i&gt;Flavobacterium&lt;/i&gt;. Moreover, approximately 50% of the sequences from MDT were affiliated with potential novel species (&lt;98.65% identity to type strains), and 27% with potential novel genera (&lt;95% identity). Strain verification by Sanger sequencing confirmed 12 of 17 isolates as candidate novel species, among which one strain represented a potential novel genus within &lt;i&gt;Devosiaceae&lt;/i&gt;. This study demonstrates that MDT is a powerful platform for accessing the uncultured majority of polar soil microbiota and establishes a pipeline for high-throughput isolation of novel cold-adapted bacteria.IMPORTANCEArctic soils harbor a vast reservoir of microbial diversity that remains largely inaccessible due to the extreme oligotrophic conditions and low temperatures characteristic of polar environments, leading to slow growth and extended lag phases in most microbes. Conventional plate-based methods (CPM) inherently favor fast-growing copiotrophs while suppressing rare or slow-growing lineages. Here, we demonstrate that microfluidic droplet technology (MDT) overcomes these fundamental constraints, representing its first systematic application to polar microbiology. By physically isolating individual cells into microliter-scale bioreactors, MDT provides independent microenvironments that allow slow-growing and oligotrophic taxa to proliferate without being outcompeted by fast-growing copiotrophs in bulk cultures. The water-in-oil emulsion format further enables extended low-temperature incubation without evaporative loss or airborne fungal contamination, issues that frequently compromise long-term plate-based cultivation of Arctic samples. Relative to CPM, MDT increased r","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0112426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149073519","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 slow decay to extinction: cold temperatures and reduced microbial complexity prolong the persistence of planktonic <i>Francisella tularensis</i>.","authors":"Johanna Thelaus, Dawn Birdsell, Stina Bäckman, Malin Granberg, Emelie Salomonsson, Igor Golovliov, Eva Lundmark, David Sundell, Jonas Näslund, Laila Noppa, Anna-Lena Johansson, Karin Wallgren, Joseph D Busch, Jason W Sahl, Anders Johansson, Mats Forsman, David M Wagner","doi":"10.1128/aem.01261-26","DOIUrl":"https://doi.org/10.1128/aem.01261-26","url":null,"abstract":"<p><p><i>Francisella tularensis</i> is a zoonotic pathogen transmitted to humans through contact with infected animals, arthropod vectors, or contaminated environmental sources. Although replication occurs primarily within eukaryotic host cells, persistence outside a host is thought to be critical for long-term maintenance and transmission in natural ecosystems. To better understand persistence in aquatic habitats outside of mammalian hosts, we studied virulent strains of <i>F. tularensis</i> subspecies <i>tularensis</i> (type A) and subspecies <i>holarctica</i> (type B) incubated in a planktonic state (free living in water) under various axenic aquatic conditions. After 1 year in cold, nutrient-poor treatments, the type B strain (FSC200) caused disease in mice and remained culturable on laboratory media, whereas the type A strain (Schu S4) caused disease but with delayed onset and became non-responsive to laboratory growth conditions. In 1.5-year persistence experiments, type B still caused disease in mice, but with delayed onset, whereas type A no longer caused disease. The rate of bacterial decline depended on subspecies, temperature, and the initial inoculum size. We further explored the persistence of type A and type B populations in natural pond water, which corroborated findings from axenic conditions and revealed that both strains perpetuated disease from a non-replicative inactive persistent state. This study provides timeframes for the persistence of virulent planktonic <i>F. tularensis</i> subspecies <i>tularensis</i> and <i>holarctica</i> populations in various aquatic conditions, contributing to increased understanding of host-independent survival as a component of the perpetuation of tularemia.</p><p><strong>Importance: </strong>Long-term persistence of planktonic (free living in water) <i>Francisella tularensis</i> subspecies tularensis (type A) and subspecies <i>holarctica</i> (type B) requires low temperatures and reduced microbial complexity. These conditions are typical of water wells, supporting the epidemiological observations that drinking water reservoirs may serve as sources of human <i>F. tularensis</i> infections (specifically type B). Importantly, persistence of types A and B did not correlate with molecular viability assays and culturability. This suggests that risk assessment of contagious bacteria based on these methods may not be appropriate. This is the first study to perform side-by-side comparisons of fully virulent strains of type A (Schu S4) and type B (FSC200), to evaluate persistence (defined by the capability to cause tularemia in mice) outside the host-restricted niche under stress conditions in water. The results contribute to the understanding of long-term persistence of <i>F. tularensis</i> between tularemia outbreaks in humans and other mammals.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0126126"},"PeriodicalIF":4.2,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149073552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative evaluation of viability assays and functional analysis of <i>bbi29</i> in <i>Borrelia burgdorferi</i>.","authors":"Connor Waldron, Sierra George, Zhiming Ouyang","doi":"10.1128/aem.01574-26","DOIUrl":"10.1128/aem.01574-26","url":null,"abstract":"<p><p><i>In vitro</i> viability assays are essential for studying the survival of <i>Borrelia burgdorferi</i> after exposure to stressful conditions. In contrast to the cumbersome and tedious manual microscopic counting method, fluorescence-based assays are more rapid and convenient and thus can be used in a high-throughput format. In the SYBR Green I/propidium iodide (PI) assay, spirochetes are labeled with different fluorescent dyes, and fluorescence ratios are then compared to calculate the ratio between live and dead spirochetes. Stained spirochetes are also manually counted under a fluorescence microscope or analyzed via flow cytometry to obtain the live/dead ratio. In this study, we compared these methods to determine the most accurate technique for quantifying spirochete viability. Our results showed that, compared with the SYBR Green I/PI assay that carries inherent caveats, both the fluorescent microscopic counting method and the flow cytometry method provide more reliable and accurate results for <i>B. burgdorferi</i> viability assays, and flow cytometry offers significant advantages in speed and reduced labor compared to manual microscopic counting. Leveraging the flow cytometry-based viability assay, we investigated the role of gene <i>bbi29</i>, encoding a putative virulence-associated lipoprotein, in <i>B. burgdorferi</i> stress response. The contribution of <i>bbi29</i> to <i>B. burgdorferi</i> mammalian infection was also examined using a murine model of Lyme disease.</p><p><strong>Importance: </strong>Lyme disease, caused by <i>Borrelia burgdorferi</i>, is the most common tick-borne disease in the United States. Assessment of <i>B. burgdorferi</i> growth and viability has been traditionally challenging due to the slow growth and unique morphology of the spirochete. Recently, an optimized SYBR Green I/PI assay was developed and has since been used by a number of laboratories to assess <i>B. burgdorferi</i> viability. We herein surprisingly found that the SYBR Green I/PI assay has significant caveats and does not provide accurate quantification of <i>B. burgdorferi</i> viability. Rather, our data showed that flow cytometry is a superior alternative to quantify spirochete viability, providing a valuable methodological framework for future studies. Additionally, by investigating the role and requirement for gene <i>bbi29</i>, we have refined our understanding of hypothetical proteins in <i>B. burgdorferi</i> pathogenesis. Together, this work highlights the importance of developing and validating experimental approaches and functionally characterizing <i>B. burgdorferi</i> genes with unknown functions.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0157426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149073476","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":"Activity and diversity of sulfate- and methane-based pathways of anaerobic chitin and N-acetylglucosamine degradation in marine sediments.","authors":"Sujung Lim, Ranjani Murali, Daan R Speth, Rachel E Szabo, Otto X Cordero, Victoria J Orphan","doi":"10.1128/aem.01280-26","DOIUrl":"https://doi.org/10.1128/aem.01280-26","url":null,"abstract":"<p><p>Sulfate reduction is estimated to account for half of the organic carbon respiration in anoxic, organic-rich ocean sediments. Sulfate-reducing microorganisms (SRMs) typically oxidize simple carbon compounds, such as primary alcohols, or small fatty acids. However, much of the organic input to the seafloor is complex, driving interactions between terminal respirers, such as SRMs and methanogens, and primary degraders that initiate the breakdown of complex organic carbon. To explore how these interactions shape sediment microbiomes, we conducted multi-month microcosm experiments using serially diluted sediments in deep 96-well plates. Sediments from a former deep-sea whalefall site were amended with either the insoluble polymer chitin or its soluble monomer N-acetylglucosamine. The high replication in these experiments allowed us to evaluate the effects of complex versus labile carbon on degradation activity, microbial diversity, community structure, and functional redundancy over time. Geochemical analysis, combined with 16S rRNA gene sequencing and metagenomics, revealed that chitin addition preserved higher microbial diversity and increased predicted interactions among microorganisms. Despite anaerobic chitin degradation producing N-acetylglucosamine, microbial communities enriched by these substrates showed low nestedness over the 7-month experiment. Complex carbon inputs fostered unique microbial assemblages and functional interactions, including the emergence of diverse methanogenic lineages at medium to high dilutions-less apparent in monomer treatments. In microoxic sediments, methanogens and other rare biosphere members co-exist with SRM and dynamically respond to complex carbon inputs. Our results highlight the contribution of carbon complexity and recalcitrance in stimulating metabolically diverse community members in sediments, driving the assembly of functional microbial networks.</p><p><strong>Importance: </strong>Deep-sea sediments cover over 60% of the planet's surface and harbor diverse microbial communities that are important contributors to the carbon and nitrogen budget of the ocean. Despite their importance, the mechanisms by which these communities maintain diversity are poorly understood. In this work, we discuss the contribution of complex carbon to the community structure of marine sediment microbial consortia through the establishment of highly replicated anaerobic incubations provided with either the complex cosmopolitan carbon source chitin or its monomer N-acetylglucosamine.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0128026"},"PeriodicalIF":4.2,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069311","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}