Applied and Environmental Microbiology最新文献

{"title":"Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere.","authors":"Xinqi Li, Hongzhen Wang, Yu Zang, Song Xue, Jiayi Xin, Lei Liu, Xuexi Tang, Jun Chen","doi":"10.1128/aem.02437-24","DOIUrl":"10.1128/aem.02437-24","url":null,"abstract":"<p><p>Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (<i>Zostera marina</i> and <i>Phyllospadix iwatensis</i>). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0243724"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482023","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 strain of <i>Streptococcus mitis</i> inhibits biofilm formation of caries pathogens via abundant hydrogen peroxide production.","authors":"Isabella Williams, Jacob S Tuckerman, Daniel I Peters, Madisen Bangs, Emily Williams, Iris J Shin, Justin R Kaspar","doi":"10.1128/aem.02192-24","DOIUrl":"10.1128/aem.02192-24","url":null,"abstract":"<p><p>Commensal oral streptococci that colonize supragingival biofilms deploy mechanisms to combat competitors within their niche. Here, we determined that <i>Streptococcus mitis</i> more effectively inhibited biofilm formation of <i>Streptococcus mutans</i> compared to other oral streptococci. This phenotype was common among all isolates of <i>S. mutans</i>, but was specific to a single strain of <i>S. mitis</i>, ATCC 49456. We documented ATCC 49456 to accumulate four to five times more hydrogen peroxide (H₂O₂) than other <i>Streptococcus</i> species tested, and 5-18 times more than other <i>S. mitis</i> strains assayed. <i>S. mutans</i> biofilm formation inhibition was dependent on cell contact/proximity and reduced when grown in media containing catalase or with a <i>S. mitis</i> mutant of pyruvate oxidase (<i>spxB; pox</i>), confirming that SpxB-dependent H₂O₂ production was a major antagonistic factor. Addition of <i>S. mitis</i> within hours after <i>S. mutans</i> inoculation was effective at reducing biofilm biomass, but not for 24 h pre-formed biofilms in an SpxB-dependent manner. Transcriptome analysis revealed responses for both <i>S. mitis</i> and <i>S. mutans</i>, with several <i>S. mutans</i> differentially expressed genes following a gene expression pattern we have previously described, while others being unique to the interaction with <i>S. mitis</i>. Finally, we show that <i>S. mitis</i> also affected coculture biofilm formation of several other commensal streptococci as well as cariogenic <i>Streptococcus sobrinus</i>. Our study shows that strains with abundant H₂O₂ production are effective at inhibiting initial growth of caries pathogens like <i>S. mutans</i>, but are less effective at disrupting pre-formed biofilms and have the potential to influence the stability of other oral commensal strains.IMPORTANCEAntagonistic properties displayed by oral bacteria have been sought as therapeutic approaches against dental caries pathogens like <i>Streptococcus mutans</i>. An emergent theme has been the ability of select strains that produce high amounts of hydrogen peroxide to effectively inhibit the growth of <i>S. mutans</i> within <i>in vitro</i> and <i>in vivo</i> models. Our study builds on these previous findings by determining that <i>Streptococcus mitis</i> ATCC 49456 is a high hydrogen peroxide producer, compared to other <i>Streptococcus</i> species as well as additional strains of <i>S. mitis</i>. In addition to <i>S. mutans</i>, we show that ATCC 49456 also affects biofilm formation of other oral streptococci, a non-desirable trait that should be weighed heavily for strains under consideration as probiotics. Further phenotypic characterization of strains like <i>S. mitis</i> ATCC 49456 in mixed-species settings will allow us to hone in on qualities that are optimal for probiotic strains that are intended to prevent the emergence of odontopathogens.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0219224"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490483","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":"Deciphering reductive dehalogenase specificity through targeted mutagenesis of chloroalkane reductases.","authors":"Katherine J Picott, Connor M Bowers, Elizabeth A Edwards","doi":"10.1128/aem.01501-24","DOIUrl":"10.1128/aem.01501-24","url":null,"abstract":"<p><p>Reductive dehalogenases (RDases) are essential in the anaerobic degradation of various organohalide contaminants. This family of enzymes has broad sequence diversity, but high structural conservation. There have been few studies assessing how RDase amino acid sequences affect their substrate selectivity. Here, we focus on two chloroalkane RDases, CfrA and DcrA, which have 95% protein sequence identity but have diverged to have opposite substrate preferences. CfrA dechlorinates chloroform (CF) and 1,1,1-trichloroethane (TCA) but not 1,1-dichloroethane (DCA), while DcrA will dechlorinate 1,1-DCA but not CF or 1,1,1-TCA. We mutated several residues in the active site of CfrA to investigate a change in substrate preference and to identify which wild-type residues contribute the most to substrate specialization. We determined that no individual residue solely dictates substrate discrimination, but both Y80W and F125W mutations were needed to force CfrA to prefer 1,1-DCA as a substrate. When using 1,1,2-TCA as a substrate, CfrA predominately performs hydrogenolysis to 1,2-DCA, yet the introduction of the double mutant changed this preference to dihaloelimination (forming vinyl chloride). We use predictive protein models and substrate docking to predict what interactions are made between the enzyme and substrate to aid in selection. The residues of significance identified in this study are consistent with those identified from chloroethene RDases, suggesting residue locations with a particularly high impact on activity.IMPORTANCEReductive dehalogenases (RDases) play an integral role in the removal of chlorinated solvents from the environment. These enzymes have specificity toward different chlorinated compounds, and it is known that natural variants of highly similar RDases can have distinct activities. How specific differences in protein sequence influence activity is largely unknown. In this study, we demonstrate that mutating a few residues within the active site of CfrA-a chloroform and trichloroethane-specific dehalogenase-changes its substrate preference to dichloroethane. We determine that only two mutations are needed to disrupt the native activity, underscoring the nuances in substrate-structure relationships in RDases. Though we are still far from predicting function from the sequence, this knowledge can give some insight into engineering RDases for new target contaminants.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0150124"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143405039","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":"<i>Campylobacter jejuni</i> ST353 and ST464 cause localized gut inflammation, crypt damage, and extraintestinal spread during large- and small-scale infection in broiler chickens.","authors":"Heather M Chick, Lisa K Williams, Nick Sparks, Farina Khattak, Paul Vermeij, Inge Frantzen, Mandy Peeters, Jetta J E Bijlsma, Daniel John, Timothy Ogunrin, Keioni Essex, Caroline Cayrou, Venkateswarlu Kanamarlapudi, Christopher D Bayliss, Julian M Ketley, Thomas J Humphrey, Steven P Rushton, Thomas S Wilkinson","doi":"10.1128/aem.01614-24","DOIUrl":"10.1128/aem.01614-24","url":null,"abstract":"<p><p><i>Campylobacter</i> infections in humans and chickens are a significant burden to health services and the poultry industry. In the UK, over 75% of chicken products are <i>Campylobacter</i>-positive at retail, but the knowledge of the mechanisms responsible for extraintestinal spread into edible tissues remains incomplete. This work aimed to establish if two chicken-associated lineages of <i>Campylobacter jejuni</i>, ST353 and ST464, have the potential for extraintestinal spread. Large- and small-scale chicken colonization trials investigated the infection biology of <i>C. jejuni</i> ST353 (three strains) and ST464 (four strains). Both lineages strongly colonized the ileum and ceca and were detected in liver and spleen. <i>C. jejuni</i> ST353 and ST464 spleen load were significantly increased compared to <i>C. jejuni</i> M1 controls. Immune responses in cecal tonsils exhibited early induction of IFN-γ and suppressed TGFβ at 7 days post-infection with <i>C. jejuni</i> ST464. Histochemistry of gut tissue demonstrated significant decreases in intestinal crypt depth in ileal tissue with increasing severity relative to <i>Campylobacter</i> lineage, M1 <ST353<ST464. Pairwise correlation analysis confirmed strong interdependencies between \"cecal <i>Campylobacter</i> load,\" \"CXCLi1,\" \"CXCLi2,\" and \"splenic <i>Campylobacter</i> load.\" Furthermore, linear discriminant analysis confirmed that cecal tonsil-derived IFNγ, TGFβ, and CXCLi1 could predict splenic invasion at 71% accuracy. This work demonstrates that two chicken specialist <i>C. jejuni</i> lineages, ST353 and ST464, cause extraintestinal spread to liver and spleen and modeling suggests distinct routes from ileum and cecum, respectively. Recognition of these two routes of <i>Campylobacter</i> extraintestinal spread (ileal/liver and cecal/spleen) provides a better understanding of this food-derived pathogen for academia and the industry.IMPORTANCEThe UK is self-sufficient in chicken meat production, which remains a cheap and healthy source of dietary protein. However, <i>Campylobacter</i> species are present in 75% of raw chicken products at retail sales, resulting in increased human gut infections. Currently, it is not clear which members of the <i>Campylobacter jejuni</i> species can leave the digestive tract and reach edible tissues. Using industry-relevant conditions, two <i>C. jejuni</i> lineages (ST353 and ST464) isolated from chicken gut and liver were shown to cause infections outside the gut. The underlying mechanisms involve inducing inflammation and gut damage to structures required for cell renewal (crypts) of the intestine. Modeling this data leads to our proposal that <i>C. jejuni</i> uses two invasion pathways; one where spread is from ileum to liver and the other between ceca and spleen. Knowledge of these two routes of extraintestinal spread will help the industry develop control measures to improve food biosecurity in poultry.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0161424"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921347/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439854","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":"Branched-chain amino acid metabolism supports Roseobacteraceae positive interactions in marine biofilms.","authors":"Han Cui, Shuaitao Wang, Shen Fan, Hongan Long, Jinshui Lin, Wei Ding, Weipeng Zhang","doi":"10.1128/aem.02411-24","DOIUrl":"10.1128/aem.02411-24","url":null,"abstract":"<p><p>Interspecies interactions are key factors affecting the stability of microbial communities. However, microbial interactions in marine biofilms, which constitute up to 80% of the microbial biomass in certain marine environments, are not well understood. We addressed this knowledge gap by coculturing four marine biofilm-derived Roseobacteraceae strains (<i>Leisingera aquaemixtae</i> M597, <i>Roseibium aggregatum</i> S1616, <i>Alloyangia pacifica</i> T6124, and <i>Sulfitobacter indolifex</i> W002) in 14 single carbon sources. Overall, 140 coculture experiments revealed 39.3% positive interactions compared to 8.3% negative interactions. When the carbon source was consumed by only one strain, the interaction between the strains was more likely to be positive. The interaction between S1616 and M597, when cultured in D-gluconic acid, was further studied as an example. S1616-M597 coculture displayed a higher D-gluconic acid consumption rate than S1616 monoculture, whereas M597 could not use D-gluconic acid as the sole carbon source. The supernatant of S1616 monoculture supported the growth of M597, and branched-chain amino acids in the supernatant were consumed. Transcriptomic analysis suggested that M597 induced the expression of genes for branched-chain amino acid biosynthesis in S1616. Additionally, metagenomic analysis revealed the wide distribution and a strongly correlated co-occurrence of the four strains in global oceanic biofilms. Together, our findings show that interspecies positive interactions are prevalent among marine-biofilm Roseobacteraceae, and the interactions are likely to be mediated by branched-chain amino acids metabolism.</p><p><strong>Importance: </strong>Interspecies interactions are crucial for microbial community structure and function. Despite well-studied social behaviors in model microorganisms, species interactions in natural marine biofilms especially Roseobacteraceae with complex metabolic pathways are not well understood. Our findings suggest that positive microbial interactions, which can be mediated by branched-chain amino acid biosynthesis, are common among marine-biofilm Roseobacteraceae. This study provides new insights into microbial interactions and the ecology of marine biofilms.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0241124"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389999","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":"Inhibition of pneumococcal growth and biofilm formation by human isolates of <i>Streptococcus mitis</i> and <i>Streptococcus oralis</i>.","authors":"João Borralho, Sara Handem, João Lança, Bárbara Ferreira, Catarina Candeias, Adriano O Henriques, N Luisa Hiller, Carina Valente, Raquel Sá-Leão","doi":"10.1128/aem.01336-24","DOIUrl":"10.1128/aem.01336-24","url":null,"abstract":"<p><p>In a world facing the unprecedented threat of antibiotic-resistant bacteria, targeted approaches to control colonization and prevent disease caused by common pathobionts offer a promising solution. <i>Streptococcus pneumoniae</i> (pneumococcus) is a leading cause of infections worldwide, affecting both children and adults despite available antimicrobials and vaccines. Colonization, which occurs in the form of a biofilm in the upper respiratory tract, is frequent and a prerequisite for disease and transmission. The use of live bacterial strains as biotherapeutics for infectious diseases is actively being explored. Here, we investigated the potential of commensal streptococci to control <i>S. pneumoniae</i>. Screening of over 300 human isolates led to the identification of seven strains (one <i>Streptococcus oralis</i> and six <i>Streptococcus mitis</i>, designated A22 to G22) with inhibitory activity against <i>S. pneumoniae</i> of multiple serotypes and genotypes. Characterization of A22 to G22 cell-free supernatants indicated the involvement of secreted proteins or peptides in the inhibitory effect of all <i>S. mitis</i> isolates. Genome analyses revealed the presence of 64 bacteriocin loci, encoding 70 putative bacteriocins, several of which are novel and absent or rare in over 7,000 publicly available pneumococcal genomes. Deletion mutants indicated that bacteriocins partially or completely explained the anti-pneumococcal activity of the commensal strains. Importantly, strains A22 to G22 were further able to prevent and disrupt pneumococcal biofilms, a proxy for nasopharyngeal colonization. These results highlight the intricacy of the interactions among nasopharyngeal colonizers and support the potential of strains A22 to G22 to be used as live biotherapeutics, alone or in combination, to control <i>S. pneumoniae</i> colonization.</p><p><strong>Importance: </strong><i>Streptococcus pneumoniae</i> (pneumococcus) infections remain a major public health issue despite the use of vaccines and antibiotics. Pneumococci asymptomatically colonize the human upper respiratory tract, a niche shared with several commensal <i>Streptococcus</i> species. Competition for space and nutrients among species sharing the same niche is well documented and tends to be more intense among closely related species. Based on this rationale, a screening of several commensal streptococci isolated from the human upper respiratory tract led to the identification of strains of <i>Streptococcus mitis</i> and <i>Streptococcus oralis</i> capable of inhibiting most pneumococcal strains, across diverse serotypes and genotypes. This inhibition was partially or wholly linked to the expression of novel bacteriocins. The selected <i>S. mitis</i> and <i>S. oralis</i> strains significantly disrupted pneumococcal biofilms, indicating a potential for using commensals as biotherapeutics to control pneumococcal colonization, a key step in preventing disease and transmission.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0133624"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143498060","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":"Phylogenetic analysis of plant-pathogenic and non-pathogenic <i>Trichoderma</i> isolates on maize from plants, soil, and commercial bio-products.","authors":"Annette Pfordt, Clovis Douanla-Meli, Bernhard C Schäfer, Gritta Schrader, Eike Tannen, Madhav Jatin Chandarana, Andreas von Tiedemann","doi":"10.1128/aem.01931-24","DOIUrl":"10.1128/aem.01931-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Fungi of the genus &lt;i&gt;Trichoderma&lt;/i&gt; are primarily associated with the mycobiome of dead wood but can also be occasionally found in soil and plant rhizospheres. Several &lt;i&gt;Trichoderma&lt;/i&gt; spp. are used in crop health management to promote growth and control plant diseases. Although widely considered beneficial to plants, some members have been reported to be pathogenic to maize, causing a disease called &lt;i&gt;Trichoderma&lt;/i&gt; ear rot. Since 2018, &lt;i&gt;Trichoderma afroharzianum&lt;/i&gt; has caused significant infections of maize cobs in Germany, France, and Italy. This study aimed to investigate the pathogenicity and phylogenetic relationships among different &lt;i&gt;Trichoderma&lt;/i&gt; strains from diverse sources and geographical origins. While previous studies primarily identified &lt;i&gt;T. afroharzianum&lt;/i&gt; as the main species causing &lt;i&gt;Trichoderma&lt;/i&gt; ear rot, this study found that isolates of &lt;i&gt;T. asperellum&lt;/i&gt;, &lt;i&gt;T. atroviride,&lt;/i&gt; and &lt;i&gt;T. guizhouense&lt;/i&gt; may also exhibit pathogenicity on maize cobs. Additionally, &lt;i&gt;Trichoderma&lt;/i&gt; strains from commercial biocontrol products displayed unexpected pathogenicity inducing up to 92% disease severity on maize cobs. Most &lt;i&gt;T. afroharzianum&lt;/i&gt; strains induced high levels of disease severity, although some isolates of the same species did not cause any disease, indicating a large heterogeneity in pathogenicity within the species. Notably, phylogeny reconstruction based on the &lt;i&gt;tef1-α&lt;/i&gt; and &lt;i&gt;rpb2&lt;/i&gt; genes did not result in any discernible clustering between pathogenic and non-pathogenic isolates. A further novel finding is the isolation of pathogenic &lt;i&gt;Trichoderma&lt;/i&gt; isolates from agricultural soil, demonstrating that soil can serve as a reservoir for pathogenic species. This study highlights the need for biosecurity assessment and monitoring of &lt;i&gt;Trichoderma&lt;/i&gt; strains for agricultural use, considering their beneficial and pathogenic potential.IMPORTANCEIn this study, we explored the ability of different &lt;i&gt;Trichoderma&lt;/i&gt; species to infect maize plants. &lt;i&gt;Trichoderma&lt;/i&gt; is a group of fungi known for its beneficial role in agriculture, often used as a biological pesticide to control fungal plant diseases. However, some species within this genus can also act as pathogens, causing infections in crops like maize. We found that one species, &lt;i&gt;T. afroharzianum&lt;/i&gt;, is particularly aggressive, capable of infecting maize without the plant being wounded first. This makes it a potentially serious threat to crop health. In contrast, other species, such as &lt;i&gt;T. atroviride&lt;/i&gt; and &lt;i&gt;T. asperellum&lt;/i&gt;, only caused infections when maize plants were injured before. Our research suggests that pathogenic &lt;i&gt;Trichoderma&lt;/i&gt; species not only effectively infect plants but can also survive well in soil, making their control difficult. These findings highlight the need for better understanding of how these fungi operate in order to manage the risks they pose to important crops like maize, while still taking advan","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0193124"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514470","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":"Cometabolism of ferrihydrite reduction and methyl-dismutating methanogenesis by <i>Methanosarcina mazei</i>.","authors":"Chaojie Guo, Yahai Lu","doi":"10.1128/aem.02238-24","DOIUrl":"10.1128/aem.02238-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Recent discoveries have shown that some &lt;i&gt;Methanosarcina&lt;/i&gt; species can reduce Fe(III), reshaping our understanding of &lt;i&gt;Methanosarcina&lt;/i&gt; ecophysiology. However, the specific minerals reduced, the products formed, and the underlying metabolic mechanisms remain elusive. Here, we report on the cometabolic process of Fe(III) reduction and methylotrophic methanogenesis in &lt;i&gt;Methanosarcina mazei&lt;/i&gt; zm-15. Biogeochemical and mineralogical analyses were conducted to investigate Fe(III) reduction from three mineral preparations-ferrihydrite, goethite, and hematite. The results revealed that 38% of the 6 mM Fe(III) in ferrihydrite was reduced within 4 days, and this percentage increased to 75% with the addition of 100 µM anthraquinone-2,6-disulfonate (AQDS). Active Fe(III) reduction occurred immediately and preceded rapid methanogenesis. The addition of ferrihydrite and AQDS together significantly enhanced the maximal CH₄ production rate. However, Fe(III) reduction did not occur in goethite or hematite, even with the addition of 100 µM AQDS. Vivianite was identified as the major product from ferrihydrite reduction. Transcriptomic analysis revealed that gene expression related to the oxidation branch of the methyl-dismutating pathway and the membrane-associated electron transport chain (ETC) was significantly upregulated, whereas the expressions of genes associated with the reduction branch of the methyl-dismutating pathway were downregulated. In conclusion, &lt;i&gt;M. mazei&lt;/i&gt; zm-15 demonstrates a strong ability to reduce poorly crystalline ferrihydrite, but not highly crystalline goethite and hematite. During the cometabolism of Fe(III) reduction and CH₄ production from methanol, the methyl-oxidation and membrane ETC pathways are enhanced, while the methyl-reduction pathway is downregulated. The mechanism of electron relay from cells to ferrihydrite, however, remains unclear and warrants further investigation.IMPORTANCEThe recent discovery that certain &lt;i&gt;Methanosarcina&lt;/i&gt; species can grow by reducing Fe(III) challenges the traditional understanding of methanogens. However, the underlying metabolic mechanisms remain largely unexplored. Using a combination of biogeochemical, mineralogical, and microbiological approaches, we investigated the ability of &lt;i&gt;Methanosarcina mazei&lt;/i&gt; zm-15. It exhibited a strong capacity to reduce poorly crystalline ferrihydrite but not highly crystalline goethite and hematite. The formation of vivianite from ferrihydrite reduction is likely due to the high rate of Fe(III) reduction and the presence of excess phosphorus in incubations. During the cometabolism of Fe(III) reduction and CH&lt;sub&gt;4&lt;/sub&gt; production from methanol, the methyl-oxidation and membrane electron transport pathways are upregulated, while the methyl-reduction pathway is downregulated. Our research uncovers a differential regulation of metabolic pathways during the cometabolism of Fe(III) reduction and CH&lt;sub&gt;4&lt;/sub&gt; production from methanol. The fi","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0223824"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143405012","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":"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}