Applied and Environmental Microbiology最新文献

{"title":"Assessing horizontal gene transfer in the rhizosphere of <i>Brachypodium distachyon</i> using fabricated ecosystems (EcoFABs).","authors":"Shweta Priya, Silvia Rossbach, Thomas Eng, Hsiao-Han Lin, Peter F Andeer, Jenny C Mortimer, Trent R Northen, Aindrila Mukhopadhyay","doi":"10.1128/aem.01505-24","DOIUrl":"https://doi.org/10.1128/aem.01505-24","url":null,"abstract":"<p><p>Horizontal gene transfer (HGT) is a major process by which genes are transferred between microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant-associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provide the first demonstration of gene transfer via a triparental conjugation system in the <i>Brachypodium distachyon</i> rhizosphere in an EcoFAB using <i>Pseudomonas putida</i> KT2440 as both donor and recipient bacterial strain with the donor containing a mobilizable and non-self-transmissible plasmid. We observed that the frequency of plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage and the composition and amount of root exudates. The frequency of plasmid transfer also increased with higher numbers of donor cells. We demonstrate the transfer of plasmid from <i>P. putida</i> to another <i>B. distachyon</i> root colonizer, <i>Burkholderia</i> sp. OAS925, showing HGT within a rhizosphere microbial community. Environmental stresses also influenced the rate and efficiency of HGT in the rhizosphere between different species and genera. This study provides a robust workflow to evaluate transfer of engineered plasmids in the rhizosphere when such plasmids are potentially introduced in a field or other plant-associated environments.IMPORTANCEWe report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbe interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells, and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567832","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":"Elevated incidence of infant botulism in a 17-county area of the Mid-Atlantic region in the United States, 2000-2019, including association with soil types.","authors":"Haydee A Dabritz, Ingrid K Friberg, Jessica R Payne, Camille Moreno-Gorrin, Kristy Lunquest, Deepam Thomas, Alexandra P Newman, Elizabeth A Negrón, Patrick J Drohan","doi":"10.1128/aem.01063-24","DOIUrl":"10.1128/aem.01063-24","url":null,"abstract":"<p><p>We sought to identify counties in the northeastern United States where the incidence of infant botulism (IB) is elevated compared to the nationwide incidence and to assess associations with soil type at the case residence. IB cases were identified through the distribution of the orphan drug Human Botulism Immune Globulin Intravenous for treatment of IB by state and national surveillance systems and were subsequently confirmed by laboratory testing. IB incidence by county was calculated as the number of IB cases divided by the number of live births in the county from 2000 to 2019. Cases were spatially mapped and assigned to soil types using the US Department of Agriculture's online soils database. Possible association with soil type was evaluated with the Chi-squared test. We identified a rectangular area consisting of 17 contiguous counties in Delaware, Maryland, New Jersey, New York, and Pennsylvania, approximately 80 km by 250 km, in which the 20-year incidence of IB was nearly seven times greater than that of the remaining counties in those five states. Within this area, case residences were strongly associated with certain soil types (<i>P</i> ≤ 0.003). From 2000 to 2019, IB occurred with disproportionate incidence in a rectangular area encompassing the lower Delaware and Raritan River Valley and parts of five adjacent states. Further investigation of the soils in counties from this area could assess whether <i>C. botulinum</i> is more prevalent in certain soil types and whether isolation of <i>C. botulinum</i> is more common in counties with higher IB incidence.</p><p><strong>Importance: </strong>Infant botulism occurs more frequently in 17 counties within and adjacent to the Delaware and Raritan River watersheds. This study should alert physicians and pediatricians in the area to the higher likelihood of encountering cases of this otherwise rare disease that manifests with constipation, poor feeding, loss of head control, weak suck/cry, generalized weakness, and descending bilateral paralysis.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a <i>Limosilactobacillus reuteri</i> therapeutic delivery platform with reduced colonization potential.","authors":"Laura M Alexander, Saima Khalid, Gina M Gallego-Lopez, Theresa J Astmann, Jee-Hwan Oh, Mark Heggen, Phil Huss, Renee Fisher, Amitava Mukherjee, Srivatsan Raman, In Young Choi, Morgan N Smith, Claude J Rogers, Michael W Epperly, Laura J Knoll, Joel S Greenberger, Jan-Peter van Pijkeren","doi":"10.1128/aem.00312-24","DOIUrl":"10.1128/aem.00312-24","url":null,"abstract":"<p><p>Bacterial biotherapeutic delivery vehicles have the potential to treat a variety of diseases. This approach obviates the need to purify the recombinant effector molecule, allows delivery of therapeutics <i>in situ</i> via oral or intranasal administration, and protects the effector molecule during gastrointestinal transit. Lactic acid bacteria have been broadly developed as therapeutic delivery vehicles though risks associated with the colonization of a genetically modified microorganism have so-far not been addressed. Here, we present an engineered <i>Limosilactobacillus reuteri</i> strain with reduced colonization potential. We applied a dual-recombineering scheme for efficient barcoding and generated mutants in genes encoding five previously characterized and four uncharacterized putative adhesins. Compared with the wild type, none of the mutants were reduced in their ability to survive gastrointestinal transit in mice. CmbA was identified as a key protein in <i>L. reuteri</i> adhesion to HT-29 and enteroid cells. The nonuple mutant, a single strain with all nine genes encoding adhesins inactivated, had reduced capacity to adhere to enteroid monolayers. The nonuple mutant producing murine IFN-β was equally effective as its wild-type counterpart in mitigating radiation toxicity in mice. Thus, this work established a novel therapeutic delivery platform that lays a foundation for its application in other microbial therapeutic delivery candidates and furthers the progress of the <i>L. reuteri</i> delivery system towards human use.IMPORTANCEOne major advantage to leverage gut microbes that have co-evolved with the vertebrate host is that evolution already has taken care of the difficult task to optimize survival within a complex ecosystem. The availability of the ecological niche will support colonization. However, long-term colonization of a recombinant microbe may not be desirable. Therefore, strategies need to be developed to overcome this potential safety concern. In this work, we developed a single strain in which we inactivated the encoding sortase, and eight genes encoding characterized/putative adhesins. Each individual mutant was characterized for growth and adhesion to epithelial cells. On enteroid cells, the nonuple mutant has a reduced adhesion potential compared with the wild-type strain. In a model of total-body irradiation, the nonuple strain engineered to release murine interferon-β performed comparable to a derivative of the wild-type strain that releases interferon-β. This work is an important step toward the application of recombinant <i>L. reuteri</i> in humans.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543189","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":"Application of sodium hypochlorite for human norovirus and hepatitis A virus inactivation in groundwater.","authors":"Eun Bi Jeon, Anamika Roy, Shin Young Park","doi":"10.1128/aem.01405-24","DOIUrl":"10.1128/aem.01405-24","url":null,"abstract":"<p><p>In this study, the effect of sodium hypochlorite (10-200 ppm of Cl₂) on the inactivation of human norovirus (HuNV) GII.4 and hepatitis A virus (HAV) in groundwater was investigated using propidium monoazide (PMA)/reverse transcription quantitative real-time PCR (RT-qPCR). Initially, 4.00 log₁₀ genome copies/μL of HuNV GII.4 or 5.50 log₁₀ genome copies/μL of HAV were artificially inoculated in groundwater. The titers of HuNV GII.4 and HAV decreased significantly (<i>P</i> < 0.05) with increasing Cl₂ concentrations. Groundwater was treated with 10, 30, 50, 100, 150, and 200 ppm of Cl₂, and the viable HuNV GII.4 was significantly (<i>P</i> < 0.05) reduced to 3.28 (0.21-log reduction), 3.18 (0.31-log reduction), 3.01 (0.48 log reduction), 2.75 (0.74 log reduction), 2.54 (0.95 log reduction), and 2.34 (1.15 log reduction) log₁₀ genome copies/μL, respectively. The viable HAV was also significantly (<i>P</i> < 0.05) reduced to 4.99 (0.23 log reduction), 4.76 (0.46 log reduction), 4.55 (0.67 log reduction), 4.21 (1.01-log reduction), 3.89 (1.33 log reduction), and 3.64 (1.58 log reduction) log₁₀ genome copies/μL, respectively. The decimal reduction times (<i>D</i> values) (1-log₁₀ genome reduction) of HuNV GII.4 and HAV infectivity in groundwater were predicted as 116.7 and 98.9 ppm of Cl₂, respectively, using the first-order kinetics model (HuNV GII.4: <i>y</i> = -0.0054<i>x</i> + 3.3585, correlation coefficient (<i>R</i>²) = 0.97; HAV: <i>y</i> = -0.0091<i>x</i> + 5.0470, <i>R</i>² = 0.97). The result specifically suggests that 150- to 200-ppm Cl₂ can potentially be used for the inactivation of >1-log₁₀ genome copy/μL HuNV GII.4 and HAV in groundwater.IMPORTANCEGroundwater represents a vital component of the global water supply, serving as a crucial source of potable water for humans. It serves as a source of potable water for up to 50% of the global population and accounts for 43% of all water used for irrigation. It thus follows that the sustainable management of groundwater represents a pivotal solution. However, the regrowth of pathogens in water that is not treated with chlorine or where proper residual chlorine is not maintained represents a risk to public health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome divergence of marine gastropod species separated by the Isthmus of Panama.","authors":"Alexander T Neu, Mark E Torchin, Eric E Allen, Kaustuv Roy","doi":"10.1128/aem.01003-24","DOIUrl":"10.1128/aem.01003-24","url":null,"abstract":"<p><p>The rise of the Isthmus of Panama separated the populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and the Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped the compositions of their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera <i>Cerithium</i> and <i>Cerithideopsis</i> to those of congeneric outgroups. Our results suggest that the effects of ~3 million years of separation and isolation on microbiome composition varied among host genera and between sample types within the same hosts. In the whole-body samples, microbiome compositions of geminate species pairs tended to be similar, likely due to host filtering, although the strength of this relationship varied among the two groups and across similarity metrics. Shell-surface microbiomes show contrasting patterns, with co-divergence between the host taxa and a small number of microbial clades evident in <i>Cerithideopsis</i> but not <i>Cerithium</i>. These results suggest that (i) isolation of host populations after the rise of the Isthmus of Panama affected microbiomes of geminate hosts in a complex and host-specific manner, and (ii) host-associated microbial taxa respond differently to vicariance events than the hosts themselves.IMPORTANCEWhile considerable work has been done on evolutionary divergences of marine species in response to the rise of the Isthmus of Panama, which separated two previously connected oceans, how this event shaped the microbiomes of these marine hosts remains poorly known. Using whole-body and shell-surface microbiomes of closely related gastropod species from opposite sides of the Isthmus, we show that divergences of microbial taxa after the formation of the Isthmus are often not concordant with those of their gastropod hosts. Our results show that evolutionary responses of marine gastropod-associated microbiomes to major environmental perturbations are complex and are shaped more by local environments than host evolutionary history.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543207","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":"Corynebacterial membrane vesicles disrupt cariogenic interkingdom assemblages.","authors":"Puthayalai Treerat, Tanner Rozendal, Camilla de Mattos, Anli Davis, Emily Helliwell, Justin Merritt, Jens Kreth","doi":"10.1128/aem.00885-24","DOIUrl":"10.1128/aem.00885-24","url":null,"abstract":"<p><p>Polymicrobial diseases such as periodontal disease and caries pose significant treatment challenges due to their resistance to common approaches like antibiotic therapy. These infections exhibit increased resilience, due to microbial interactions that also disrupt host immune responses. Current research focuses on virulence and disease-promoting interactions, but less is known about interactions that could inhibit or prevent disease development. Normally human-associated microbiomes maintain homeostasis, preventing pathobionts from becoming dominant. In conditions like chronic disseminated candidiasis or severe early childhood caries (s-ECC), an overgrowth of microbes such as <i>Candida albicans</i> disrupts this balance. Typically, <i>C. albicans</i> coexists benignly within the microbial community but can become pathogenic, forming biofilms and interacting with other microbes such as cariogenic <i>Streptococcus mutans</i>. This interaction is particularly significant in s-ECC, where it exacerbates the disease's progression and severity. Here, we present that <i>Corynebacterium durum</i>, itself and through its extracellular membrane vesicles disrupts interkingdom assemblages between <i>C. albicans</i> and <i>S. mutans</i>. Mechanistically the interaction interference occurs at the genetic level with downregulated HWP1 expression, a surface protein specifically induced in the presence of <i>S. mutans</i> promoting the interkingdom interaction. Additionally, we show that <i>C. durum</i> can impede <i>C. albican</i>s systemic virulence in the <i>Galleria mellonella</i> infection model. This suggests that oral corynebacteria may act as a beneficial commensal species, exerting antifungal effects within polymicrobial communities and opening new avenues for managing polymicrobial diseases.IMPORTANCEPolymicrobial diseases such as severe early childhood caries (s-ECC) lack effective treatment options. Prevention, requiring a deeper understanding of ecological processes before the onset of disease symptoms, could be a potential strategy. In this context, we investigated how relatively abundant oral biofilm <i>Corynebacterium</i> species, which are associated with oral health, can interfere with the interkingdom partnership of <i>Streptococcus mutans</i> and <i>Candida albicans</i>. This partnership is a significant driver of tooth decay in s-ECC due to synergistic activities that increase cariogenicity. Our study reveals that oral corynebacteria, through the production of extracellular membrane vesicles, can disrupt the <i>S. mutans</i> and <i>C. albicans</i> partnership by inhibiting fungal hyphae formation. Additionally, the fatty acid cargo within these vesicles exhibits antifungal properties, suggesting that corynebacteria play a role in shaping microbial dynamics within the oral biofilm.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a suite of <i>Proteus mirabilis</i>-derived urea-inducible promoters.","authors":"Madison J Fitzgerald, Abigail Scavone, Chaitra Moolaveesala, Melanie M Pearson, Harry L T Mobley","doi":"10.1128/aem.01273-24","DOIUrl":"https://doi.org/10.1128/aem.01273-24","url":null,"abstract":"<p><p>Catheter-associated urinary tract infections (CAUTIs) are a significant burden on healthcare systems, accounting for up to 40% of hospital-acquired infections globally. A prevalent CAUTI pathogen, <i>Proteus mirabilis,</i> is an understudied Gram-negative bacterium. One sequela of <i>P. mirabilis</i> CAUTI is the production of urinary stones, which complicates treatment and clearing of the infection. Stone formation is induced by the activity of urease, a nickel-metalloenzyme that is regulated by UreR in a urea-dependent manner. As urea is abundant in the urinary tract, urease genes are highly expressed during experimental UTI. We sought to leverage the urease promoter to create an expression system that would enable urea-inducible expression of genes during <i>in vitro</i> experiments as well as during experimental UTI. During preliminary studies, we observed unexpectedly high levels of basal expression of the urease promoter. This was somewhat dependent on the presence of regulator UreR. To further develop this expression system, we generated a series of reporter constructs to assess the impact of specific promoter elements on promoter activity in the presence and absence of urea. Elements of interest included known regulatory binding sites, alternative translational start sites, and single-nucleotide polymorphisms identified through comparative genomics. This work describes a suite of urea-inducible promoters, constructed during this study, that exhibit a variety of expression dynamics, providing a customizable platform for gene expression.IMPORTANCEUrea is an inexpensive molecule that can easily be supplied during <i>in vitro</i> experiments. A urea-inducible promoter would also be activated by environments where urea naturally occurs, such as in the urinary tract. Thus, the development of a urea-inducible system for selective gene expression is of great interest to the field of uropathogenesis as it would enable selective gene induction during experimental urinary tract infection. This expression system would also have important applications for recombinant protein production in biotech and manufacturing.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543190","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":"Genomic characterization of a clonal emergent <i>Salmonella</i> Minnesota lineage in Brazil reveals the presence of a novel megaplasmid of resistance and virulence.","authors":"Anamaria M P Dos Santos, Pedro Panzenhagen, Rafaela G Ferrari, Ana Beatriz Portes, Ana Carolina de Jesus, Alan Ochioni, Dália Rodrigues, Magaly Toro, Jianghong Meng, Marc Allard, Carlos A Conte-Junior","doi":"10.1128/aem.01579-24","DOIUrl":"https://doi.org/10.1128/aem.01579-24","url":null,"abstract":"<p><p><i>Salmonella</i> Minnesota has emerged in Brazil as the predominant serovar in poultry and poultry products, along with <i>Salmonella</i> Heidelberg. To understand the emergence of <i>Salmonella</i> Minnesota over the last few years in Brazil, we performed a comparative analysis between 69 selected <i>S</i>. Minnesota genomes from Pathogen Detection database and 65 clonal emergent genomes isolated from Brazil. We demonstrate the presence of multidrug resistance genes against tetracycline [<i>tet</i>(A)], sulfonamide (<i>sul2</i>), and AmpC beta-lactamase (<i>bla</i>_CMY-2) in emergent genomes, along with the carriage of a megaplasmid of resistance and virulence (~210 kb), designated pESM (plasmid for emergent <i>Salmonella</i> Minnesota). pESM is an IncC/A2 plasmid predicted to increase <i>S</i>. Minnesota environmental tolerance to mercury (<i>mer</i> operon) and provide resistance to tetracycline and ampicillin due to the presence of <i>tet</i>(A) and <i>bla</i>_CMY-2, respectively. Moreover, pESM carries the yersiniabactin siderophore (high-pathogenicity island of <i>Yersinia</i>) related to the iron uptake. The temporal inference demonstrated that the most recent common ancestor dated from ~1978 and that the clonal emergent genomes carrying the pESM belong to a completely different lineage of <i>S</i>. Minnesota. Our results indicate that the presence of pESM likely contributes to the emergence of <i>S</i>. Minnesota and is precisely related to the successful spread of this particular clonal lineage in Brazil.IMPORTANCE<i>Salmonella</i> Minnesota has emerged in Brazil as one of the leading serovars related to human and animal infection, presenting high virulence and antibiotic resistance to drugs classified as the highest priority for clinical treatment in humans. This study performed whole-genome sequencing, temporal analysis, and phylogenetics to understand the genetic insights related to the emergence of <i>Salmonella</i> Minnesota in Brazil. Long-read sequencing has led to the identification and characterization of a unique megaplasmid carrying virulence, antibiotic resistance, and heavy-metal tolerance genes, which may play a central role in <i>S</i>. Minnesota's successful emergence in Brazil and possibly worldwide. The potentially high transmissibility of this plasmid between clones and serovars represents a risk to public health since its acquisition may increase <i>Salmonella</i>'s fitness, virulence, resistance, and persistence. Understanding the genetic aspects related to the emergence of serovars can help devise measures to mitigate the spread of hazardous multidrug-resistant strains.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543206","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 wildfire on soil microbial communities in karst forest ecosystems of southern Guizhou Province, China.","authors":"Xu Li, Yanfeng Han, Yunlin Zhang, Qiuyu Shao, Chunbo Dong, Jianfeng Li, Bo Ding, Yanwei Zhang","doi":"10.1128/aem.01245-24","DOIUrl":"https://doi.org/10.1128/aem.01245-24","url":null,"abstract":"<p><p>Wildfires are unpredictable disturbances with profound effects on soil properties and microbial communities within forest ecosystems. However, knowledge of post-fire microbial communities in karst forests remains limited. In this study, microbial amplicon sequencing techniques were employed to investigate the impact of wildfires on the composition, diversity, function, and co-occurrence network of soil microbial communities in karst forest landscapes and to identify the key soil physicochemical factors affecting the post-fire microbial communities. The wildfire affected the fungal community to a greater extent than the bacterial community, with the former shifting from a dominance of Basidiomycota to Ascomycota at the phylum level, while the relative abundance of Actinobacteria increased significantly in the bacterial community. Moreover, the wildfire increased the α-diversity of the microbial community and changed the β-diversity. Network analysis indicated significant reductions in the complexity of microbial community networks and the hub microbiome in burned soils compared to those of unburned soils. Functional predictions indicated an increase in the highly abundant functional taxa of chemoheterotrophic and aerobic chemoheterotrophic bacteria, along with a significant rise in saprotrophic functional fungal taxa following the fire. In addition, soil organic matter, total nitrogen, total phosphorus, and soil water content emerged as key soil physicochemical factors affecting post-fire soil microbial communities in the karst forest. Overall, this study revealed the structural and functional characteristics of soil microbial communities and their key influencing factors after a fire in a karst forest, which will provide a valuable theoretical basis for ecosystem restoration after a wildfire.IMPORTANCEDespite the significant impacts of wildfires on forest ecosystems, most existing studies have largely focused on boreal and Mediterranean coniferous forest types, with limited research on the impacts of coniferous and broadleaf forest types in subtropical karst regions. This study reveals the effects of wildfires on soil microbial communities of coniferous and broadleaf forest types in a karst forest. The results of this study not only improve the understanding of the effects of wildfires on the composition, diversity, function, and network of soil microbial communities but also provide a meaningful theoretical basis for post-fire ecosystem restoration in the karst forest.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543192","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":"Directed evolution of bacteriophages: thwarted by prolific prophage.","authors":"Tracey Lee Peters, Jacob Schow, Emma Spencer, James T Van Leuven, Holly Wichman, Craig Miller","doi":"10.1128/aem.00884-24","DOIUrl":"10.1128/aem.00884-24","url":null,"abstract":"<p><p>Various directed evolution methods exist that seek to procure bacteriophages with expanded host ranges, typically targeting phage-resistant or non-permissive bacterial hosts. The general premise of these methods involves propagating phage(s) on multiple bacterial hosts, pooling the lysate, and repeating this process until phage(s) can form plaques on the target host(s). In theory, this produces a lysate containing input phages and their evolved phage progeny. However, in practice, this lysate can also include prophages originating from bacterial hosts. Here, we describe our experience implementing one directed evolution method, the Appelmans protocol, to study phage evolution in the <i>Pseudomonas aeruginosa</i> phage-host system, where we observed rapid host-range expansion of the phage cocktail. Further experimentation and sequencing revealed that the observed host-range expansion was due to a <i>Casadabanvirus</i> prophage originating from a lysogenic host that was only included in the first three rounds of the experiment. This prophage could infect five of eight bacterial hosts initially used, allowing it to persist and proliferate until the termination of the experiment. This prophage was represented in half of the sequenced phage samples isolated from the Appelmans experiment, but despite being subjected to directed evolution conditions, it does not appear to have evolved. This work highlights the impact of prophages in directed evolution experiments and the importance of genetically verifying output phages, particularly for those attempting to procure phages intended for phage therapy applications. This study also notes the usefulness of intraspecies antagonism assays between bacterial host strains to establish a baseline for inhibitory activity and determine the presence of prophage.IMPORTANCEDirected evolution is a common strategy for evolving phages to expand the host range, often targeting pathogenic strains of bacteria. In this study, we investigated phage host-range expansion using directed evolution in the <i>Pseudomonas aeruginosa</i> system. We show that prophages are active players in directed evolution and can contribute to observation of host-range expansion. Since prophages are prevalent in bacterial hosts, particularly pathogenic strains of bacteria, and all directed evolution approaches involve iteratively propagating phage on one or more bacterial hosts, the presence of prophage in phage preparations is a factor that needs to be considered in experimental design and interpretation of results. These results highlight the importance of screening for prophages either genetically or through intraspecies antagonism assays during selection of bacterial strains and will contribute to improving the experimental design of future directed evolution studies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543191","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}