Applied and Environmental Microbiology最新文献

{"title":"Antibiotic resistome in the glacier forelands of polar regions.","authors":"Jabir Thajudeen, Siddarthan Venkatachalam, Puthiya Veettil Vipindas","doi":"10.1128/aem.00762-25","DOIUrl":"https://doi.org/10.1128/aem.00762-25","url":null,"abstract":"<p><p>Antibiotic resistance genes (ARGs) pose a significant threat, exacerbated by climate change impacts on polar regions, particularly melting glaciers and permafrost. While ancient antibiotic resistance exists in the environments, the release and dissemination of ARGs remain poorly understood. This study investigated ARG composition and distribution in 43 metagenomes from Arctic and Antarctic glacier forelands. We identified 154 ARGs, predominantly bacitracin resistance, followed by rifamycin, fosfomycin, vancomycin, tetracycline, and beta-lactam resistance genes. Significant correlations were observed between ARGs and mobile genetic elements (MGEs), with 20 ARGs associated with <i>tnpA</i> MGEs. Actinomycetota and Pseudomonadota were the primary ARG-carrying phyla. Metagenome-assembled genomes revealed <i>Mycobacterium</i> sp., <i>Pseudomonas</i> sp., and <i>Tatlockia</i> sp. as major ARG-harboring pathogens in the glacier forelands. Evolutionarily adapted, distinct ancient ARGs were abundant in the polar environments, varying between different geographic regions. The environmental parameters such as pH and total organic carbon significantly influenced the ARG distribution in the Arctic and Antarctic glacier forelands. This study provides crucial baseline data on antimicrobial resistance, highlighting potential risks associated with rapid environmental change in the regions.</p><p><strong>Importance: </strong>Antibiotic resistance poses a significant global health threat, exacerbated by the release of antibiotic resistance genes from melting glaciers and permafrost due to climate change. This study provides crucial baseline data on the composition and distribution of antibiotic resistance genes in these vulnerable polar environments, which is essential for understanding and mitigating the risks associated with their release. The findings have far-reaching implications for global health security and emphasize the need for further research to address this emerging threat.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0076225"},"PeriodicalIF":3.9,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075344","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":"Designing synthetic microbial communities for enhanced anaerobic waste treatment.","authors":"Lisa Jourdain, Wenyu Gu","doi":"10.1128/aem.00404-25","DOIUrl":"https://doi.org/10.1128/aem.00404-25","url":null,"abstract":"<p><p>Synthetic microbial communities (SynComs) are powerful tools for investigating microbial interactions and community assembly by focusing on minimal yet functionally representative members. Here, we will highlight key principles for designing SynComs, specifically emphasizing the anaerobic digestion (AD) microbiome for waste treatment and upcycling. The AD process has traditionally been used to reduce organic waste volume while producing biogas as a renewable energy source. Its microbiome features well-defined trophic layers and metabolic groups. There has been growing interest in repurposing the AD process to produce value-added products and chemical precursors, contributing to sustainable waste management and the goals of a circular economy. Optimizing the AD process requires a better understanding of microbial interactions and the influence of both biotic and abiotic parameters, where SynComs offer great promise. Focusing on AD microbiomes, we review the principles of SynComs' design, including keystone taxa and function, cross-feeding interactions, and metabolic redundancy, as well as how modeling approaches could guide SynComs design. Furthermore, we address practical considerations for working with AD SynComs and examine constructed SynComs designed for anaerobic waste digestion. Finally, we discuss the challenges associated with designing and applying SynComs to enhance our understanding of the AD process. This review aims to explore the use of synthetic communities in studying anaerobic digestion and highlights their potential for developing innovative biotechnological processes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0040425"},"PeriodicalIF":3.9,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075365","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":"Bacterial genome-wide association studies: exploring the genetic variation underlying bacterial phenotypes.","authors":"Qiuping Yang, Xiaoqi Wang, Mengting Han, Huanjing Sheng, Yulu Sun, Li Su, Wenjing Lu, Mei Li, Siyue Wang, Jia Chen, Shenghui Cui, Bao-Wei Yang","doi":"10.1128/aem.02512-24","DOIUrl":"https://doi.org/10.1128/aem.02512-24","url":null,"abstract":"<p><p>With the continuous advancements in high-throughput genome sequencing technologies and the development of innovative bioinformatics tools, bacterial genome-wide association studies (BGWAS) have emerged as a transformative approach for investigating the genetic variations underlying diverse bacterial phenotypes at the population genome level. This review provides a comprehensive overview of the application of BGWAS in elucidating genetic determinants of bacterial drug resistance, pathogenicity, host specificity, biofilm formation, and probiotic fermentation characteristics. We systematically summarize the BGWAS workflow, including study design, data analysis pipelines, and the bioinformatics software employed at various stages. Furthermore, we highlight specialized tools tailored for BGWAS and discuss their unique features and applications. We also discuss confounding factors that can influence the accuracy and reliability of BGWAS results, including population structure, linkage disequilibrium, and multiple testing. By incorporating recent advancements, this review serves as a comprehensive reference for researchers utilizing BGWAS to uncover the genetic basis of bacterial phenotypes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0251224"},"PeriodicalIF":3.9,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075347","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":"Determinism and stochasticity drive microbial community assembly and microbial interactions in calcareous glacier forefields.","authors":"Edoardo Mandolini, Maraike Probst, Anusha Telagathoti, Beat Frey, Luis M Rodriguez-R, Flavio Fornasier, Nadine Praeg, Paul Illmer, Ursula Peintner","doi":"10.1128/aem.00302-25","DOIUrl":"https://doi.org/10.1128/aem.00302-25","url":null,"abstract":"<p><p>Calcareous glacier forefields challenge prevailing ecological frameworks on microbial biodiversity and community assembly due to their unique bedrock. Early stages of soil development in these environments are notorious for their high turnover rates, demanding a high degree of replication for obtaining conclusive data. However, studies across different calcareous glaciers are still missing. Here, we robustly investigated both bacterial and fungal diversity, association networks, and assembly processes in four calcareous glacier forefields of the Alps, focusing on the earliest soil developmental stages (<25 years) early in the snow-free season. We found a diverse community of bacteria and fungi, potentially involved in P and N nutrient cycling. A core microbiome existing across all four locations suggests that certain microbes might be more successful colonizers of these ecosystems than others. Nearest taxon index revealed phylogenetically clustered microbial communities. These findings suggest that the distribution and colonization of some microbes were influenced by selective forces such as geography and climate during the early stages of soil development in calcareous glaciers. Interestingly, there were no common bacterial-fungal associations across the four locations, indicating that this habitat does not select for specific bacterial-fungal associations and that associations were driven by neutral processes. We discuss microbial communities and their interactions in these special calcareous glacier forefield habitats. Moreover, we present innovative approaches for studying microbial assembly that address both deterministic, intrinsic drivers, like specific microbial traits, and stochastic, extrinsic drivers, such as the opportunistic behavior of microbes.IMPORTANCEOur study is based on three fundamental and unique approaches: (i) we utilize the early stages of soil development in four glacier forefields across the Alpine range. This design implies high replicability in a natural setting, which is crucial for drawing general conclusions. (ii) Our study investigates glacier forefields with calcareous bedrock directly after snowmelt. These habitats and periods remain surprisingly underexplored. (iii) Our results underline the relevance of bacterial-fungal associations in microbial community assembly alongside dispersal, drift, and natural selection. Taken together, our study provides new insights into the development of complex microbial communities, their stabilization and predictability, including ecological implications.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0030225"},"PeriodicalIF":3.9,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075443","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":"An obligate symbiont of <i>Haematomyzus elephantis</i> with a strongly reduced genome resembles symbiotic bacteria in sucking lice.","authors":"Jana Martin Říhová, Roman Vodička, Václav Hypša","doi":"10.1128/aem.00220-25","DOIUrl":"https://doi.org/10.1128/aem.00220-25","url":null,"abstract":"<p><p>The parvorder Rhynchophthirina with a single genus <i>Haematomyzus</i> is a small group of ectoparasites of unclear phylogenetic position, related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated that <i>Haematomyzus</i> harbors a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the smallest known genomes are found in the symbionts associated with sucking lice, which feed exclusively on mammal blood, compared to the generally larger genomes of the symbionts inhabiting chewing lice, which feed on skin derivatives. In this study, we investigate the genome characteristics of the symbiont associated with <i>Haematomyzus elephantis</i>. We sequenced and assembled the <i>H. elephantis</i> metagenome, extracted a genome draft of its symbiotic bacterium, and showed that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice and also with <i>Wigglesworthia glossinidia</i>, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, the <i>H. elephantis</i> symbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.IMPORTANCERhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, i.e., mammals' blood vs vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role is not known. In this study, we assemble the genome of symbiotic bacterium from <i>Haematomyzus elephantis</i> (Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other sucking louse symbionts, it retains essential pathways for the synthesis of several B vitamins.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0022025"},"PeriodicalIF":3.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959408","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 protozoan perspective on climate change and biosafety threats: differences in testate amoebae in lakes in forest-swamp and forest-steppe zones in Western Siberia.","authors":"Olga N Zagumyonnaya, Dmitry G Zagumyonnyi, Elena A Gerasimova, Denis V Tikhonenkov","doi":"10.1128/aem.00330-25","DOIUrl":"https://doi.org/10.1128/aem.00330-25","url":null,"abstract":"<p><p>The problem of increasing salinity and mineralization in natural and artificial freshwater bodies with climate warming is very relevant nowadays, as it leads to changes in the species composition of planktonic organisms. Testate amoebae are one of the responsive bioindicators that are sensitive to even minor changes in environmental conditions. In this study, a comparative analysis of the species diversity of planktonic testate amoebae was carried out in a number of lakes in the forest-steppe and forest-swamp natural zones of Western Siberia using microscopy and metabarcoding. One new species, <i>Pseudodifflugia siemensmai</i> sp. nov., was described. The detection frequency and the number of reads of amplicon sequence variants of potentially pathogenic testate amoebae belonging to the genera <i>Rhogostoma</i> and <i>Fisculla</i> were higher in forest-steppe lakes. Universal eukaryotic primers for the 18S rRNA gene are well suited for identifying testate amoebae from the supergroup Cercozoa but are practically not applicable for identifying Amoebozoa testaceans. The plankton of the lakes with the highest mineralization and salinity was characterized by the most specific species composition. These results should be taken into account when predicting changes in aquatic communities with further climate warming, which may also be associated with an increase in the occurrence of pathogenic testaceans that pose biosafety threats.IMPORTANCEMicroscopic and metabarcoding analyses reveal important differences in testate amoebae communities in lakes in two natural and climatic zones of Western Siberia that should be taken into account when predicting changes in aquatic communities with further climate warming, which may also be associated with an increase in the occurrence of pathogenic testaceans that pose biosafety threats.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0033025"},"PeriodicalIF":3.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952833","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":"Optimizing experimental conditions: the role of buffered environments in microbial isolation, physiological studies, and taxonomic characterization.","authors":"Om Prakash, Ujjwala Waghmare, Ashvini Chauhan, Yogesh Patil","doi":"10.1128/aem.01728-24","DOIUrl":"https://doi.org/10.1128/aem.01728-24","url":null,"abstract":"<p><p>Using a buffered medium is considered essential for enriching and cultivating novel microbial taxa, studying their pH range and optima, and conducting different physiological experiments. Experimental evidence showed that different buffer compounds impact microbial physiology and cell growth differently, and some of them exert toxic and inhibitory effects on organisms under study. Laboratory growth media supplemented with incompatible buffers could also suppress the organism's growth. Therefore, the selection of buffers without the knowledge of their implications on cell growth and physiology in such experiments yields an inaccurate estimate of their physiological abilities and pH range and optima. In this paper, the authors argue against the use of buffered medium to enrich and isolate novel taxa and suggest determining the pH range and optima using unbuffered medium for taxonomic description and physiological characterization. Based on previous literature and our observations, we recommend the use of rich universal laboratory growth medium with their pH adjusted using 1 N NaOH and/or 1 N HCl for such studies, except in cases where the organism cannot grow in such media. However, the pH of the growth medium must be continuously monitored, and in cases where the medium's buffering capacity is compromised, a suitable pH buffer with only a neutral effect on cell growth must be used for more accurate physiological experiments with that organism in the future. Based on the inhibitory effects of buffers on different cells (prokaryotes and eukaryotes) and physiological activities, in this manuscript, we also recommend that the compatibility of the buffers should be first screened before starting any physiological experiments, and any buffer compound should be avoided in the culture medium during the designing of the culturomics protocols for the cultivation of novel taxa from natural samples.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0172824"},"PeriodicalIF":3.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957399","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":"Analysis of the SARS-CoV-2 inactivation mechanism using violet-blue light (405 nm).","authors":"Davide Amodeo, Serena Marchi, Lia Fiaschi, Luisa Raucci, Camilla Biba, Valentina Salvestroni, Claudia Maria Trombetta, Ilaria Manini, Maurizio Zazzi, Emanuele Montomoli, Ilaria Vicenti, Gabriele Cevenini, Gabriele Messina","doi":"10.1128/aem.00403-25","DOIUrl":"https://doi.org/10.1128/aem.00403-25","url":null,"abstract":"<p><p>The study evaluated the effects of violet-blue light (VBL) on cell viability and replication, carbonylation of three structural proteins (S, E, and N) and one non-structural protein (NSP13), and direct damage to the RNA of SARS-CoV-2. The virus was exposed to increasing doses of VBL along with influenza A and B viruses to compare their susceptibility. At the highest dose (21.6 J/cm²), SARS-CoV-2 was significantly more susceptible to VBL than the influenza viruses, with a reduction in viral titer of 2.33 log₁₀. Viral RNA did not show significant changes after exposure to VBL, as demonstrated by next-generation sequencing and real-time PCR quantification, suggesting that the inactivation process does not involve direct nucleic acid damage. To exclude the role of the culture suspension in the inactivation process, virus viability experiments were performed using different dilutions of Dulbecco's modified Eagle's medium (DMEM) in phosphate-buffered saline (PBS). The results indicated that the suspension medium played a secondary role in virus inactivation, as viability did not increase with increasing DMEM dilution. Subsequent tests with three different antioxidants (NAC, AsA, and SOD) at different concentrations prevented viral inactivation, from 99.99% to 85.43% (with SOD 0.003 mM). Carbonylation of S and E proteins was more pronounced when viruses were suspended in DMEM rather than PBS, although the tests demonstrated that the intrinsic properties of the viral membrane were a crucial element to consider in relation to its susceptibility to VBL.IMPORTANCELight-based disinfection methods are often used in combination with other cleaning methods due to their non-invasive nature, versatility, and environmental benefits. VBL is an effective approach as it induces the production of reactive oxygen species that reduce microbial viability. In this study, lipid peroxidation was identified as an important factor affecting the structural integrity and function of the viral envelope, reducing its ability to interact with host cells and consequently its ability to be infectious. The lipid envelope of SARS-CoV-2, composed mainly of glycerophospholipids and lacking cholesterol and sphingolipids, appears to be the critical factor in its susceptibility, distinguishing it from influenza viruses, which have a lipid profile richer in components that protect against oxidative stress.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0040325"},"PeriodicalIF":3.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143972815","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":"Citric acid impairs type B trichothecene biosynthesis of <i>Fusarium graminearum</i> but enhances its growth and pigment biosynthesis: transcriptomic and proteomic analyses.","authors":"Luzhou Cai, Ling Li, Dong Li, Yanping Wu, Jinrong Bai, Kai Zhong, Hong Gao","doi":"10.1128/aem.01531-24","DOIUrl":"https://doi.org/10.1128/aem.01531-24","url":null,"abstract":"<p><p><i>Fusarium graminearum</i> is a pathogenic fungus that causes devastating plant diseases such as Fusarium head blight, leading to significant food waste and posing a threat to human health due to the accumulation of mycotoxins. As a soil-borne fungus, <i>F. graminearum</i> interacts closely with plants and soil, completing its life cycle in an intricate environment. In this investigation, citric acid (CA), a plant root exudate and heavy metal chelator, was investigated for its effect on <i>F. graminearum</i> at concentrations of 2.5, 5, 10, and 20 mM. The fungus treated with this CA gradient exhibited different growth conditions and mycelial colors. Integrative analysis of transcriptomics and proteomics found that the growth of the fungus was accelerated by the upregulation of carbon source metabolism-related enzymes such as phosphoenolpyruvate carboxykinase (PEPCK), Glpk, and LAI12, and the mycelial pigments were altered by polyketide biosynthetic enzymes like AurF, AurJ, and AurT, which were responsible for the production of aurofusarin and rubrofusarin. Interestingly, many <i>Tri</i> genes and their corresponding proteins along with type B trichothecene biosynthesis were significantly downregulated, though the fungal growth was promoted. In this study, the CK, 2.5, and 5 mM groups had similar expression patterns of RNA and protein, while the 10 and 20 mM groups were alike. With the validation of CK, 5, and 10 mM groups, the discovery of CA as a type B trichothecene biosynthesis inhibitor and growth promoter was expected to facilitate its reasonable application and contribute to further research for the prevention of <i>F. graminearum</i>.</p><p><strong>Importance: </strong><i>Fusarium graminearum</i> is a challenging phytopathogen that causes plant disasters worldwide, such as Fusarium head blight and ear rot in small grain crops like wheat and maize. Besides, the invasion of the fungus on plants is often accompanied by the production of health-threatening mycotoxins-trichothecenes. Therefore, the control of <i>Fusarium graminearum</i> has always been a hot area of research. However, currently, the prevalence of these plant diseases around the world and the mycotoxin accumulation beyond safety limits indicate the necessity for more related research. In the last decades, researchers have sought to identify the key substances associated with the growth, propagation, and mycotoxin production of the fungus, such as carbon and nitrogen sources. Organic acids have always been considered antifungal agents due to their abundant H+ content. However, their comprehensive impact on fungi has been rarely investigated. This research focused on the effect of citric acid, a type of crop exudate and a common heavy-metal chelator, on the metabolism of <i>Fusarium graminearum</i>. The result was expected to provide a theoretical basis for further studies on plants-soil-fungi interactions and the reasonable utilization of citric acid in agriculture.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0153124"},"PeriodicalIF":3.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959077","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":"Lydicamycins induce morphological differentiation in actinobacterial interactions.","authors":"Scott A Jarmusch, Morten D Schostag, Zhijie Yang, Jinglin Wang, Aaron J C Andersen, Tilmann Weber, Ling Ding","doi":"10.1128/aem.00295-25","DOIUrl":"https://doi.org/10.1128/aem.00295-25","url":null,"abstract":"<p><p><i>Streptomyces</i> are major players in soil microbiomes; however, their interactions with other actinobacteria remain largely unexplored. Given the complex developmental cycle of actinobacteria, a multi-omics approach is essential to unravel the interactions. This study originated from the observation of induced morphogenesis between two environmental isolates from the same site, <i>Kitasatospora</i> sp. P9-2B1 and <i>Streptomyces</i> sp. P9-2B2. When co-cultivated on potato dextrose agar, P9-2B2 triggered a wave-like sporulation pattern in strain P9-2B1. Mass <i>s</i>pectrometry imaging revealed that a suite of lydicamycins accumulated in the induced sporulation zone. Using CRISPR base editing, lydicamycin-deficient mutants were generated, and the inducible sporulation was ceased, confirming the role of lydicamycin in triggering morphological differentiation. In agar diffusion assays, pure lydicamycin was inhibitory when added concurrently with bacterial inoculation but induced sporulation when added later. The same inducible sporulation wave phenomenon was also observed in additional environmental isolates and <i>Streptomyces coelicolor</i> M145 and M1146. Transcriptomics analysis revealed differential gene expression linked to early aerial mycelium development at 4 days into co-culture, the transitional genes responsible for the development of spores at day 9, together with numerous genes for overall stress responses, particularly cell envelope stress responses. These findings highlight previously unrecognized actinobacteria interactions mediated by lydicamycins, suggesting a broader ecological role of bioactive metabolites in microbiomes.</p><p><strong>Importance: </strong>Moving beyond an antibiotic discovery mindset, exploring the chemical ecology of secondary metabolites is key to maximizing their biotechnological potential. Dual cultures offer reduced complexity, enabling an in-depth analysis of these interactions via multi-omics, which provides complementary data for more robust conclusions. This study sheds light on the role of lydicamycins in dual cultures with other actinobacteria and establishes an integral roadmap for future chemical ecology work between microorganisms, particularly through mass spectrometry imaging.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0029525"},"PeriodicalIF":3.9,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967259","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}