Applied and Environmental Microbiology最新文献

{"title":"7β-Hydroxysteroid dehydratase Hsh3 eliminates the 7-hydroxy group of the bile salt ursodeoxycholate during degradation by <i>Sphingobium</i> sp. strain Chol11 and other <i>Sphingomonadaceae</i>.","authors":"Phil Richtsmeier, Ruslan Nedielkov, Malte Haring, Onur Yücel, Lea Elsner, Rebekka Herdis Lülf, Lars Wöhlbrand, Ralf Rabus, Heiko Moeller, Bodo Philipp, Franziska Maria Mueller","doi":"10.1128/aem.00185-25","DOIUrl":"10.1128/aem.00185-25","url":null,"abstract":"<p><p>Bile salts are steroids with distinctive hydroxylation patterns that are produced and excreted by vertebrates. In contrast to common human bile salts, ursodeoxycholate (UDCA) has a 7-hydroxy group in β-configuration and is used in large amounts for the treatment of diverse gastrointestinal diseases. We isolated the 7β-hydroxysteroid dehydratase Hsh3 that is involved in UDCA degradation by <i>Sphingobium</i> sp. strain Chol11. Hsh3 eliminates the 7β-hydroxy group as water, leading to a double bond in the B-ring. This is similar to 7α-hydroxysteroid dehydratases in this and other strains, but Hsh3 is evolutionarily different from these. Purified Hsh3 accepted steroids with and without side chains as substrates and had minor activity with 7α-hydroxy groups. The deletion mutant strain Chol11 Δ<i>hsh3</i> had impacted growth with UDCA and accumulated a novel compound. The compound was identified as 3',5-dihydroxy-H-methyl-hexahydro-5-indene-1-one-propanoate, consisting of steroid rings C and D with a C₃-side chain carrying the former 7β-hydroxy group, indicating that Hsh3 activity is important especially for the later stages of bile salt degradation. Hsh3 homologs were found in other sphingomonads that were also able to degrade UDCA as well as in environmental metagenomes. Thus, Hsh3 adds to the bacterial enzyme repertoire for degrading a variety of differently hydroxylated bile salts.IMPORTANCEThe bacterial degradation of different bile salts is not only important for the removal of these steroidal compounds from the environment but also harbors interesting enzymes for steroid biotechnology. The 7β-hydroxy bile salt ursodeoxycholate (UDCA) naturally occurs in high concentration in the feces of black bears and has important pharmaceutical relevance for the treatment of different liver-related diseases, for which it is administered in high and increasing amounts. Additionally, it is present in the bile salt pool of humans in trace amounts. While UDCA degradation is environmentally important, the enzyme Hsh3 modifies the hydroxy group that confers the medically relevant properties and thus might be interesting for microbiome analyses and biotechnological applications.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0018525"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060932","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":"Survival and spread of engineered <i>Mycobacterium smegmatis</i> and associated mycobacteriophage in soil microcosms.","authors":"Megan S Fleeharty, Kate B R Carline, Bilalay V Tchadi, Bjorn B Shockey, Emma C Holley, Margaret S Saha","doi":"10.1128/aem.00212-25","DOIUrl":"10.1128/aem.00212-25","url":null,"abstract":"<p><p>The inoculation of microbes into soil environments has numerous applications for improving soil quality and crop health; however, the ability of exogenous and engineered microbes to survive and spread in soil remains uncertain. To address this challenge, we assayed the survival and spread of <i>Mycobacterium smegmatis</i>, engineered with either plasmid transformation or genome integration, as well as its mycobacteriophage Kampy, in both sterilized and non-sterilized soil microcosms over a period of 49 days. Although engineered <i>M. smegmatis</i> and Kampy persisted in all soil microcosms, there was minimal evidence of spread to 5 cm away from the inoculation site. There was a higher prevalence of Kampy observed in sterilized soil than in non-sterilized soil, suggesting a detrimental effect of the native soil biotic and viral community on the ability of this phage to proliferate in the soil microcosm. Additionally, a higher abundance of the genome-integrated bacteria relative to the plasmid-carrying bacteria, as well as evidence for loss of plasmid over the duration of the experiment, suggests a burden associated with bacteria harboring plasmids, although plasmids were still retained across 49 days. To our knowledge, this is the first study to simultaneously measure the persistence and spread of bacteria and their associated phage in both sterilized and non-sterilized soil microcosms, employing bacteria with plasmid-based and genome-integrated engineered circuits. As such, this study provides a novel understanding of challenges associated with the deployment of bioengineered microbes into soil environments.</p><p><strong>Importance: </strong>Healthy soil is essential to sustain life, as it provides habitable land, enables food production, promotes biodiversity, sequesters and cycles nutrients, and filters water. Given the prevalence of soil degradation, treatment of soil with microbes that promote soil and crop health could improve global soil sustainability; furthermore, the application of bioengineering and synthetic biology to these microbes allows fine-tunable and robust control of gene-of-interest expression. These solutions require the introduction of bacteria into the soil, an environment in which abundant competition and often limited nutrients can result in bacterial death or dormancy. This study employs <i>Mycobacterium smegmatis</i> as a chassis alongside its bacteriophage Kampy in soil microcosms to assess the ability of non-native microbes to survive and spread in soil. Insights from this experiment highlight important challenges, which must be overcome for successful deployment of engineered microbes in the field.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0021225"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109517","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":"Bacterial conjugation in the ruminant pathogen <i>Mycoplasma agalactiae</i> is influenced by eukaryotic host factors.","authors":"M'hamed Derriche, Laurent Xavier Nouvel, Maria Gaudino, Eveline Sagné, Elisa Simon, Hortensia Robert, Gwendoline Pot, Gilles Meyer, Christian de la Fe, Yonathan Arfi, Renaud Maillard, Christine Citti, Eric Baranowski","doi":"10.1128/aem.00868-25","DOIUrl":"10.1128/aem.00868-25","url":null,"abstract":"<p><p>Horizontal gene transfer (HGT) plays a pivotal role in the evolution and adaptation of genome-reduced mycoplasmas. The conjugative properties of these organisms are key in this phenomenon but are largely understudied, particularly <i>in vivo</i>. In the present study, the ruminant pathogen <i>Mycoplasma agalactiae</i> was used as a model organism to document mycoplasma conjugation in environments of increasing complexity, from axenic to cell and organotypic culture conditions. Compared to axenic mating conditions, mycoplasma co-cultivation with goat epithelial cells or bovine precision-cut lung slices resulted in enhanced mating frequencies with high rates of <i>M. agalactiae</i> integrative and conjugative element (ICEA) self-dissemination. These results were conditioned by the presence of eukaryotic cells in the culture and influenced by competition between mating partners but were not limited to <i>M. agalactiae</i>, as similar results were observed with <i>Mycoplasma bovis</i>. Mycoplasma conjugation <i>ex vivo</i> was further characterized by analyzing mycoplasma chromosomal transfer (MCT), a newly discovered mechanism of horizontal exchange of chromosomal DNA that generates mosaic genomes. Compared to ICEA transfer, MCT was detected at lower rates under cell and organotypic culture conditions, suggesting a negative impact of these cellular environments on MCT or its progeny. Finally, mating experiments under nutrient-deprived conditions identified nucleotide stress as a potential factor influencing the modulation of mycoplasma conjugation by eukaryotic host cells. In conclusion, these results suggest that HGT <i>in vivo</i> is likely underestimated and provide valuable models to further study mycoplasma conjugation <i>ex vivo</i>.IMPORTANCEConjugation is an evolutionary shortcut that bacteria use to exchange genetic information with their neighbors. Despite the fast evolution rate of the genome-reduced mycoplasmas, their conjugative properties remain largely understudied, particularly <i>in vivo</i>. Here we used the ruminant pathogen <i>Mycoplasma agalactiae</i> to study how mycoplasmas conjugate in co-culture with host-derived cells and tissues. Interestingly, conjugation was stimulated when mycoplasmas were co-cultured with eukaryotic cells. This was documented by monitoring the self-propagation of a mobile genetic element known as integrative and conjugative element (ICE) and the exchange of chromosomal DNA leading to the formation of mosaic genomes. While ICE transfer was observed at high frequency, only a few mosaic genomes were detected in the presence of eukaryotic cells. Further data point toward nucleotide stress as a possible factor modulating mycoplasma conjugation in cellular environments. These results suggest that mycoplasma-host interactions may stimulate conjugation <i>in vivo</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0086825"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149023","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":"Chemoautotrophy in subzero environments and the potential for cold-adapted Rubisco.","authors":"Kaitlin Harrison, Josephine Z Rapp, Alexander L Jaffe, Jody W Deming, Jodi Young","doi":"10.1128/aem.00604-25","DOIUrl":"10.1128/aem.00604-25","url":null,"abstract":"<p><p>The act of fixing inorganic carbon into the biosphere is largely facilitated by one enzyme, Rubisco. Beyond well-studied plants and cyanobacteria, many bacteria use Rubisco for chemolithoautotrophy in extreme environments on Earth. Here, we characterized the diversity of autotrophic pathways and chemolithoautotrophic Rubiscos from two distinct subzero, hypersaline Arctic environments: 40-kyr relic marine brines encased within permafrost (cryopeg brines) and first-year sea ice. The Calvin-Benson-Bassham (CBB) cycle was widely found in both environments, although with different predominant Rubisco forms. From cryopeg brine, reconstructions of metagenome-assembled genomes (MAGs) uncovered four MAGs with the potential for chemolithoautotrophy, of which the CBB-containing genus <i>Thiomicrorhabdus</i> was most abundant. A broader survey of <i>Thiomicrorhabdus</i> genomes from diverse environments identified a core complement of three Rubisco forms (II, IAc, IAq) with a complex pattern of gain and loss, with form II constitutively present in genomes from subzero environments. Using representative kinetic data, we modeled carboxylation rates of Rubisco forms II, IAc, and IAq across CO₂, O₂, and temperature conditions. We found that form II outcompetes form I at low O₂, but cold temperatures minimize this advantage. Inspection of form II from genomes from cold environments identified signals of potential thermal adaptation due to key amino acid substitutions, which resulted in a more exposed active site. We argue that subzero form II from <i>Thiomicrorhabdus</i> warrants further study as it may have unique kinetics or thermal stability. This work can help address the limits of autotrophic functionality in extreme environments on Earth and other planetary bodies.<b>IMPORTANCE</b>Autotrophy, or the fixation of inorganic carbon to biomass, is a key factor in life's ability to thrive on Earth. Research on autotrophy has focused on plants and algae, but many bacteria are also autotrophic and can survive and thrive under more extreme conditions. These bacteria are a window to past autotrophy on Earth, as well as potential autotrophy in extreme environments elsewhere in the universe. Our study focused on dark, cold, saline environments, which are likely to be found on Enceladus and Europa, as well as in the Martian subsurface. We found evidence for potential cold adaptation in a key autotrophic enzyme, Rubisco, which could expand the known boundaries of autotrophy in rapidly disappearing icy environments on Earth. We also present a novel model framework that can be used to probe the limits of autotrophy not only on Earth but also on key astrobiological targets like Enceladus and Europa.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0060425"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186333","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":"ARTP mutagenesis for genome-wide identification of genes important for biofilm regulation in spoilage bacterium <i>Pseudomonas fluorescens</i> PF08.","authors":"Feifei Wang, Shenjia Chen, Jinjing Zhou, Ruiyu Zhu, Jian Chen, Yanbo Wang","doi":"10.1128/aem.00218-25","DOIUrl":"10.1128/aem.00218-25","url":null,"abstract":"<p><p><i>Pseudomonas fluorescens</i> is a vital food spoilage bacterium and commonly spoils foods in the form of biofilms. Yet its biofilm regulation strategies have not been fully revealed. Here, we conducted a genome-wide screen of genes important for biofilm regulation using atmospheric and room temperature plasma mutagenesis together with the whole-genome resequencing technology. Three genes (<i>D7M10_RS02105</i>, <i>D7M10_RS27690,</i> and <i>D7M10_RS25705</i>) encoding GGDEF-EAL domain-containing proteins were found to have different mutation manifestations between biofilm cells and free cells. On direct testing, null mutants of <i>D7M10_RS02105</i> and especially <i>D7M10_RS27690</i> exhibited significantly elevated cyclic di-GMP (c-di-GMP) levels. Further studies indicated that a higher level of c-di-GMP caused by the null mutant of <i>D7M10_RS27690</i> triggered cell growth, the production of siderophore and exopolysaccharide as well as autoaggregation, and hindered cell motility, all of which together promote biofilm formation. RNA-sequencing analysis revealed the transcription profile regulated by <i>D7M10_RS27690</i>, mostly including flagellar assembly and peptidoglycan biosynthesis pathways. Therein, the downregulated genes enriched in flagellar assembly were verified by qRT-PCR; the result of which was in agreement with the decreased cell motility.IMPORTANCEBiofilms formed by spoilage bacterium <i>Pseudomonas fluorescens</i> will bring about food quality and safety issues. In this study, we present the establishment of a genetic method and verified its reliability and efficiency for identifying genes associated with biofilm regulation. The genes we discovered offer new perspectives on the mechanisms of biofilm regulation in spoilage bacterium <i>P. fluorescens</i>. Moreover, the gene screen method based on atmospheric and room temperature plasma mutagenesis and whole-genome resequencing-coupled technology overcomes the labor-intensive issues caused by traditional methods and should generally be suitable for identifying genes associated with biofilm formation or dispersion in other bacteria.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":"91 6","pages":"e0021825"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324335","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":"Marked reduction of SARS-CoV-2 infection and improved recovery following supplementation with a probiotic mix of four strains and two strains of <i>Bifidobacterium breve</i> in hamsters.","authors":"Edgar Torres-Maravilla, Marine Wasniewski, Aurélie Wauquier, Alexandre Servat, Evelyne Picard-Meyer, Elodie Monchatre-Leroy, Sandrine Auger, Sophie Holowacz, Franck Boué, Philippe Langella, Elsa Jacouton, Anne-Judith Waligora-Dupriet","doi":"10.1128/aem.00648-25","DOIUrl":"10.1128/aem.00648-25","url":null,"abstract":"<p><p>Only a few studies have shown that certain probiotics have beneficial effects on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In this study, two strains of <i>Bifidobacterium breve</i>, CNCM I-5644 and CNCM I-5979, selected for their <i>in vitro</i> immunomodulatory properties demonstrated in a screening of 20 strains and a mixture of 4 probiotic strains selected based on its immunomodulatory and antiviral properties were evaluated in a hamster model of SARS-CoV-2 infection. Supplementation with these probiotics (7 days before plus 7 days after infection) reduced SARS-CoV-2 infection with a significantly reduced viral load in the upper respiratory tract and lungs and improved weight recovery. Probiotics also counteracted the increase in inflammatory markers and intestinal permeability. The impact of these probiotics was independent of microbiota composition and short-chain fatty acid production. Overall, these data suggest that the probiotics tested, in particular the mix containing <i>Bifidobacterium longum</i> LA101, <i>Lactobacillus helveticus</i> LA102, <i>Lactococcus lactis</i> LA103, and <i>Streptococcus thermophilus</i> LA104, can facilitate recovery from SARS-CoV-2 infection (as shown by weight regain in infected hamsters) by reducing viral load and inflammation.</p><p><strong>Importance: </strong>Our study investigated the potential benefits of specific probiotics in fighting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19). We tested two strains of <i>Bifidobacterium breve</i> selected based on their immune-boosting properties, along with a commercial mix of four probiotic strains chosen for its antiviral and immune-modulating effects. These probiotics were administered to hamsters over a week before and a week after infection. Supplementation with these probiotics significantly reduced the viral load in the upper respiratory tract and lungs, promoting recovery as demonstrated by the weight regain observed. In addition to reducing viral presence, the probiotics also helped lower inflammation and improved gut health by counteracting increased intestinal permeability. Our findings suggest that probiotics, particularly the mix of four strains, could support recovery from SARS-CoV-2 infection by reducing inflammation, viral load, and enhancing overall health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0064825"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143969199","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":"Antibiotic resistome in the glacier forelands of polar regions.","authors":"Jabir Thajudeen, Siddarthan Venkatachalam, Puthiya Veettil Vipindas","doi":"10.1128/aem.00762-25","DOIUrl":"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":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175520/pdf/","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":"OA","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":"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":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175522/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics-based insights into <i>Pantoea ananatis</i> strains, isolated from white spot diseased leaves of maize with plant growth-promoting attributes.","authors":"Fenghuan Yang, Miao Li, Hanxiang Wu, Chao Yu, Wende Liu, Huamin Chen","doi":"10.1128/aem.00329-25","DOIUrl":"10.1128/aem.00329-25","url":null,"abstract":"<p><p><i>Pantoea ananatis</i> is a member of the Enterobacteriaceae family known for its broad host adaptability. This study isolated 10 <i>P</i>. <i>ananatis</i> strains from white spot (MWS)-diseased leaves of maize (<i>Zea mays</i>) grown in Yunnan Province, China, and analyzed their putative functions, genomic diversity, and variation. The inoculation tests revealed that none of the 10 isolates caused MWS symptoms in maize. Nine maize isolates, except for S47, induced a hypersensitive response (HR) in tobacco and caused rot symptoms in onion. Most isolates exhibited plant growth-promoting characteristics, with strains JCC14, JCY1, and S47 significantly enhancing maize seedling growth parameters. Genomic sequencing of 10 maize isolates and two rice isolates revealed that 12 isolates clustered into three groups, with an open pan-genome identified. Ancestral reconstruction indicated that the genome size increased in Group A and then decreased in Group B, with significant gains in orthologous groups at Node 14, the most recent common ancestor (MRCA) of Group A and Group B, and at Node 19, the MRCA of seven maize-isolated strains and other Group B strains. Additionally, 11 single-copy orthologous groups were under positive selection. Furthermore, the HIVir (high virulence, also known as PASVIL, <i>P. ananatis</i>-specific virulence locus) cluster and type VI secretion system-related genes were conserved in certain <i>P. ananatis</i> strains but were not related to their group divergences. This study not only reveals the diverse functions of MWS-diseased maize <i>P. ananatis</i> isolates, but also enhances our understanding of divergent genome evolution and environmental adaptation across <i>P. ananatis</i> species.IMPORTANCE<i>Pantoea ananatis</i> is a bacterium commonly found in various agronomic crops. Maize white spot (MWS) has been one of the most destructive diseases affecting maize, leading to significant economic losses. This study clarified that <i>P. ananatis</i> strains colonized maize leaves but were not the causal agents of MWS in Yunnan Province, China. Moreover, most of these <i>P. ananatis</i> strains exhibited plant growth-promoting (PGP) activities, induced hypersensitive response (HR) activity on tobacco, and caused rot symptoms in onion. Notably, the analysis of divergence throughout the evolutionary process revealed significant genomic evolution and environmental adaptation in these <i>P. ananatis</i> strains. This highlights the genetic exchange that has shaped the genome of <i>P. ananatis</i>. These findings improve our understanding of the functional diversity of <i>P. ananatis</i> strains across different hosts and their positions within the evolutionary lineages of <i>P. ananatis</i> species.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0032925"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092669","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 tale of two vineyards: parsing site-specific differences in bacterial and fungal communities of wine grapes from proximal vineyards and their changes during processing in a single winery.","authors":"Reid G Griggs, Lena Flörl, Michael Swadener, Rodrigo Hernández-Velázquez, David A Mills, Nicholas A Bokulich","doi":"10.1128/aem.00526-25","DOIUrl":"10.1128/aem.00526-25","url":null,"abstract":"<p><p>Wine is a microbial product, naturally transformed through fermentation by a consortium of fungi and bacteria that originate from the vineyard and the cellar, in addition to any microorganisms that are intentionally inoculated. Previous work has shown that grapevine-associated microbiota follow distinct biogeographic patterns, associated with climate and soil properties, and that even neighboring vineyards can harbor distinct microbial communities, but it is unclear whether these differences persist when controlling for variations in farming practices, cultivar, and climate and whether site-specific microbial profiles change during processing in the winery. Here, we investigated the bacterial and fungal microbiota of fruits pre- and post-harvest from two neighboring vineyards planted to a single variety, geographically close to one another, and farmed the same way and then processed in a single winery. These communities underwent subtle changes during processing, yet retained distinct site-specific signatures, indicating the partial contribution of the winery environment to the microbiota of grape must and juice pre-fermentation. We also profiled the microbiota of key microbial sources in the winery environment, including fruit flies (<i>Drosophila</i> spp.) and processing equipment, demonstrating that the microbiota at these sites reflect contact with the plant material, harbor communities distinct from the fruit, and appear to partially contribute to the fermentation assemblage, especially via the contribution of fermentative yeasts that are rare or missing in the vineyard environment. These results bolster previous reports of site-specific microbial signatures in winegrowing and make a first estimation of the changes to the grape-associated microbiome during early processing.IMPORTANCENative wine fermentations are driven by microbes carried over from the vineyard or introduced in the winery. In this study, we tracked the microbiome dynamics of wine fermentations from two Chardonnay vineyards planted in close proximity in order to examine the relative contribution of vineyard- and winery-resident microbiota on microbial succession during wine fermentation. By tracking microbial changes from the vineyard to winery, we show that the winery environment, including processing equipment and fruit flies, contributes to the fermentation microbiome but does not override vineyard-specific microbial differences. These findings support the concept of microbial terroir and highlight the importance of vineyard microbiomes in shaping wine fermentation. This work advances our understanding of how microbial diversity influences wine production and provides insights into the ecological dynamics of fermentation. By identifying key microbial sources and their contributions, this study lays the groundwork for future research on microbiomes in viticulture and winemaking.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0052625"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960155","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}