FEMS microbiology reviews最新文献

Seven Critical Challenges in Synthetic One-Carbon Assimilation and Their Potential Solutions.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-04-02 DOI: 10.1093/femsre/fuaf011

Òscar Puiggené, Giusi Favoino, Filippo Federici, Michele Partipilo, Enrico Orsi, Maria V G Alván-Vargas, Javier M Hernández-Sancho, Nienke K Dekker, Emil C Ørsted, Eray U Bozkurt, Sara Grassi, Julia Martí-Pagés, Daniel C Volke, Pablo I Nikel

{"title":"Seven Critical Challenges in Synthetic One-Carbon Assimilation and Their Potential Solutions.","authors":"Òscar Puiggené, Giusi Favoino, Filippo Federici, Michele Partipilo, Enrico Orsi, Maria V G Alván-Vargas, Javier M Hernández-Sancho, Nienke K Dekker, Emil C Ørsted, Eray U Bozkurt, Sara Grassi, Julia Martí-Pagés, Daniel C Volke, Pablo I Nikel","doi":"10.1093/femsre/fuaf011","DOIUrl":"https://doi.org/10.1093/femsre/fuaf011","url":null,"abstract":"Synthetic C1 assimilation holds the promise of facilitating carbon capture while mitigating greenhouse gas emissions, yet practical implementation in microbial hosts remains relatively limited. Despite substantial progress in pathway design and prototyping, most efforts stay at the proof-of-concept stage, with frequent failures observed even under in vitro conditions. This review identifies seven major barriers constraining the deployment of synthetic C1 metabolism in microorganisms and proposes targeted strategies for overcoming these issues. A primary limitation is the low catalytic activity of carbon-fixing enzymes, particularly carboxylases, which restricts the overall pathway performance. In parallel, challenges in expressing multiple heterologous genes-especially those encoding metal-dependent or oxygen-sensitive enzymes-further hinder pathway functionality. At the systems level, synthetic C1 pathways often exhibit poor flux distribution, limited integration with the host metabolism, accumulation of toxic intermediates, and disruptions in redox and energy balance. These factors collectively reduce biomass formation and compromise product yields in biotechnological setups. Overcoming these interconnected challenges is essential for moving synthetic C1 assimilation beyond conceptual stages and enabling its application in scalable, efficient bioprocesses towards a circular bioeconomy.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771732","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}

引用次数: 0

Ambrosia gall midges (Diptera: Cecidomyiidae) and their microbial symbionts as a neglected model of fungus-farming evolution.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-04-02 DOI: 10.1093/femsre/fuaf010

Petr Pyszko, Hana Šigutová, Jan Ševčík, Michaela Drgová, Denisa Hařovská, Pavel Drozd

{"title":"Ambrosia gall midges (Diptera: Cecidomyiidae) and their microbial symbionts as a neglected model of fungus-farming evolution.","authors":"Petr Pyszko, Hana Šigutová, Jan Ševčík, Michaela Drgová, Denisa Hařovská, Pavel Drozd","doi":"10.1093/femsre/fuaf010","DOIUrl":"https://doi.org/10.1093/femsre/fuaf010","url":null,"abstract":"Ambrosia gall midges (AGM) represent an intriguing group within the Cecidomyiidae, one of the most diversified dipteran families. AGM form galls on plants, where they cultivate and consume fungal symbionts (phytomycetophagy). This mutualistic relationship may play a critical role in larval nutrition, gall morphogenesis, and protection against natural enemies. Although most other fungus-farming taxa have been intensively studied, AGM have largely been neglected. This review synthesises current knowledge on the diversity, biology, and ecological interactions of AGM, highlighting the intricate relationships with their fungal symbionts. The implications for adaptive radiation and speciation are critically considered, including how fungal associations may have facilitated ecological flexibility and diversification. We also tackle the processes of coevolution, not only between AGM and their fungal symbionts but also involving plants and parasitoids. We identify the most pressing issues and discrepancies in the current understanding the AGM-fungi interactions. Key areas of future research should include elucidating fungal acquisition and transmission mechanisms, determining the specificity and diversity of AGM-associated fungal communities, understanding the evolutionary pathways leading to phytomycetophagy, and addressing taxonomic challenges within the AGM group, where species identification has been complicated by reliance on gall morphology and host specificity.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771668","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}

引用次数: 0

Plant Exudates Driven Microbiome Recruitment and Assembly Facilitates Plant Health Management.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-03-29 DOI: 10.1093/femsre/fuaf008

Chang-Xin Yang, Shi-Jie Chen, Xiao-Yu Hong, Lv-Zhuang Wang, Hai-Ming Wu, Yang-Yang Tang, Yang-Yang Gao, Ge-Fei Hao

{"title":"Plant Exudates Driven Microbiome Recruitment and Assembly Facilitates Plant Health Management.","authors":"Chang-Xin Yang, Shi-Jie Chen, Xiao-Yu Hong, Lv-Zhuang Wang, Hai-Ming Wu, Yang-Yang Tang, Yang-Yang Gao, Ge-Fei Hao","doi":"10.1093/femsre/fuaf008","DOIUrl":"https://doi.org/10.1093/femsre/fuaf008","url":null,"abstract":"Plant-microbiome symbiotic interactions play a crucial role in regulating plant health and productivity. To establish symbiotic relationships, the plant secretes a variety of substances to facilitate microbial community recruitment and assembly. In recent years, important progress has been made in studying how plant exudates attract beneficial microorganisms and regulate plant health. However, the mechanisms of plant exudates-mediated microbial community recruitment and assembly and their effects on plant health are no comprehensive review. Here, we summaries the interaction mechanisms among plant exudates, microbial community recruitment and assembly, and plant health. First, we systematically evaluate the type and distribution of plant exudates, as well as their role in microbiome recruitment and assembly. Second, we summarize the mechanisms of plant exudates in terms of microbiome recruitment, diversity regulation and chemotaxis. Finally, we list some typical examples for elucidating the importance of plant exudates in promoting plant health and development. This review contributes to utilizing plant exudate or beneficial microbiome resources to manage plant health and productivity.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751818","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}

引用次数: 0

Electrical signaling in fungi: past and present challenges.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-03-21 DOI: 10.1093/femsre/fuaf009

Matteo Buffi, Julia M Kelliher, Aaron J Robinson, Diego Gonzalez, Guillaume Cailleau, Justine A Macalindong, Eleonora Frau, Silvia Schintke, Patrick S G Chain, Claire E Stanley, Markus Künzler, Saskia Bindschedler, Pilar Junier

{"title":"Electrical signaling in fungi: past and present challenges.","authors":"Matteo Buffi, Julia M Kelliher, Aaron J Robinson, Diego Gonzalez, Guillaume Cailleau, Justine A Macalindong, Eleonora Frau, Silvia Schintke, Patrick S G Chain, Claire E Stanley, Markus Künzler, Saskia Bindschedler, Pilar Junier","doi":"10.1093/femsre/fuaf009","DOIUrl":"https://doi.org/10.1093/femsre/fuaf009","url":null,"abstract":"Electrical signaling is a fundamental mechanism for integrating environmental stimuli and coordinating responses in living organisms. While extensively studied in animals and plants, the role of electrical signaling in fungi remains a largely under-explored field. Early studies suggested that filamentous fungi generate action potential-like signals and electrical currents at hyphal tips, yet their function in intracellular communication remained unclear. Renewed interest in fungal electrical activity has fueled developments such as the hypothesis that mycorrhizal networks facilitate electrical communication between plants and the emerging field of fungal-based electronic materials. Given their continuous plasma membrane, specialized septal pores, and insulating cell wall structures, filamentous fungi possess architectural features that could support electrical signaling over long distances. However, studying electrical phenomena in fungal networks presents unique challenges due to the microscopic dimensions of hyphae, the structural complexity of highly modular mycelial networks, and the limitations of traditional electrophysiological methods. This review synthesizes current evidence for electrical signaling in filamentous fungi, evaluates methodological approaches, and highlights experimental challenges. By addressing these challenges and identifying best practices, we aim to advance research in this field and provide a foundation for future studies exploring the role of electrical signaling in fungal biology.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673305","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}

引用次数: 0

Multidisciplinary methodologies used in the study of cable bacteria. 电缆细菌研究中使用的多学科方法。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae030

Michaela M H Wawryk, Philip Ley, Diana Vasquez-Cardenas, Rico F Tabor, Perran L M Cook

引用次数: 0

Bile acids as germinants for Clostridioides difficile spores, evidence of adaptation to the gut?

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf005

Gianni Vinay, Jurgen Seppen, Peter Setlow, Stanley Brul

{"title":"Bile acids as germinants for Clostridioides difficile spores, evidence of adaptation to the gut?","authors":"Gianni Vinay, Jurgen Seppen, Peter Setlow, Stanley Brul","doi":"10.1093/femsre/fuaf005","DOIUrl":"10.1093/femsre/fuaf005","url":null,"abstract":"Bacterial spores formed upon metabolic stress have minimal metabolic activity and can remain dormant for years. Nevertheless, they can sense the environment and germinate quickly upon exposure to various germinants. Germinated spores can then outgrow into vegetative cells. Germination of spores of some anaerobes, especially Clostridioides difficile, is triggered by cholic acid and taurocholic acid. Elevated levels of these bile acids are thought to correlate with a perturbed gut microbiome, which cannot efficiently convert primary bile acids into secondary bile acids. That bile acids are germination-triggers suggests these bacteria have a life cycle taking place partially in the mammalian digestive tract where bile acids are plentiful; notably bile acids can be made by all vertebrates. Thus, spores survive in the environment until taken up by a host where they encounter an environment suitable for germination and then proliferate in the largely anaerobic large intestine; some ultimately sporulate there, regenerating environmentally resistant spores in the C. difficile life cycle. This review summarizes current literature on the effects of bile acids and their metabolites on spore germination in the gut and evidence that adaptation to bile acids as germinants is a consequence of a life cycle both inside and outside the digestive tract.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382098","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}

引用次数: 0

Correction to: Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf002

引用次数: 0

Evolving spectrum of Pneumocystis host specificity, genetic diversity, and evolution.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf006

Liang Ma, Christiane Weissenbacher-Lang, Alice Latinne, Spenser Babb-Biernacki, Barbara Blasi, Ousmane H Cissé, Joseph A Kovacs

{"title":"Evolving spectrum of Pneumocystis host specificity, genetic diversity, and evolution.","authors":"Liang Ma, Christiane Weissenbacher-Lang, Alice Latinne, Spenser Babb-Biernacki, Barbara Blasi, Ousmane H Cissé, Joseph A Kovacs","doi":"10.1093/femsre/fuaf006","DOIUrl":"10.1093/femsre/fuaf006","url":null,"abstract":"Following over a century's worth of research, our understanding of Pneumocystis has significantly expanded in various facets, spanning from its fundamental biology to its impacts on animal and human health. Its significance in public health has been underscored by its inclusion in the 2022 WHO fungal priority pathogens list. We present this review to summarize pivotal advancements in Pneumocystis epidemiology, host specificity, genetic diversity and evolution. Following a concise discussion of Pneumocystis species classification and divergence at the species and strain levels, we devoted the main focus to the following aspects: the epidemiological characteristics of Pneumocystis across nearly 260 mammal species, the increasing recognition of coinfection involving multiple Pneumocystis species in the same host species, the diminishing host specificity of Pneumocystis among closely related host species, and the intriguingly discordant evolution of certain Pneumocystis species with their host species. A comprehensive understanding of host specificity, genetic diversity, and evolution of Pneumocystis can provide important insights into pathogenic mechanisms and transmission modes. This, in turn, holds the potential to facilitate the development of innovative strategies for the prevention and control of Pneumocystis infection.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457360","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}

引用次数: 0

Insight into the environmental cues modulating the expression of bacterial toxin-antitoxin systems.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf007

Emeline Ostyn, Yoann Augagneur, Marie-Laure Pinel-Marie

{"title":"Insight into the environmental cues modulating the expression of bacterial toxin-antitoxin systems.","authors":"Emeline Ostyn, Yoann Augagneur, Marie-Laure Pinel-Marie","doi":"10.1093/femsre/fuaf007","DOIUrl":"10.1093/femsre/fuaf007","url":null,"abstract":"Bacteria require sophisticated sensing mechanisms to adjust their metabolism in response to stressful conditions and survive in hostile environments. Among them, toxin-antitoxin (TA) systems play a crucial role in bacterial adaptation to environmental challenges. TA systems are considered as stress-responsive elements, consisting of both toxin and antitoxin genes, typically organized in operons or encoded on complementary DNA strands. A decrease in the antitoxin-toxin ratio, often triggered by specific stress conditions, leads to toxin excess, disrupting essential cellular processes and inhibiting bacterial growth. These systems are categorized into eight types based on the nature of the antitoxin (RNA or protein) and the mode of action of toxin inhibition. While the well-established biological roles of TA systems include phage inhibition and the maintenance of genetic elements, the environmental cues regulating their expression remain insufficiently documented. In this review, we highlight the diversity and complexity of the environmental cues influencing TA systems expression. A comprehensive understanding of how these genetic modules are regulated could provide deeper insights into their functions and support the development of innovative antimicrobial strategies.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572557","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}

引用次数: 0

Microbial functional diversity and redundancy: moving forward. 微生物功能多样性和冗余：向前发展。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae031

Pierre Ramond, Pierre E Galand, Ramiro Logares

引用次数: 0