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Annual review of microbiology最新文献

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Horizontal Gene Transfer and Recombination in Cyanobacteriota. 蓝藻的水平基因转移与重组。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-09-10 DOI: 10.1146/annurev-micro-041522-100420
Devaki Bhaya, Gabriel Birzu, Eduardo P C Rocha
{"title":"Horizontal Gene Transfer and Recombination in Cyanobacteriota.","authors":"Devaki Bhaya, Gabriel Birzu, Eduardo P C Rocha","doi":"10.1146/annurev-micro-041522-100420","DOIUrl":"10.1146/annurev-micro-041522-100420","url":null,"abstract":"<p><p>Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"685-711"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Mutagenesis: Insights from Single-Cell, Real-Time Approaches. 诱变：从单细胞实时方法的见解。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-09-16 DOI: 10.1146/annurev-micro-050224-093623
Marina Elez, Chiara Enrico Bena, Lydia Robert
{"title":"Mutagenesis: Insights from Single-Cell, Real-Time Approaches.","authors":"Marina Elez, Chiara Enrico Bena, Lydia Robert","doi":"10.1146/annurev-micro-050224-093623","DOIUrl":"10.1146/annurev-micro-050224-093623","url":null,"abstract":"<p><p>All genetic variation fueling evolution depends on mutations. Although mutations have been extensively studied for almost a century, until a decade ago the investigation of mutations was limited to population-level analysis. This constraint has hampered the exploration of cellular heterogeneity in mutation processes and its evolutionary implications. To overcome these limitations, quantitative visualization methods for studying mutations in the bacterium <i>Escherichia coli</i> at the single-cell level have been developed. These approaches offer the possibility of accessing a major source of mutations, DNA polymerase errors, and their fate, i.e., repair versus conversion to mutation. In addition, such methods allow for quantitative characterization of the effects of mutations on cell fitness. This article discusses insights into the mutation process derived from these new single-cell mutagenesis approaches.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"773-793"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Decoding Microbial Community Assembly: Insights on Vectors of Infectious Diseases. 解码微生物群落组装：对传染病载体的见解。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 DOI: 10.1146/annurev-micro-082024-094943
Dasiel Obregon, Apolline Maitre, Elianne Piloto-Sardiñas, Alejandra Wu-Chuang, Lianet Abuin-Denis, Ana Laura Cano-Argüelles, Justė Aželytė, Ivan Corona-Guerrero, Lourdes Mateos-Hernández, Myriam Kratou, Štefánia Skičková, Karolína Svobodová, Alejandro Cabezas-Cruz
{"title":"Decoding Microbial Community Assembly: Insights on Vectors of Infectious Diseases.","authors":"Dasiel Obregon, Apolline Maitre, Elianne Piloto-Sardiñas, Alejandra Wu-Chuang, Lianet Abuin-Denis, Ana Laura Cano-Argüelles, Justė Aželytė, Ivan Corona-Guerrero, Lourdes Mateos-Hernández, Myriam Kratou, Štefánia Skičková, Karolína Svobodová, Alejandro Cabezas-Cruz","doi":"10.1146/annurev-micro-082024-094943","DOIUrl":"10.1146/annurev-micro-082024-094943","url":null,"abstract":"<p><p>Vector-borne diseases (VBDs), which are caused by pathogens transmitted by vectors such as mosquitoes and ticks, account for more than 17% of infectious diseases and more than 700,000 deaths annually. The complexity of VBDs arises from ecological interactions among hosts, vectors, pathogens, and the environment, with vector microbiota playing a pivotal role in the modulation of vector competence. Advances in sequencing and in microbiome analysis have deepened our understanding of microbial community assembly within vectors and revealed opportunities for novel control strategies. Network analysis has become essential for uncovering microbial interactions and identifying keystone species that affect community stability and pathogen transmission. Despite progress, key challenges remain in deciphering the drivers of vector microbiota assembly. This review highlights factors shaping microbiota assembly, the potential of network analysis, and promising interventions such as antimicrobiota vaccines and paratransgenesis to reduce pathogen transmission. Future research should focus on standardizing methodologies and leveraging emerging technologies for effective and sustainable VBD control.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"79 1","pages":"547-572"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
The Structure and Mechanism of Energy Transfer in Phycobilisomes. 藻胆体能量传递的结构和机制。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-07-29 DOI: 10.1146/annurev-micro-051024-074722
Jindong Zhao, Yuxiang Weng, Zhenggao Zheng
{"title":"The Structure and Mechanism of Energy Transfer in Phycobilisomes.","authors":"Jindong Zhao, Yuxiang Weng, Zhenggao Zheng","doi":"10.1146/annurev-micro-051024-074722","DOIUrl":"10.1146/annurev-micro-051024-074722","url":null,"abstract":"<p><p>Phycobilisomes (PBSs) are the major light-harvesting antenna of photosynthesis in cyanobacteria and red algae. Different types of PBSs exhibit a basic structure: a central core that interacts with photosystem II (PSII) and peripheral rods that are attached to the core and that expand the light-absorption cross-section area. This review summarizes recent progress in the study of PBS structures, with an emphasis on protein-bilin chromophore interactions. We describe the mechanisms of excitation energy transfer (EET) in PBSs with near-unity efficiency, as recent studies using two-dimensional electron spectroscopy showed that both Förster EET and coherent EET are involved in this process. Recent studies that provided insights into the mechanism of the PBS-thylakoid membrane association, particularly of PBS-PSII interactions, are also described. In addition, we discuss progress and some unsettled issues from studies on state transitions, which regulate energy distribution between PSII and PSI, in PBS-containing organisms.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"263-285"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144741010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Kin Recognition Systems and Their Role in Multicellular Behaviors. 亲属识别系统及其在多细胞行为中的作用。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-08-20 DOI: 10.1146/annurev-micro-051724-092527
Karin Yaniv, Karine A Gibbs
{"title":"Kin Recognition Systems and Their Role in Multicellular Behaviors.","authors":"Karin Yaniv, Karine A Gibbs","doi":"10.1146/annurev-micro-051724-092527","DOIUrl":"10.1146/annurev-micro-051724-092527","url":null,"abstract":"<p><p>Interactions between individuals are at the foundation of every community. Furthermore, multicellular behaviors can emerge when individuals come together. Microbes-bacteria, fungi, archaea, and parasites-can engage in multicellular behaviors, which help with population dispersal, infections, and protection from environmental threats. A critical interaction in collectives is determining whether the interacting neighbor is a sibling (kin) or a nonsibling (nonkin). Multiple molecular ways exist to achieve kin recognition and discrimination, especially when fitness is essential. This review considers four bacterial and eukaryotic microorganisms that engage in collective migration and where recognition is known or implied as part of their emergent behavior. This comparative analysis considers shared themes about recognition behaviors among these social microbes, as well as open questions. As more is learned about why kin recognition occurs in different species, a greater understanding will emerge about its evolutionary history and the potential for exogenous control of microbial social groups.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"475-495"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Temperature as a Driver of Phage Ecology and Evolution. 温度是噬菌体生态学和进化的驱动因素。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 DOI: 10.1146/annurev-micro-042424-040029
Samuel T E Greenrod, Tobias E Hector, Michael Blazanin, Daniel Cazares, Kayla C King
{"title":"Temperature as a Driver of Phage Ecology and Evolution.","authors":"Samuel T E Greenrod, Tobias E Hector, Michael Blazanin, Daniel Cazares, Kayla C King","doi":"10.1146/annurev-micro-042424-040029","DOIUrl":"10.1146/annurev-micro-042424-040029","url":null,"abstract":"<p><p>Bacteriophages (phages) are virtually ubiquitous and play a fundamental role in the ecological and evolutionary dynamics of their bacterial hosts. While phages are found across many thermal environments, they can be highly sensitive to changes in temperature. Moreover, phages are expected to face increasingly frequent and intense thermal perturbations with global climate change. In this review, we combine theoretical and empirical evidence to assess the impact of the thermal environment on phage biology at the global scale. We identify key thermal environments that phages inhabit, and we discuss the role of temperature in determining phage life-history strategies, ecological interactions, and evolutionary dynamics. We then explore the potential effects of thermal variation on phage functions in natural microbial communities and the application of phages as biomedical therapeutics.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"79 1","pages":"497-522"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Prokaryotic Circadian Systems: Cyanobacteria and Beyond. 原核生物昼夜系统：蓝藻及其他。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-08-26 DOI: 10.1146/annurev-micro-041222-022934
Mingxu Fang, Carrie L Partch, Andy LiWang, Susan S Golden
{"title":"Prokaryotic Circadian Systems: Cyanobacteria and Beyond.","authors":"Mingxu Fang, Carrie L Partch, Andy LiWang, Susan S Golden","doi":"10.1146/annurev-micro-041222-022934","DOIUrl":"10.1146/annurev-micro-041222-022934","url":null,"abstract":"<p><p>Circadian clocks are biological timekeeping mechanisms that synchronize physiology with the 24-h day-night cycle and provide temporal order to cellular events that recur daily as circadian rhythms. The cyanobacterium <i>Synechococcus elongatus</i> displays robust circadian rhythms and for more than 30 years has served as a model organism for uncovering the principles of prokaryotic timekeeping. The fundamental driving force behind these rhythms is a three-protein oscillator composed of KaiA, KaiB, and KaiC. In this review, we summarize current knowledge of the molecular mechanism of the Kai oscillator and focus on the dynamic conformational changes of these proteins over the period of a day. We also discuss how timing information is relayed from the oscillator to regulate downstream gene expression, thereby influencing cellular physiology. Furthermore, we explore circadian or circadian-like timing systems identified in other prokaryotes. We hope this review can inspire the discovery of new clock mechanisms in the microbial world and beyond.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"523-545"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
The Corrinoid Model for Dissecting Microbial Community Interactions Across Scales. 跨尺度解剖微生物群落相互作用的Corrinoid模型。
IF 12.2 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-06-27 DOI: 10.1146/annurev-micro-051024-044734
Zoila I Alvarez-Aponte, Rebecca R Procknow, Michiko E Taga
{"title":"The Corrinoid Model for Dissecting Microbial Community Interactions Across Scales.","authors":"Zoila I Alvarez-Aponte, Rebecca R Procknow, Michiko E Taga","doi":"10.1146/annurev-micro-051024-044734","DOIUrl":"10.1146/annurev-micro-051024-044734","url":null,"abstract":"<p><p>Microbial communities in different environments have major impacts on global nutrient cycling and on the health of host organisms. However, the complexity of microbial communities complicates the investigation of how interactions among numerous microbial species, each with distinct features and metabolic capabilities, affect global processes. In this review, we describe the corrinoid model for investigating microbial community interactions across scales, from individual microbes to complex natural communities. Corrinoids are the vitamin B<sub>12</sub> (cobalamin) family of organometallic cofactors. While numerous metabolic processes across all domains of life require corrinoids, only a fraction of bacterial and archaeal species produce them. This structurally diverse set of shared nutrients influences community structure in different ways. Knowledge about corrinoid biology at each scale informs and reinforces a robust model that can be expanded to increase our understanding of microbial communities.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"149-169"},"PeriodicalIF":12.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12416548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144511381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Clock Regulation and Fungal Physiology: Molecular Mechanisms Underpinning the Timely Control of Just About Everything. 时钟调节和真菌生理学：支持及时控制一切的分子机制。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-07-10 DOI: 10.1146/annurev-micro-060424-051158
José I Costa, Felipe Muñoz-Guzmán, Luis F Larrondo
{"title":"Clock Regulation and Fungal Physiology: Molecular Mechanisms Underpinning the Timely Control of Just About Everything.","authors":"José I Costa, Felipe Muñoz-Guzmán, Luis F Larrondo","doi":"10.1146/annurev-micro-060424-051158","DOIUrl":"10.1146/annurev-micro-060424-051158","url":null,"abstract":"<p><p>Circadian clocks enable organisms to anticipate daily environmental changes. In fungi, <i>Neurospora crassa</i> has been the premier model for studying these rhythms, allowing the revelation of intricate phosphorylation dynamics, protein interactions, and the pivotal role of Casein Kinase 1 in clock regulation. FREQUENCY, an intrinsically disordered protein, plays a central role in the spatial and temporal control of <i>N. crassa</i> and coordinates interactions that define clock function at large. Recent findings highlight the extent of circadian regulation in <i>N. crassa</i> and span transcriptional and translational processes that dynamically reshape the daily proteome. Additionally, circadian control of metabolism and organismal interactions has emerged as a vibrant area of research, and multiple efforts have focused on uncovering circadian mechanisms in fungi other than <i>Neurospora</i>. And while the study of <i>Neurospora</i> will remain central to advancing the field, comparative studies across fungal systems offer unique perspectives on the evolution of clock mechanisms and further position fungi as a platform for unraveling the intricacies of complex eukaryotic systems.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"191-214"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Motility in Filamentous Cyanobacteria. 丝状蓝藻的运动。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-06-10 DOI: 10.1146/annurev-micro-051024-033328
Douglas D Risser
{"title":"Motility in Filamentous Cyanobacteria.","authors":"Douglas D Risser","doi":"10.1146/annurev-micro-051024-033328","DOIUrl":"10.1146/annurev-micro-051024-033328","url":null,"abstract":"<p><p>Filamentous cyanobacteria are multicellular organisms that perform oxygenic photosynthesis and frequently exhibit surface motility. This review discusses the underlying mechanism facilitating motility in these organisms, with a focus on recent molecular and genetic studies. While previous explanations for this motility have proposed exotic mechanisms, the current data indicate that all filamentous cyanobacteria produce a similar motility-associated extracellular polysaccharide (EPS) or slime essential for movement and employ a type IV pilus (T4P) motor to power motility. The (<i>a</i>) regulation of the motor to facilitate coordinated polarity and phototaxis and (<i>b</i>) possible bidirectional feedback between the T4P and motility-associated polysaccharide are discussed as well. Finally, the role of motility in promoting diverse biological phenomena, including dispersal, phototaxis, biofilm formation, granulation, and symbiosis, is explored.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"69-85"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144265100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
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