Annual review of microbiology最新文献

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.

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.

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 B₁₂ (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.

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.

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 Synechococcus elongatus 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.

Gliotoxin (GT) is a sulfur-containing secondary metabolite that belongs to a class of naturally occurring 2,5-diketopiperazines produced by fungi. Although GT production has been observed only in a few species, GT is the most studied fungal secondary metabolite, and the GT biosynthetic gene cluster (BGC) is broadly present in filamentous fungi. GT has a multitarget mechanism of action: It is fungicidal and bacteriostatic, it induces apoptosis in mammalian cells, and it modulates phagocytosis and neutrophil attraction. GT is important for Aspergillus fumigatus virulence and pathogenesis in humans and in animals and for Trichoderma spp. symbiotic and antagonistic behavior. GT is also toxic for producer and nonproducer organisms. Consequently, very sophisticated mechanisms of GT self-protection have evolved in producers; some of these protective mechanisms are also found in nonproducer organisms. This review discusses the distribution of the GT BGC among filamentous fungi and discusses GT biosynthesis, mechanisms of action and self-defense, and ecological properties.

Circadian clocks enable organisms to anticipate daily environmental changes. In fungi, Neurospora crassa 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 N. crassa and coordinates interactions that define clock function at large. Recent findings highlight the extent of circadian regulation in N. crassa 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 Neurospora. And while the study of Neurospora 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.

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 (a) regulation of the motor to facilitate coordinated polarity and phototaxis and (b) 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.

Developmental processes are carefully regulated programs that are present in multiple kingdoms of life and that generally result in cell differentiation and specialization. This regulation can be mediated in part by checkpoints that monitor the progression of development to ensure that earlier steps occur successfully before later steps are initiated. Bacterial endospore formation (i.e., sporulation) is a well-studied developmental program that transforms a progenitor cell into a dormant cell type in response to environmental stress and that serves as a model for the discussion of checkpoint mechanisms used to monitor development. This review focuses on the checkpoints monitoring bacterial sporulation, with an emphasis on the model gram-positive bacterium Bacillus subtilis, to highlight general strategies that may be broadly conserved among disparate developmental programs.

Prevalent in marine and freshwater ecosystems, cyanophages compose a class of double-stranded DNA viruses that specifically infect cyanobacteria. During billions of years of coevolution, cyanophages and cyanobacteria have significantly contributed to the biogeochemical cycling and genetic diversity of aquatic ecosystems. As natural predators of cyanobacteria, cyanophages hold promise as eco-friendly agents against harmful cyanobacterial blooms. Recent technical advances in omics and cryo-electron microscopy have revealed the remarkable diversity of cyanophages in genome sequence and tail morphology. In this review, we summarize the genomic and metagenomic data, phylogenetic analyses, and diverse three-dimensional structures of cyanophages, in addition to their interplays with hosts. We also discuss the in vivo assembly processes of cyanophages, the exploration of uncultured cyanophages and host pairing, and the synthetic engineering and potential applications of cyanophages.