Annual review of microbiology最新文献

Despite the ubiquity of fungi in nature, only a small fraction are pathogenic to humans, and the majority of these fungi are opportunistic and affect immunocompromised individuals. In general, pathogen emergence is restricted by the ability of fungi to sense and withstand human host environmental cues and stresses. These stress responses in fungi involve immediate survival reactions as well as long-term adaptations. Additionally, some opportunistic pathogenic behavior suggests that virulence traits evolved for environmental survival, a concept known as exaptation. This review covers recent advances in examining fungal responses to host environments and focuses on stress pathways including HOG (high osmolarity glycerol) and CWI (cell wall integrity), thermotolerance mechanisms, CO₂ and oxygen sensing, nutrient and metal stresses, pH adaptation, and antimicrobial defenses. By focusing on both conserved and specialized responses, we highlight the critical role of stress adaptation in pathogenicity and potential avenues for further research and therapeutic intervention.

Members of the genus Akkermansia are the only cultured representatives of Verrucomicrobiota within the gastrointestinal tract. Akkermansia muciniphila, the best-characterized representative of the genus, is a mucin-degrading specialist that has emerged as a microbe of significant interest due to its influence on the health of its hosts. We describe emerging themes in the biology of Akkermansia species, including their diversity; cellular structures; physiology; interactions with other intestinal microbes; responses to diet; and effects on mammalian hosts, particularly their role in modulating immune responses. We also describe some of the tools available to explore the molecular biology of Akkermansia and discuss its increasingly complex interactions with other members of the microbiota and their implications for gastrointestinal health.

While reproduction in Leishmania is primarily clonal, genomic analyses of natural isolates provide evidence for hybridization within and between species. Genetic exchange has been formally demonstrated via the generation of hybrids in the laboratory. Experimentally, genetic exchange in Leishmania is nonobligatory, relatively rare, and naturally confined to life cycle stages present in the sandfly midgut. Per whole genome sequencing, allele inheritance is Mendelian and involves meiosis-like recombination of the nuclear genome. Deletion of meiosis- and plasmogamy-related genes reveals their requirement for successful hybridization. Mitochondrial DNA inheritance appears uniparental for maxicircle kinetoplast DNA (kDNA) but biparental for minicircle kDNA. To account for the current absence of identified haploid gametes and for the hybridization of aneuploid genomes, alternative modes of genetic exchange have been proposed. Future studies will need to confirm the existence of gametes, explore the conditions promoting their development, and exploit the generation of sexual recombinants to map genes controlling important traits.

The ability to synthesize lichen symbioses in vitro from pure cultures of transformable symbionts would be a game changer for experiments to identify the metabolic interplay that underpins the success of lichens. However, despite multiple reports of successful lichen resynthesis, no lichen lab model system exists today. We reviewed 150 years of in vitro lichen studies and found that the term resynthesis is applied to many types of fungal-photobiont cocultures that do not resemble lichens. Some of the most lichen-like results, for their part, were obtained from nonaxenic tissue culture. Only a few studies reported obtaining natural-looking lichens from axenic input cultures, but all appear to have been isolated successes obtained against the background of extensive contamination. We suggest revisiting resynthesis experiments in light of recent advances in our understanding of lichen microbial composition to test whether in vitro lichen morphogenesis requires microbial inputs beyond those of the canonical fungal and algal symbionts.

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.

Most of our current knowledge about yeast is based on the workhorse Saccharomyces cerevisiae. However, can this yeast represent the vast array of natural yeast life-forms? This review discusses significant recent advances in the study of non-Saccharomyces yeasts, also known as non-conventional yeasts (NCYs). We (a) review recent literature on bioprospecting methodologies and on population genomics that have expanded our understanding of NCY diversity, (b) highlight critical species with industrial applications, and (c) offer insights into how NCYs' genetic diversity translates into phenotypic plasticity and adaptation to extreme environments. We assess the limitations that are delaying the widespread use of NCYs in biotechnology, including the need for ambitious bioprospecting efforts and robust genetic tools in the scaling up of NCY-based processes for industry. NCYs could offer novel sustainable solutions in the food, beverage, pharmaceutical, and bioenergy sectors and could open a new frontier of commercial opportunities.

Streptomyces are among the most well-studied and important groups of bacteria, largely owing to their prolific production of biomedically important compounds like antibiotics and antifungals. Research over more than a half-century has elucidated the molecular and mechanistic details of Streptomyces multicellular development and the production of secondary metabolites. In contrast, the evolutionary and ecological mechanisms that underlie these phenotypes are comparatively understudied. Our aim in this review is to examine these aspects of Streptomyces biology, with a focus on the benefits associated with their complex life cycle, their multicellular architecture and development, and their production of antibiotics. In addition to highlighting existing studies, we point to clear knowledge gaps that can serve to motivate further research on these bacteria. A greater understanding of Streptomyces evolution and ecology is needed to improve our ability to exploit these organisms for biomedical and agricultural applications.

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.

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 Escherichia coli 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.