Annual review of microbiology最新文献

Circadian rhythms play a fundamental role in regulating biological processes across the tree of life. While these 24-h cycles are well-characterized in model organisms, their role in parasitic organisms has remained largely unexplored until recently. Here, we review emerging evidence that parasites possess intrinsic timekeeping abilities, focusing particularly on the malaria parasite Plasmodium. We examine two principal paradigms of biological timing: transcriptional-translational feedback loops and posttranscriptional feedback loops. Despite lacking canonical clock genes found in other eukaryotes, Plasmodium employs sophisticated regulatory machinery, including ApiAP2 transcription factors, chromatin regulators, and noncoding RNAs, that could form novel timing circuits. We discuss how these mechanisms might enable parasites to synchronize with host rhythms and optimize their development and transmission. Understanding these temporal regulatory networks could reveal new therapeutic strategies and expand our knowledge of biological timing mechanisms across evolution.

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.

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.

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.

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.

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.

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.