Explore the vast range of titles available.

Light controls important physiological and morphological responses in fungi. Fungi can sense near-ultraviolet, blue, green, red and far-red light using up to 11 photoreceptors and signalling cascades to control a large proportion of the genome and thereby adapt to environmental conditions. The blue-light photoreceptor functions directly as a transcriptional regulator in the nucleus, whereas the red-light-sensing and far-red-light-sensing phytochrome induces a signalling pathway to transduce the signal from the cytoplasm to the nucleus. Green light can be sensed by retinal-binding proteins, known as opsins, but the signalling mechanisms are not well understood. In this Review, we discuss light signalling processes in fungi, their signalling cascades and recent insights into the integration of light signalling pathways with other regulatory circuits in fungal cells.

Key Points Fungi have crucial ecological roles — as microbial saprotrophs, pathogens and mutualists — in both terrestrial and aquatic ecosystems. Advances in DNA sequencing have facilitated the ecological exploration of the 'mycobiome' and begun to change our view of fungal taxonomic and functional diversity. Molecular-based work has shown that fungal communities are more diverse than previously known across a range of spatial scales, from the diversity of local communities to biogeographical differences across continents. In contrast with earlier ideas, mycobiome studies have suggested that dispersal has an important role in both local community assembly and in generating large-scale biogeographical diversity patterns. The identification of key functional traits is helping to make predictions about the newly discovered diversity of the mycobiome and decode its role in the health of plants, animals and ecosystems. Molecular-based studies of fungal biodiversity have revealed fundamental differences from the biodiversity of bacteria, plants and animals. In this Review, Peay and colleagues consider the roles of ecology and fungal biology in determining fungal biodiversity at different spatial scales. Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of ecosystem processes. Large-scale DNA-sequencing datasets are beginning to reveal the dimensions of fungal biodiversity, which seem to be fundamentally different to bacteria, plants and animals. In this Review, we describe the patterns of fungal biodiversity that have been revealed by molecular-based studies. Furthermore, we consider the evidence that supports the roles of different candidate drivers of fungal diversity at a range of spatial scales, as well as the role of dispersal limitation in maintaining regional endemism and influencing local community assembly. Finally, we discuss the ecological mechanisms that are likely to be responsible for the high heterogeneity that is observed in fungal communities at local scales.

The yeast Saccharomyces cerevisiae has been an essential component of human civilization because of its long global history of use in food and beverage fermentation. However, the diversity and evolutionary history of the domesticated populations of the yeast remain elusive. We show here that China/Far East Asia is likely the center of origin of the domesticated populations of the species. The domesticated populations form two major groups associated with solid- and liquid-state fermentation and appear to have originated from heterozygous ancestors, which were likely formed by outcrossing between diverse wild isolates primitively for adaptation to maltose-rich niches. We found consistent gene expansion and contraction in the whole domesticated population, as well as lineage-specific genome variations leading to adaptation to different environments. We show a nearly panoramic view of the diversity and life history of S. cerevisiae and provide new insights into the origin and evolution of the species. An understanding of the domestication of the yeast Saccharomyces cerevisiae has important implications for studying its evolution and diversity. Here, the authors show that Far East Asia is likely the center of origin of the domesticated populations of the yeast based on genomic and phenotypic characterization of a large collection of isolates.

During the diversification of Fungi and the rise of conifer-dominated and angiosperm-dominated forests, mutualistic symbioses developed between certain trees and ectomycorrhizal fungi that enabled these trees to colonize boreal and temperate regions. The evolutionary success of these symbioses is evident from phylogenomic analyses that suggest that ectomycorrhizal fungi have arisen in approximately 60 independent saprotrophic lineages, which has led to the wide range of ectomycorrhizal associations that exist today. In this Review, we discuss recent genomic studies that have revealed the adaptations that seem to be fundamental to the convergent evolution of ectomycorrhizal fungi, including the loss of some metabolic functions and the acquisition of effectors that facilitate mutualistic interactions with host plants. Finally, we consider how these insights can be integrated into a model of the development of ectomycorrhizal symbioses.

The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, we study its spread and evolution by analyzing a global sample of 172 mildew genomes. Our analyses show that B.g. tritici emerged in the Fertile Crescent during wheat domestication. After it spread throughout Eurasia, colonization brought it to America, where it hybridized with unknown grass mildew species. Recent trade brought USA strains to Japan, and European strains to China. In both places, they hybridized with local ancestral strains. Thus, although mildew spreads by wind regionally, our results indicate that humans drove its global spread throughout history and that mildew rapidly evolved through hybridization. The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, Sotiropoulos et al. analyze a global sample of 172 mildew genomes, providing evidence that humans drove global spread of the pathogen throughout history and that mildew rapidly evolved through hybridization with local fungal strains.

Fungal pathogens cause more than a billion human infections every year, resulting in more than 1.6 million deaths annually. Understanding the natural history and evolutionary ecology of fungi is helping us understand how disease-relevant traits have repeatedly evolved. Different types and mechanisms of genetic variation have contributed to the evolution of fungal pathogenicity and specific genetic differences distinguish pathogens from non-pathogens. Insights into the traits, genetic elements, and genetic and ecological mechanisms that contribute to the evolution of fungal pathogenicity are crucial for developing strategies to both predict emergence of fungal pathogens and develop drugs to combat them. Understanding the mechanisms and evolution of pathogenicity in fungi will bring us a step closer to reducing the annual toll of 1.6 million deaths from fungal disease.

Key Points Ustilago maydis is a member of the smut fungi (phylum Basidiomycota) that infect maize. This group of plant pathogens is characterized by their biotrophic lifestyle and narrow host range. The establishment of a biotrophic, compatible interaction between U. maydis and maize depends on the secretion of specialized fungal proteins termed effectors. A large proportion of these effectors are completely novel, as they do not contain any annotated domains, and most of them are species-specific or lineage-specific. Many of the novel effector genes are arranged in gene clusters, which arose through gene duplications and represent genomic islands with accelerated evolution. Many of these clusters are important for virulence. Effector genes that markedly contribute to virulence are conserved among the smut fungi. For a few effectors their mode of action has been elucidated. They counteract defence responses, re-route metabolic pathways and stimulate plant cell division. The expression of effector genes is regulated by a hierarchical network of transcription factors and is coupled to sexual development and spore formation. The plant signals that induce the expression of effector genes are largely unknown. Biotrophic fungal plant pathogens secrete protein effectors that support colonization of the host. Here, Kahmann and colleagues discuss new insights into the effector repertoire of smut fungi, the molecular mechanisms whereby effectors of Ustilago maydis change plant cell processes, how the respective genes are regulated and how effectors evolve. Biotrophic fungal plant pathogens establish an intimate relationship with their host to support the infection process. Central to this strategy is the secretion of a range of protein effectors that enable the pathogen to evade plant immune defences and modulate host metabolism to meet its needs. In this Review, using the smut fungus Ustilago maydis as an example, we discuss new insights into the effector repertoire of smut fungi that have been gained from comparative genomics and discuss the molecular mechanisms by which U. maydis effectors change processes in the plant host. Finally, we examine how the expression of effector genes and effector secretion are coordinated with fungal development in the host.

Endosymbioses have profoundly impacted the evolution of life and continue to shape the ecology of a wide range of species. They give rise to new combinations of biochemical capabilities that promote innovation and diversification 1 , 2 . Despite the many examples of known endosymbioses across the tree of life, their de novo emergence is rare and challenging to uncover in retrospect 3 – 5 . Here we implant bacteria into the filamentous fungus Rhizopus microsporus to follow the fate of artificially induced endosymbioses. Whereas Escherichia coli implanted into the cytosol induced septum formation, effectively halting endosymbiogenesis, Mycetohabitans rhizoxinica was transmitted vertically to the progeny at a low frequency. Continuous positive selection on endosymbiosis mitigated initial fitness constraints by several orders of magnitude upon adaptive evolution. Phenotypic changes were underscored by the accumulation of mutations in the host as the system stabilized. The bacterium produced rhizoxin congeners in its new host, demonstrating the transfer of a metabolic function through induced endosymbiosis. Single-cell implantation thus provides a powerful experimental approach to study critical events at the onset of endosymbiogenesis and opens opportunities for synthetic approaches towards designing endosymbioses with desired traits. A study presents an approach to establish and track a new endosymbiotic partnership by implanting bacteria in a non-host fungus and shows that stable inheritance of the implanted bacteria is possible with positive selection.

Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with reductions in plant cell wall-degrading enzymes, but whether this is true of lichen fungal symbionts (LFSs) is unknown. Here, we predict genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 46 genomes from the Lecanoromycetes , the largest extant clade of LFSs. All LFSs possess a robust CAZyme arsenal including enzymes acting on cellulose and hemicellulose, confirmed by experimental assays. However, the number of genes and predicted functions of CAZymes vary widely, with some fungal symbionts possessing arsenals on par with well-known saprotrophic fungi. These results suggest that stable fungal association with a phototroph does not in itself result in fungal CAZyme loss, and lends support to long-standing hypotheses that some lichens may augment fixed CO 2 with carbon from external sources. Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. Here, Resl et al. show that, contrary to other fungal symbioses, fungal association with a phototroph in lichens does not result in loss of fungal enzymes for plant cell-wall degradation.

Anthracnose caused by Colletotrichum is one of the most severe diseases that can afflict Camellia sinensis . However, research on the diversity and geographical distribution of Colletotrichum in China remain limited. In this study, 106 Colletotrichum isolates were collected from diseased leaves of Ca. sinensis cultivated in the 15 main tea production provinces in China. Multi-locus phylogenetic analysis coupled with morphological identification showed that the collected isolates belonged to 11 species, including 6 known species ( C. camelliae , C. cliviae , C. fioriniae , C. fructicola , C. karstii , and C. siamense ), 3 new record species ( C. aenigma , C. endophytica , and C. truncatum ), 1 novel species ( C. wuxiense ), and 1 indistinguishable strain, herein described as Colletotrichum sp. Of these species, C. camelliae and C. fructicola were the dominant species causing anthracnose in Ca. sinensis . In addition, our study provided further evidence that phylogenetic analysis using a combination of ApMat and GS sequences can be used to effectively resolve the taxonomic relationships within the C. gloeosporioides species complex. Finally, pathogenicity tests suggested that C. camelliae , C. aenigma , and C. endophytica are more invasive than other species after the inoculation of the leaves of Ca. sinensis .