Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

Temperature contributes to host specialization of coffee wilt disease (Fusarium xylarioides) on arabica and robusta coffee crops

Coffee wilt disease, caused by the fungus Fusarium xylarioides, is a vascular wilt disease that has affected coffee production in sub-Saharan Africa over the past century. Today, the disease has two host-specific populations specialising on arabica and robusta coffee crops, which grow at high and low altitude, respectively. Here we test whether adaptation to different temperatures contributes to specialisation of the fungi on each crop. Firstly, climate models show that the severity of the arabica and robusta populations of coffee wilt disease correlates with temperature. The robusta population shows higher peak severity than the arabica population overall, but the latter has greater cold tolerance. Secondly, growth assays of thermal performance of fungal strains in vitro show that, while robusta strains grow faster than arabicas at intermediate temperatures, the arabica strains have higher sporulation and spore germination rates at temperatures below 15ºC. The match between environmental patterns of severity in nature with thermal performance of fungal cultures in the laboratory supports a role for temperature adaptation in specialisation on arabica and robusta coffee. Extrapolating our temperature-models to future climate change predicts that disease severity could decline on average due to increased temperature but could increase in some coffee-growing regions.

Age-Related Rhizosphere Analysis of Coffea arabica Plants

The analysis of large-scale sequence data has revealed that plants over time recruit certain microbes that are efficient colonizers of the rhizosphere. This enrichment phenomenon is especially seen in annual crops, but we suggest that there could have been some type of enrichment in perennial crops such as coffee plants. To verify this hypothesis, we performed a metagenomic and chemical analysis in rhizosphere with three different plant ages (young, mature, and old) and cultivated on the same farm. We verified that from mature to old plants, there was a decrease in diversity, particularly Fusarium and Plenodomus, while there was an increase in Aspergillus, Cladosporium, Metarhizium, and Pseudomonas. We also detected that the abundance of anti-microbials and ACC-deaminase grows as plants age, although denitrification and carbon fixation had reduced abundances. In summary, we detected an enrichment in the microbial community, especially in the great increase in the participation of Pseudomonas, passing from 50% of the relative abundance as the plants get older. Such enrichment can occur through the dynamics of nutrients such as magnesium and boron.

Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures

The fungal genus Fusarium (Ascomycota) includes well-known plant pathogens that are implicated in diseases worldwide, and many of which have been genome sequenced. The genus also encompasses other diverse lifestyles, including species found ubiquitously as asymptomatic-plant inhabitants (endophytes). Here, we produced structurally annotated genome assemblies for five endophytic Fusarium strains, including the first whole-genome data for Fusarium chuoi. Phylogenomic reconstruction of Fusarium and closely related genera revealed multiple and frequent lifestyle transitions, the major exception being a monophyletic clade of mutualist insect symbionts. Differential codon usage bias and increased codon optimisation separated Fusarium sensu stricto from allied genera. We performed computational prediction of candidate secreted effector proteins (CSEPs) and carbohydrate-active enzymes (CAZymes)—both likely to be involved in the host–fungal interaction—and sought evidence that their frequencies could predict lifestyle. However, phylogenetic distance described gene variance better than lifestyle did. There was no significant difference in CSEP, CAZyme, or gene repertoires between phytopathogenic and endophytic strains, although we did find some evidence that gene copy number variation may be contributing to pathogenicity. Large numbers of accessory CSEPs (i.e., present in more than one taxon but not all) and a comparatively low number of strain-specific CSEPs suggested there is a limited specialisation among plant associated Fusarium species. We also found half of the core genes to be under positive selection and identified specific CSEPs and CAZymes predicted to be positively selected on certain lineages. Our results depict fusarioid fungi as prolific generalists and highlight the difficulty in predicting pathogenic potential in the group.

Using structural variants to understand the ecological and evolutionary dynamics of fungal plant pathogens

Deletions, duplications, insertions, inversions and translocations are commonly referred to as structural variants (SVs). Fungal plant pathogens have compact genomes, facilitating the generation of accurate maps of SVs for these species in recent studies. Structural variants have been found to constitute a significant proportion of the standing genetic variation in fungal plant pathogen populations, potentially leading to the generation of accessory genes, regions or chromosomes enriched in pathogenicity factors. Structural variants are involved in the rapid adaptation and ecological traits of pathogens, including host specialization and mating. Long-read sequencing techniques coupled with theoretical and experimental approaches have considerable potential for elucidating the phenotypic effects of SVs and deciphering the evolutionary and genomic mechanisms underlying the formation of SVs in fungal plant pathogens.

Comprehensive Review of Fungi on Coffee

Coffee is grown in more than 80 countries as a cash crop and consumed worldwide as a beverage and food additive. It is susceptible to fungal infection during growth, processing and storage. Fungal infections, in particular, can seriously affect the quality of coffee and threaten human health. The data for this comprehensive review were collected from the United States Department of Agriculture, Agricultural Research Service (USDA ARS) website and published papers. This review lists the fungal species reported on coffee based on taxonomy, life mode, host, affected plant part and region. Five major fungal diseases and mycotoxin-producing species (post-harvest diseases of coffee) are also discussed. Furthermore, we address why coffee yield and quality are affected by fungi and propose methods to control fungal infections to increase coffee yield and improve quality. Endophytic fungi and their potential as biological control agents of coffee disease are also discussed.