Fungi associated with coffee in Bolivia: biodiversity of Fusarium and Trichoderma

This thesis investigates fungal diversity associated with coffee in the Bolivian Yungas, focusing on Fusarium and Trichoderma spp., and assesses their potential for pathogenicity and biocontrol, respectively. It also investigates the transcriptomic responses of a native Trichoderma cf. brasiliensis against the coffee pathogens (mycohosts) Colletotrichum gloeosporioides, Fusarium xylarioides, and Phoma costaricensis, which are taxonomically distinct and cause different disease types in coffee. Multilocus DNA barcoding and phylogenetic analyses identified seven Fusarium species, dominated by Fusarium oxysporum and Neocosmospora solani (synonym: Fusarium solani), with intraspecific variation in their ability to cause disease in coffee seedlings. Fifty-one Trichoderma species consisting of four unambiguously identified species, 47 with ambiguous identification [22 T. cf. (confer) and 25 T. aff. (affinis)], and 41 isolates potentially representing new species were identified. The distribution varied by ecosystem and altitude, with rhizosphere
soils supporting the highest Trichoderma diversity, and ecosystem type (P < 0.001), soil texture (P ≤ 0.006), and organic carbon (P ≤ 0.034) content significantly contributing to diversity. Detached leaves assay of 100 isolates against F. oxysporum identified 70 potent antagonists, with 30 achieving 90-100% disease control.
Comparative transcriptomic analyses revealed that T. cf. brasiliensis employs both conserved and mycohost-specific transcriptional responses against the tested mycohosts. Conserved responses include increased expression of genes involved in specialised metabolite biosynthesis, membrane transport, and hydrolytic enzyme production. Mycohost-specific responses include upregulation of genes associated with transcriptional regulation, host sensing, signal transduction, and metabolic adaptation. These findings provide the first comprehensive understanding of Fusarium and Trichoderma diversity in Yungas, Bolivia, and establish a scientific foundation for investigating fungal diversity and developing locally adapted biocontrol agents. Transcriptomic analysis enhances understanding of transcriptional plasticity during mycoparasitism and provides a basis for future studies exploring the mechanisms of mycoparasitism in native Trichoderma spp. in Bolivia.