Coffee leaf rust (CLR), caused by Hemileia vastatrix, is one of the biggest economic challenges for coffee cultivation and leads to high economic losses each year. Co-occurring fungal microbial communities and their diversity in the presence of CLR are widely understudied but may harbor potential agents or indicators to reduce CLR infections. In this study, the fungal communities associated with CLR pustules in Coffea arabica L. plants across different regions of Costa Rica were analyzed. To this end, individual pustules were excised from infected leaf tissue and used as source material for DNA extraction and subsequent amplification and sequencing of the fungal taxonomic marker region ITS1. Effects of altitude and location on fungal community structure were also observed. High taxonomic variance within regions and a large proportion of unclassified taxa were detected as well as similar community structures across regions, possibly reflecting small effects of the analyzed regions on the identified taxa. However, altitude was a significant factor on the detected community structure, indicating either less favorable growth conditions for the pathogen in higher regions or favorable conditions for co-occurring taxa. This emphasizes that taxonomic identification of co-occurring fungi and their ecological relevance (e.g., potential mycoparasites) during CLR infection requires further research. This study provides a foundational framework for global coffee research by emphasizing the untapped potential of fungal community analyses to develop innovative, microbiome-informed strategies for managing coffee leaf rust and improving crop resilience.
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