Seed Grant Programs

The Implications of Cultivation Systems and Climates on Pathogen Diversity and Coffee Resilience

Principal Investigator: 

Rodrigo P. P. Almeida, Professor, UC Berkeley
Department of Environmental Science, Policy, and Management, Rausser College of Natural Resources
Hildebrand-Laumeister Chair in Plant Pathology
Chair, Division of Organisms & Environment

Research Team:

Iryna Dronova, Associate Professor, UC Berkeley
Department of Environmental Science, Policy, and Management, Rausser College of Natural Resources
Department of Landscape Architecture and Environmental Planning, College of Environmental Design
Affiliate Professor of Geography, Department of Geography

Carlos Chacon Diaz, Associate Professor, University of Costa Rica
Department of Bacteriology
Faculty of Microbiology

Funding level: $100,000


Research Summary

Plant pathogens induce extensive agricultural losses, increasing pesticide usage while reducing sustainability and resilience. Monoculture systems are hypothesized to heighten the likelihood and severity of pathogen outbreaks, as selective pressures lead to increased pathogenicity and virulence over shorter timescales.[1] Additionally, pathogen populations and outbreaks are influenced by local climate, yet the impact of climate change on pathosystems remains poorly understood. Therefore, this project has two goals: to investigate the effects of (1) cropping system and (2) climate, on pathogen evolution and disease severity. 

In Costa Rica, coffee is grown in both monoculture and polyculture across a range of altitudes, spanning different climates. Coffee leaf scorch (Crespera), a disease caused by the pathogen Xylella fastidiosa, stunts plant growth and reduces yields for Costa Rican coffee farmers. 

In partnership with local collaborators, we will collect samples of X. fastidiosa from monoculture and polyculture coffee plantations across altitudes. Genomic sequencing and analyses will quantify pathogen diversity across environments, while remote sensing techniques will classify both agricultural and landscape diversity. We expect greater genetic diversity in polyculture systems with more diverse surrounding landscapes, which could further support the benefits of more traditional shade plantations for coffee cultivation in Costa Rica. Along the altitudinal gradient, we expect to identify genetic variants linked to climate, which would aid in modeling future disease scenarios under climate change. Our multidisciplinary research will reveal how plant diseases evolve under varying environmental and agricultural settings, and contribute to building climate-resilient coffee cultivation in Costa Rica.

[1] McDonald, B.A. & Stukenbrock, E,H. (2016). Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security. Phil. Trans. R. Soc. B, 371(1709).