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Contribution short abstract

This study uses LC-MS to examine how intensive versus organic, diverse agroforestry practices in Puerto Rico shape the secondary metabolites of Coffea arabica, and how these chemical shifts affect agroecosystem resilience and economic sovereignty.

Contribution long abstract

Plant secondary metabolites (PSMs) provide a unique and underutilized lens for understanding agroecological systems and their socioeconomic and environmental outcomes. Hegemonic evaluation of agricultural systems normatively prioritizes metrics such as yield above all else; however, PSMs are fundamental to crop resilience and overall ecosystem function. This is particularly important in coffee production, where more than 70% of the global supply comes from smallholder farmers. Cultivation strategies that affect the complex chemistry underpinning healthy agroecosystems must therefore be assessed to identify practices that support economic sovereignty. In Puerto Rico, where land and labor are limited, and smallholders face strong pressure to industrialize, this issue is especially relevant. Although coffee has traditionally been cultivated in diverse, shaded agroforestry systems, growers are increasingly encouraged to adopt sun-grown monocultures with intensive synthetic agrochemical use to boost short-term yields. Yet canopy cover and agrochemical inputs have been shown to significantly affect PSM expression, with species-specific effects that cascade across trophic levels, and carry important implications for ecosystem health and farm profitability. To investigate these dynamics, we collected leaf tissue samples from sun and shade plots on both conventional and organic coffee farms in Puerto Rico. Samples included undamaged leaves, leaves damaged by Coffee Leaf Miner (Leucoptera coffeella), and leaves subjected to artificial wounding. We analyzed the quantity and diversity of secondary metabolites using targeted and untargeted LC-MS. We also gathered semi-quantitative data on chewing herbivore damage, Coffee Leaf Miner incidence (mines), Coffee Rust disease (Hemileia vastatrix), and other fungal diseases to support our analysis.