Understanding host vs. environmental effects on holobionts is challenging to do in the field due to the covariance of host diversity with environmental factors. In this project we carried out a mesocosm experiment to tease apart the effect of thermal stress, nutrient stress and host source population on the phenology and leaf endophytes of the tropical seagrass Halophila stipulacea. Seagrass functions in coastal marine ecology is related to the mitigation of global climate changes and to the support of cross kingdom biodiversity, and thus understanding their current and future dynamics, as we as the development of sensitive descriptors of their status is important.