Ecological context shapes microbial contributions to nutrition and development in Drosophila melanogaster

Microbial symbionts play a critical role in shaping insect development by supplying essential nutrients, influencing host phenotype, and mediating context-dependent mutualistic outcomes. In the fruit fly Drosophila melanogaster, larvae develop in ephemeral breeding substrates such as decaying fruits, where they acquire maternally transmitted bacterial and fungal symbionts. These substrates vary in their structural and chemical properties, potentially altering the composition and function of associated microbial communities. Here, we combine semi-natural microcosm experiments with compound-specific isotope analysis of essential amino acids to assess how variation in fruit substrate and symbiont origin affect larval nutrition, development, and adult phenotypes. We find that microbial community composition and environmental context jointly shape amino acid flow, with larvae deriving variable proportions of their nutrition from plant, bacterial, and fungal sources. These differences translate into distinct developmental outcomes, including shifts in larval development time – either delayed or accelerated, depending on the symbiont-substrate combination – and significant variation in adult body weight. Our findings introduce symbiont-environment interactions as a framework for understanding how ecological context shapes nutritional mutualisms, showing that environmental heterogeneity can alter microbial composition, nutrient sources, and larval performance. Together, these results reveal how ecological context modulates mutualistic dependence and underscores the context sensitivity of host- microbe associations.