Increased nutrient diversity can induce loss of microbial diversity through enhanced resource uptake.

The origin of biodiversity is a central question in ecology, particularly how numerous microbial species co-exist within a single community. A prevailing hypothesis holds that microbial species co-exist by specializing on different resources, thereby reducing competition. Accordingly, increasing resource diversity is expected to promote species co-existence and boost biodiversity. By integrating high-throughput experiments, ecological analysis of global microbiome data, metabolic profiling and theoretical modelling, we find that the relationship between resource diversity and microbial biodiversity is not consistently positive and can even decline with increasing resource diversity. This unexpected result emerges from a widespread physiological response across diverse microbial taxa, in which more complex environments trigger higher overall resource uptake. This intensifies competition and can lead to biodiversity loss. Updating a central ecological model to include this physiological trait accurately reproduces the observed decline. Our findings suggest that physiological changes at the individual level can substantially alter predicted diversity patterns and scale up to influence community structure.