Soil microbiomes have a central role in biogeochemical cycles, so it is important to understand the impact of global change on community function. Zhang et al. found that the functional diversity of core and accessory genes (genes required for living in a specific environment) are governed by distinct processes. The authors performed a longitudinal 5 year nitrogen and water addition experiment in the Eurasian steppe and surveyed the microbial gene diversity using metagenomics. Rises in nitrogen led to an increase in the abundance of ammonia-oxidizing bacteria, which in turn increased the relative abundance of core genes. Water addition stimulated microbial respiration such that carbon sources became limited, leading to a decrease in the diversity of accessory community genes. These findings highlight that the functional diversity of soil microbiomes is affected differently by distinct environmental change processes.