Soil aggregate fragmentation reduces microbial diversity but enhances oxidative metabolism that drives carbon loss

The escalating pace of anthropogenic activities is exacerbating soil organic carbon (SOC) loss and altering microbial community structure and ecological functions. However, how soil microbiomes reorganize under SOC dynamics and feed back to carbon depletion, especially at micro-to-millimeter scale remain unresolved. Here, croplands spanning a SOC gradient under varying cultivation duration were used to examine microbial diversity trajectories across bacteria, fungi and protists, together with carbon decomposition in bulk soils and individual aggregate fractions. Metagenomics, 13C‐tracing and literature synthesis were integrated to interlink microbial functions with alterations of carbon substrates and microenvironment. The results derived from these data imply that incorporating microscale physical structure and associated biological processes into SOC turnover models is paramount to develop practices improving biodiversity conservation and carbon persistence under intensifying anthropogenic activity and climate changes.