Protist‐Bacteria Trophic Interactions Contribute to Higher Community Stability in Subsoils Than Topsoils

ABSTRACT Climate change is reshaping ecosystem components and functions across soil profiles. In this study, we examined the effects of altered precipitation and nighttime warming on soil microbial communities in both topsoils (0–20 cm in depth) and subsoils (20–50 cm in depth) in a long‐term field experiment in Inner Mongolia, China. Unexpectedly, moisture, belowground net primary production, and NO 3 − content in subsoils were all affected more by climate changes than topsoils. Moreover, using multiple resistance metrics, including α‐diversity, β‐diversity, microbial network complexity, and network robustness, we found that both bacterial and protistan communities in subsoils exhibited greater resistance to climate change than those in topsoils, while fungal communities showed no consistent pattern. Enhanced bacterial resistance in subsoils was associated with lower 16S rRNA gene operon ( rrn ) copy number, reduced GC content, lower genome and cell size, and other oligotrophic traits, collectively supporting adaptation to nutrient‐poor and stressful environments. Protistan resistance in subsoils tracked bacterial resistance and was reinforced by stronger trophic interactions and functional traits such as protective shells, greater motility, and reduced cell size, reflecting a bottom‐up control, as soil protists are primarily phagotrophs shaped by bacterial prey supply. Abundant bacteria enhanced resistance through oligotrophic adaptations and positive intra‐community interactions, while abundant protists reduced resistance, potentially due to the dominance of negative intra‐community interactions. Partial least squares analyses revealed that microbial community resistance modulated soil heterotrophic respiration (R h ), connecting community resistance to carbon cycling. Together, these findings demonstrate that the often‐overlooked resistance of subsoil microbiomes could buffer ecosystem functions under future climate conditions, suggesting that traits (e.g., rrn copy number) and trophic interactions can outweigh diversity for community stability.