Microbial responses to changing plant community protect peatland carbon stores during Holocene drying.

Peatlands are among the most effective long-term carbon sinks. However, climate change is triggering major ecological shifts with widespread woody plant expansion in peatlands. How microbial processes regulate carbon storage under these vegetation transitions remains uncertain. Here, we integrate multi-proxy records from a subtropical fen peatland in China with a global synthesis of paleoecological data from 155 peatlands to reveal a critical carbon regulation mechanism: woody expansion within peatlands can enhance long-term carbon storage by reshaping microbial metabolism and peat organic composition. We find mid-Holocene warming- and drying-driven woody encroachment displaced herbaceous plants, suppressing bacterial heterotrophy and shifting metabolism toward autotrophy. This transition coincides with peat organic matter transformations, marked by decreased carbohydrates and increased aromatics, promoting recalcitrant carbon pools. Together, this cascade of processes amplifies carbon accumulation, with peak rates occurring alongside diminished microbial heterotrophy during woody expansions. Our findings highlight key microbial responses to vegetation shifts that protect peatland carbon storage under climatic stress.