Prokaryotic and eukaryotic microbial diversities are regulated by soil properties (e.g., soil organic matter, SOM), but their interactions and capacity to degrade carbon compounds remain unclear due to vegetation succession along elevation and climatic gradients. Fresh soils from different elevations and climates were collected from five sites covering different vegetation distributed vertically in the typical subtropical zone of Wuyishan. The community composition of microorganisms, carbon-degrading potentials and soil properties were analysed. The results showed that SOM, i.e., organic carbon, humus and fulvic acid, increased significantly along the vegetation types that existed along the elevation gradients. Prokaryotic and eukaryotic communities were distinguished by elevation and vegetation type, respectively. The pivotal role of prokaryotes in co-occurrence network was stronger than that of eukaryotes. The available potassium, organic carbon, humus, fulvic acids and humin carbons significantly affected the composition of prokaryotes and eukaryotes. In contrast, ammonium and available phosphorus alone affected the prokaryotic community composition, while pH and nitrate only affected the eukaryotic community composition. Correlations between carbon utilization potential and dominant eukaryotic taxa were more intense than those with prokaryotic taxa. Compared with prokaryotes, the carbon utilization potentials of eukaryotic taxa were more limited by changes in climate driven by increasing elevation. Our study illuminated that the differences in elevation gradient and vegetation type jointly drove the distinct diversity of the microbial communities and further affected their carbon-degrading potential. It would give insight into predict the effects of microorganisms on the carbon content transformation of different vegetation types under climate change.
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