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The cultivation of deep-rooted vegetation greatly alters the tradeoffs between water and carbon dynamics, yet their impact on microbial carbon sequestration (MCS) remains inadequately documented, particularly in thick vadose zones. This information is crucial for global climate mitigation and ecosystem service enhancement. As such, we collected triplicate samples for each land use type, exploring the abundance and structure of cbbL -harboring microbial communities within 10-m deep profiles under cultivated farmland and two apple orchards of varying ages (n = 72). Our findings indicated a shift from water-dominated (improved water retention at the expense of reduced carbon sequestration) to carbon-dominated benefits (enhanced carbon sequestration at the expense of decreased water retention) in deep soil layers (2–10 m) after the transformation from farmland to apple orchards. Despite the lack of significant differences among the three land use types, the gene abundances and microbial diversity indices reduced with soil depths because of variations in substrates, resources, and microenvironments. The cbbL -harboring microorganisms consisted of 5 phyla, 7 classes, 19 orders, 30 families, and 55 genera, with Proteobacteria as the predominant bacterial phylum. The relative contributions of different genera varied with soil depths, reflecting their distinct survival strategies. The microbial network was positively connected in various soil layers under farmland and apple orchards. Furthermore, the results of correlation, redundancy analysis, and structural equation modeling jointly indicated that plant roots and soil properties, including total nitrogen and organic carbon, governed MCS processes in deep unsaturated zones. Specifically, the low microbial variation between farmland and apple orchards can be attributed to the predominant effects of climatic and pedogenic factors on soil properties, the restricted contribution of plant roots to soil nutrient levels per unit depth, and the adverse effects of plant-induced ecohydrological consequences on root systems and microbial populations. This study offers new insights within thick vadose zones containing deep-rooted plants, thereby contributing to a better understanding of global terrestrial carbon cycle processes. [Display omitted] • Microbial carbon sequestration processes were explored in 10-m deep profiles. • The farmland-to-apple orchards conversion led to water-carbon tradeoffs. • Microbial carbon sequestration differed with depths rather than land use types. • Depth-dependent plant roots and soil nutrients affects carbon sequestration. [ABSTRACT FROM AUTHOR]