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• Irrigation and long-term cultivation (26 years) did not affect SOC stock. • SOC dynamics in the subsoil is particularly vulnerable to irrigated agriculture. • Land use favors large amounts of aliphatics products along the soil profile. • Management changes microbiological parameters, especially bacterial communities. • Changes in the bacterial community suggests alterations in groups of subsoil C. Changes in the global water cycle affect irrigation requirements and soil processes as well as the structure of soil microbial communities and function and the carbon (C) balance. The microbial structure and C sequestration under land use changing scenarios are rarely studied in the semi-arid region of Brazil. Here, we assessed the effects of land-use changes (irrigation and cultivation) on C storage in the soil and the structure of total bacteria (16S rRNA gene profile) and fungus (18S rRNA gene profile) at soil depth. We evaluated two soil profiles in the semi-arid region in northeastern Brazil. Profile P1 in an area with long-term irrigation (1,500 mm of water per year) and cultivation (small-scale farming systems, mainly with subsistence crops, which is a frequent land use system in the region of irrigated soil) for about 26 years. Profile P2 under natural conditions with 400 mm of water per year of rainfall (rain-fed hyperxerophilic Caatinga). Land-use changes showed a small influence on C storage; however, the changes strongly affected the soil organic matter (SOM) quality as well as the bacterial and fungal community structure, indicated by higher contents of labile-C and microbial biomass along with lower C-CO 2 emission. The relatively large amounts of aliphatic groups in the soil surface and subsurface in the cropped system (P1) suggested enrichment of methylene structures and probable increase of microbial-derived compounds. Methoxylic and aromatic groups tend to increase at depth (Bt horizon) indicating that the subsoil C responds to soil management changes. The structures of the bacterial community are distinct at depth in P1 and more similar at depth in P2. On the other hand, the structures of the fungal communities are more similar at depth in P1 than in P2. Furthermore, the irrigated agriculture also presented a carbon management index greater than 140% in most horizons, indicating that the soil management system did not cause soil degradation. [ABSTRACT FROM AUTHOR]