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• The α-diversity of rare bacteria was greater in the depositional zones than in the eroding slopes. • The α-diversity of abundant bacteria between the eroding slopes and depositional zones showed no difference. • The community compositions of abundant and rare bacteria differed between the eroding slopes and depositional zones. • Abundant and rare species jointly maintained the stability of co-occurrence network in eroded ecosystem. • The α-diversity of rare bacteria showed closer linkage with SCCF than abundant bacteria. Elucidating the interaction between microorganisms and soil carbon cycling functionality (SCCF) in the eroded ecosystems, can improve our understanding of the mechanisms by which soil erosion and deposition affect soil organic carbon pool. Abundant and rare sub-communities are the integral components in driving SCCF. However, changes in abundant and rare sub-communities, as well as their contributions to SCCF, remain unclear in the eroded ecosystems. In this study, changes in abundant and rare sub-communities and their correlations with SCCF were comparatively explored with respect to soil erosion and deposition in the Loess Plateau. The α-diversity of rare sub-communities in the depositional zones was 4% higher than that in the eroding slopes, but there was no significant difference in α-diversity of abundant sub-communities between the eroding slopes and depositional zones. The compositions of abundant and rare sub-communities differed between the eroding slopes and depositional zones. Regarding the co-occurrence network of the eroded ecosystems, abundant sub-communities compared with rare sub-communities presented a higher degree and betweenness centrality; however, rare sub-communities possessed more frequent interactions with other species than abundant sub-communities, especially positive interactions. The α-diversity of abundant and rare sub-communities in ecological clusters showed positive links with SCCF. The link between α-diversity of abundant sub-communities and SCCF was weaker than that with rare sub-communities, which was related to the significant disparity in the abundance of functional genes involved in SCCF and the extent of functional redundancy between abundant and rare sub-communities in the eroded ecosystems. The functional difference of abundant and rare sub-communities in improving SCCF under soil erosion and deposition, is important for accurately assessing the effects of microbial communities on soil organic carbon pool in regions predominated with fragmented eroded landscapes. [ABSTRACT FROM AUTHOR]