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To improve soil health and to aid in climate change mitigation, the quantity of soil organic matter (SOM) should be maintained or increased over the long run. In doing so, not only the total quantity of SOC but also the stability of SOC must be considered. Stability of SOC increases as a function of resistance to microbial decomposition or microbial substrate use efficiency through chemical, biological, and physical mechanisms including humification, hydrophobic moieties, molecular diversity, and formation of macroaggregates. One of the mechanisms that enhance stability confers changes in the distribution of C functional groups of SOM. To better understand and quantify how these changes are influenced by agricultural management practices, we collected 670 pairwise data from the body of literature that has evaluated changes in the distribution of C functional groups of SOM measured by solid-state 13C NMR spectroscopy. The types of agricultural managements discussed herein include (1) fertilization, (2) tillage, (3) crop rotation, (4) grazing, and (5) liming practices. Our meta-analyses show that these practices modify the distribution of C functional groups of SOM. Fertilization practices were associated with increased O-alkyl groups. Tillage resulted in increases in the SOC consisted of aromatic and carbonyl groups. Crop rotations, especially legume-based rotations, were found to increase the proportion of aromatic groups. Although there are fewer publications on tillage and crop rotation than on fertilization practices, the distribution of C functional groups may be more influenced by crop rotation and tillage practices than fertilization management—and should be a focus of future research. Supplementary Information The online version contains supplementary material available at 10.1007/s00374-021-01580-2.

Land use and tillage practices may change soil structure and undermine sustainable agriculture; however, such changes are hardly identified in the short term. In this sense, agroforestry systems have been used to reduce soil degradation and promote sustainable production in coffee plantations. These areas are expected to have well-structured soils and hence improved root distribution. This study aimed to evaluate soil quality by the morphostructural and root distribution analyses comparing open-grown coffee and coffee in agroforestry systems with rubber trees for 19 years, in an Oxisol in northern Paraná State (Brazil). Treatments consisted of open-grown coffee (OG), coffee partially shaded by rubber trees (PSH), and coffee fully shaded by rubber trees (FSH). The mapping of morphostructural features and soil resistance to penetration in “cultural profile” walls identified changes in soil structure resulting from different tillage systems. Root distribution was better in coffee plants grown in PSH and FSH systems. At greater depths, cultural profiles of FSH and PSH showed a larger numbers of roots compared to OG. Among the three systems, PSH provided a better environment for root growth and distribution. This result could be attributed to the high biological activity and interaction between roots and aggregates in that profile. The FSH agroforestry system provided less compact morphological structures and more roots throughout the soil profile. The agroforestry systems presented fewer soil structural changes by tillage operations and lower values of soil penetration resistance. Coffee root distribution was an effective indicator of soil quality and consistent with the morphostructural characterization of cultural profile.