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Maintaining soil quality for agricultural production is a critical challenge, especially in the tropics. Due to the focus on environmental performance and the provision of soil ecosystem services, organic farming and agroforestry systems are proposed as alternative options to conventional monoculture farming. Soil processes underlying ecosystem services are strongly mediated by microbes; thus, increased understanding of the soil microbiome is crucial for the development of sustainable agricultural practices. Therefore, we measured and related soil quality indicators to bacterial and fungal community structures in five cocoa production systems, managed either organically or conventionally for 12 years, with varying crop diversity, from monoculture to agroforestry. In addition, a successional agroforestry system was included, which uses exclusively on-site pruning residues as soil inputs. Organic management increased soil organic carbon, nitrogen and labile carbon contents compared to conventional. Soil basal respiration and nitrogen mineralisation rates were highest in the successional agroforestry system. Across the field sites, fungal richness exceeded bacterial richness and fungal community composition was distinct between organic and conventional management, as well as between agroforestry and monoculture. Bacterial community composition differed mainly between organic and conventional management. Indicator species associated with organic management were taxonomically more diverse compared to taxa associated with conventionally managed systems. In conclusion, our results highlight the importance of organic management for maintaining soil quality in agroforestry systems for cocoa production., Competing Interests: Declaration of competing interest The authors declare that they have no competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Farmers expect yield reduction of cash crops like cocoa when growing in agroforestry systems compared to monocultures, due to competition for resources, e.g. nutrients and water. However, complementarities between species in the use of resources may improve resource use efficiency and result in higher system performance. Cocoa trees have a shallow rooting system while the rooting characteristics of the associated trees are mainly unknown. This work investigates fine root distribution and production in five cocoa production systems: two monocultures and two agroforestry systems under conventional and organic farming, and a successional agroforestry system. In the organic systems a perennial leguminous cover crop was planted and compost was added, while herbicides and chemical fertilizers were applied in the conventional ones. We measured cocoa fine root parameters in the top 10cm of soil and annual total fine root production at 0-25 and 25-50cm depth. We related the root data with both the aboveground performance (tree and herbaceous biomass), and the cocoa and system yields. Cocoa fine roots were homogenously distributed over the plot area. Around 80% of the total fine roots were located in the upper 25cm of soil. The total fine root production was 4-times higher in the agroforestry systems and the organic monoculture than in the conventional monoculture. The roots of the associated tree species were located in the same soil space as the cocoa roots and, in principle, competed for the same soil resources. The cocoa yield was lower in the agroforestry systems, but the additional crops generated a higher system yield and aboveground biomass than the conventional cocoa monocultures, implying effective resource exploitation. The leguminous cover crop in the organic monoculture competed with the cocoa trees for nutrients, which may explain the lower cocoa yield in this system in contrast with the conventional monoculture., (Copyright © 2018 Elsevier B.V. All rights reserved.)