Cover trees associations shape bacterial diversity in coffee production systems

Traditional coffee agroforestry systems often involve shade trees, which play a crucial role in maintaining soil fertility and biodiversity. In contrast, monoculture systems negatively influence soil chemistry, microbial diversity, and overall soil health over time. Although the use of cover trees such as mango (Mangifera indica L.) and banana (Musa paradisiaca, var. Cavendish.) has been shown to have beneficial effects on the soil chemical properties, little is known about their influence on microbial communities associated with coffee production systems. The main objective of this study was to identify the bacteria inhabiting roots and soil of three coffee management systems via partial 16S rRNA sequencing, and to assess how coffee-shade tree associations, with different soil and plant parameters, influence the bacterial ecosystem. Results revealed that the association between coffee and shade trees increased alpha diversity, with the highest diversity found in the agroforestry systems. The dominant bacterial genera found in most of the samples, i.e., Kribbella, Nonomuraea, Nitrospira, Sphingobium and Neobacillus were strongly correlated with key soil chemical properties, including nitrogen content, organic matter, and available phosphorus. These correlations suggest that tree cover strategies exert beneficial effects on the bacterial microbiome. Moreover, the overall bacterial community structure was different when comparing coffee monoculture system and shade-associated systems. Our findings highlight that traditional coffee agroforestry practices involving shade trees foster more diverse bacterial communities, thereby contributing to healthier soils and more sustainable coffee production.