Comparative study of the rhizosphere microbiome of Coffea arabica grown in different countries reveals a small set of prevalent and keystone taxa

Coffee (Coffea arabica) is a globally important crop and its cultivation demands the use of agrochemicals and pesticides. Recently, plant-associated microorganisms have emerged as an unexploited resource to enhance crop performance and sustainability. In particular, the rhizosphere microbiome has been identified as a hotspot for plant health, by providing tolerance to biotic and abiotic stresses as well as regulating phenological traits. However, its composition varies widely across crops and environmental conditions. Hence, the knowledge of the “common core” taxa, which are a subset of the microbiome that is persistently associated, across different environmental gradients and conditions, to a host species, represent valuable targets for the development of microbiome-based management approaches. This study aimed to characterize and determine the rhizosphere-inhabiting microbial groups (common core and most prevalent taxa), associated with the Coffea arabica plants in different geographical locations. To assess the structure of the coffee rhizosphere microbiome, we performed the 16 S rRNA amplicon analysis of samples collected across six locations spanning four countries and grown under different climate conditions, soil type, agroecosystem management, plant vegetative stage and age. Our findings allowed us to delineate and identify a robust set of six bacterial taxa, namely Sphingobium, Rhizobium group, Acidibacter, Sphingomonas, Burkholderia group and Amycolatopsis, which are likely to play an important role for the growth and health of coffee plants. Using network analysis, we observed that some of the six “common core” taxa were highly interconnected with the resident community, being also keystone taxa of the coffee rhizosphere microbiome. Furthermore, we performed a high-throughput targeted isolation resulting into 162 rhizosphere bacterial strains, some of them related to the most prevalent taxa. These isolates represent a working bacterial culture collection to be used in the future for the development of microbiome-based solutions for a more sustainable coffee farming.