Rhizosphere and fruit microbiome variation across Coffea canephora farms representing conventional, transitional, and organic management

Abstract

Robusta coffee ( Coffea canephora Pierre ex A. Froehner) is a major global cash crop, and an increasing number of coffee farms are transitioning from conventional to organic management. To investigate how coffee-associated microbiomes vary across different management histories, bacterial communities from the rhizosphere and fruits of three farms representing conventional, transitional organic, and organic management were profiled using 16S rRNA gene amplicon sequencing, differential abundance analysis, and functional prediction. Differential abundance analysis of rhizosphere and fruit bacterial communities identified the largest number of differentially abundant taxa between the conventional and organic farms, fewer between the transitional organic and organic farms, and relatively few between the conventional and transitional organic farms. In the rhizosphere, these differences included taxa related to nitrogen cycling and contrasting soil resource conditions. Approximately 30% of bacterial taxa were shared between rhizosphere and fruit microbiomes, including lactic acid bacteria ( Lactobacillus plantarum , Leuconostoc mesenteroides ) and acetic acid bacteria ( Kozakia baliensis , Gluconobacter ) that are known to influence coffee fermentation. Shared genera accounted for more than 85% of the bacterial relative abundance detected in fruits, indicating a close correspondence between rhizosphere and fruit-associated bacterial communities. Although each management category was represented by only one farm, preventing the separation of management effects from farm-specific environmental and historical factors, these findings provide exploratory insights into microbiome variation among coffee farms with contrasting management histories and identify candidate microbial patterns for further validation in independently replicated studies.