Functional Specialisation and Diversity Shape the Rhizosphere Microbiota of Cacao and Coffee in the Amazonas Region, Peru

Cacao and coffee are the most economically important crops in the Amazonas region, Peru. Thus, characterising microbial species composition and functional profiles in these rhizospheric soils will enable a comprehensive representation of the metabolic potential of host plants in soils. Accordingly, rhizospheric soil from cacao and coffee farms was collected for both physicochemical and molecular analyses. The diversity and functional roles of the archaeal, bacterial and fungal communities were investigated through a comprehensive DNA metabarcoding analysis. It was found that each crop hosts distinct microbiomes, with a minimal shared core microbiota, underscoring the plant host's role as a primary filter. However, the assembly rules and functional responses diverged significantly across domains. Bacterial communities were compositionally and functionally homogeneous within each crop, shaped by deterministic factors. In contrast, archaeal and fungal compositions were heterogeneous but maintained stable functional profiles within their crop environment. Functionally, prokaryotes (bacteria and archaea) acted as “specialists,” exhibiting significant metabolic divergence between crops. Conversely, fungi served as “generalists,” showing no significant difference in guilds and providing a stable, redundant backbone for decomposition. This tiered microbial response highlights a fundamental ecological dichotomy and underscores the necessity of a multi‐kingdom perspective to fully understand and manage the rhizosphere ecosystem.