Disentangling environmental, irrigation, and clone effects on the cacao soil microbiome in a multi-location trial

Introduction Plant-associated microbiomes can shape host phenotypes, yet plant breeding programs rarely incorporate microbiome data into their selection criteria. For example, multi-location trials are central for studying genotype-by-environment interactions, yet the microbiome is a poorly characterized component of environmental variation. Methods This study sought to better understand effects of region, irrigation and nutrient management, and scion on variation in the cacao-associated soil microbiome within a multi-location breeding trial. Samples were sent for amplicon sequencing from four regions of Brazil and represented two cocoa scions and an irrigation trial comparing drip-irrigated and rainfed plots. Results Samples clustered by region for both prokaryotes and fungi, though the effects were not significant due to low statistical power and differences in multivariate dispersion. A conserved core microbiome was identified that included a complete prokaryotic nitrogen-cycling functional core as well as two omnipresent fungal ASVs belonging to the genus Fusarium . Irrigation and nutrient management explained 13% of fungal beta diversity and affected the relative abundance of 156 irrigation-responsive taxa across taxonomic levels. Depletion of irrigation-sensitive prokaryotes was linked to lower alpha diversity in drip-irrigated/fertigated plots relative to rainfed plots receiving surface-applied fertilizer, while fungi were more resilient to the effects of irrigation. Scion genotype did not affect alpha or beta diversity of the soil microbiome. Discussion Together, these findings can be used to guide incorporation of microbial variation in plant breeding models and inform management strategies that support productive and sustainable agroecosystems.