Pecans (Carya illinoinensis), the most valuable native North American nut crop, are commonly propagated through grafting to maintain desired traits from parent trees. Successful pecan cultivation relies on scion varieties, rootstocks, and soil conditions. This study investigated the microbial abundance and diversity in soils and roots of a southern rootstock (87MX5-1.7) and a northern provenance ('Peruque') in a rootstock test orchard, both grafted with a 'Pawnee' scion cultivar in the USDA ARS Pecan Breeding program. The 16S ribosomal RNA of bacteria and ITS of fungi were sequenced and annotated into trophic and nutrient-related groups to characterize the rhizosphere microbiota. The results showed fungal dominance over bacteria, with Peruque roots having a higher relative abundance of saprotroph fungi compared to 87MX5-1.7, while 87MX5-1.7 exhibited higher levels of nitrogen fixation-related bacteria. Despite no significant difference in diversity index, the presence of symbiotrophs, especially the ectomycorrhizal fungi, exhibited distinct ectomycorrhizal fungi, which may lead to a divergent pathway of nutrient translocation between these two rootstocks. The study suggests rootstocks from different origins shape rhizosphere microbiota differently, affecting nutrient uptake and potentially nut yield. Exploring rootstock-fungi combinations could enhance grafting success and ultimately increase nut yield.
