It is essential to understand the influence of environmental conditions on plant-associated microbial communities for improving orchard management strategies. This study characterized the bacterial and fungal microbiomes associated with pecan (Carya illinoinensis) clonal rootstock cultivated under controlled greenhouse conditions and following transplanting into field environments. Microbial profiling focused on root and rhizosphere soil compartments across four rootstock genotypes (NMU03, NMU04, NMU05, and NMU155). Preliminary findings from MiSeq of 16S rRNA and fungal ITS regions revealed that microbial community composition clustered more strongly by where it planted than by sample type (root and rhizosphere soil compartments) or host genotype. Field samples were enriched with bacterial taxa such as Micrococcaceae, Azospirillaceae, and Clostridiaceae 1, while greenhouse samples exhibited higher relative abundances of Propionibacteriaceae and Microbacteriaceae. Similarly, distinct fungal assemblages such as Tremellaceae, Trichocomaceae, and Sordariomycetes_fam_Incertae_sedis were observed from the field samples while fungal taxa including Aspergillaceae, Stachybotryaceae, and Chaetomiaceae were detected in greenhouse roots, forming separate clusters based on hierarchical analysis. Preliminary findings from alpha diversity revealed more variation in fungal than bacterial communities. Overall, this study highlights the possibile dominant role of environmental conditions over host genotype in shaping root- and soil-associated microbiomes in pecan. Our preliminary results emphasize the importance of targeted microbiome-informed management strategies in orchard systems.
