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<div>The phytobiome (here defined as the combination of the microbiome, mycobiome and viriome) not only interacts with the host, and thus may elicit or suppress a defense response, but there may be interactions amongst the constituents of the phyotbiome. To better understand these influences we have applied modified genome-wide association (GWAS) methods in order to associate host genotypic variation to the putative viral, bacterial, fungal and archaeal community composition. Metatranscriptome samples extracted from <i>Populus trichocarpa</i> xylem and leaf tissue were used to identify the different taxa present via several computational approaches. The resultant members of the phytobiome then served as phenotypes in a GWAS analysis involving 444 genotypes of <i>Populus trichocarpa</i> (against over 28 million single-nucleotide polymorphisms). We view the results as a network and network find shared associations between phytobiome phenotypes and receptor kinases, signal transduction genes, transcription factors, stress and cell organization among other functions. The resultant network provides a rich framework for biologically driven hypothesis generation. Furthermore, we have used the plant gene expression data from these genotypes as expression phenotypes for eQTN analysis. In so doing we are able to identify a significant portion of the regulatory network surrounding the genes that map to the phytobiome phenotypes described above. This unified model is a powerful tool for understanding host-phytobiome associations and the regulatory circuits that control them.</div>