Host genetics influences the root microbiome of Pinus radiata

Abstract Background and Aims Root microbiomes can benefit the health and fitness of host plants but manipulating them artificially has challenges. Instead, manipulating the host species through breeding can indirectly promote the development of a beneficial root microbiome. Information to guide root-trait-based breeding approaches in forest trees is, however, severely lacking, especially in non-juvenile trees. We aimed to investigate the relationship between host genotype and both bacterial and fungal root microbiomes in early-mature Pinus radiata D.Don. Methods We sampled roots from four clonal copies of 11 different genotypes (total of 44 trees) of 8-year-post-establishment P. radiata trees. Using amplicon-based sequencing (MiSeq Illumina) and the DADA2 pipeline, we analysed the root microbiome and tested for host genotype effects on the alpha and beta diversity of bacterial and fungal communities. Results We found evidence for an association of host genotype with fungal but not bacterial root microbiome community structure, the strength of which varied significantly among host genotypes. Both bacterial and fungal communities were highly diverse, irrespective of host genotype. Conclusion Our findings suggest there are host genetic influences on the fungal root microbiome in terms of community structure but these are likely masked by environmental effects, which are much more pronounced and variable in field trials than glasshouse experiments. Further exploration of how microbiome-associated root traits vary with host genotype, soil conditions and management regimes is required to understand the potential for microbiome-associated breeding of P. radiata .