The Role of Host Genetics in Shaping the Tree Root Microbiome

<p><strong>Plant microbiomes encompass the diverse community of microorganisms that live in and around their tissues. Conifers, with their long evolutionary history, provide an ideal system for testing whether parallel evolution between host species and their root microbiomes has produced host phylogenies that are reflected in microbiome community composition — a pattern known as phylosymbiosis. However, phylosymbiosis studies among tree species that cover a range of phylogenetic distances are limited. It is also largely unknown to what extent host genetics influences the assembly of the root microbiome for long-lived species such as conifers, especially beyond the seedling stage. In my thesis, I aimed to determine the role of host genetics in shaping the tree root microbiome. My three objectives were to 1) determine whether phylosymbiosis was present in conifers, 2) quantify how much variability in the root microbiome of Pinus radiata D.Don was attributable to host genetics, and 3) assess the range of microbial taxa that were heritable.</strong></p><p>My first objective (Chapter 2) was to investigate phylosymbiosis in conifers. I grew 196 individual plants from 23 conifer species from the Pinaceae and Cupressaceae families in a common soil for 52 weeks before measuring host traits, harvesting roots, and tag-amplicon sequencing the bacterial and fungal root microbiomes. Physicochemical soil data from each plant allowed for indirect host effects on the soil to be tested. I used two tests for phylosymbiosis that explored different aspects of the relationship among host species and similarity of their microbiomes. Both topological congruence testing and matrix correlations showed strong evidence for phylosymbiosis for both bacterial and fungal root microbiomes. There was also evidence of indirect host effects on the root microbiome composition through modification of the rhizosphere soil, particularly through variations in sulfate sulfur concentrations among hosts. The correlation of increasing genetic divergence among hosts with increasing divergence among root microbiomes may indicate coevolution among conifers and microbes.</p><p>For my second objective — to quantify how much variability in the root microbiome of P. radiata can be attributed to host genetics — I sampled roots of 48 trees, comprising four clonal copies each of 11 different genotypes from an 8-year-old genetic trial in Kinleith Forest in the central North Island of New Zealand (Chapter 3). I found subtle but significant host genotype effects on the composition of the fungal but not the bacterial root microbiome. This demonstrated that host genetic effects on the fungal root microbiome of P. radiata persist beyond the seedling stage and remain detectable in a highly variable field-trial setting, not just in tightly controlled nursery and common-garden experiments.</p><p>For my third objective, I assessed the heritability of the relative abundance of individual bacterial and fungal taxa within the root microbiome (Chapter 4). I sampled a total of 528 P. radiata trees from the same trial as Chapter 3, including four clonal copies each of 132 unique genotypes, from 28 full sibling families. In the core microbiome, i.e., taxa present in at least 80% of samples, I found that most microbial taxa were of negligible heritability. In other words, there was minimal host genetic variation associated with the abundance of these ubiquitous members of the P. radiata root microbiome. There were several non-core microbial taxa with moderate heritability, some of which have also been reported as heritable in other plant systems. Most variation in the relative abundances of heritable taxa was attributed to non-additive genetic effects, which include complex gene interactions such as dominance and epistasis. Similar to Chapter 3, I showed that host biological family influenced the fungal but not the bacterial microbiome. I found no influence of host ancestry, i.e., genetic similarity to native provenances of P. radiata, on composition of the root microbiome. My results showed evidence for broad host genetic influences on the establishment of a core root microbiome, alongside intraspecies host genetic differences that influenced the abundance of a variable non-core root microbiome. Together, these studies advance knowledge of how plant root microbiomes are influenced by host genetics in long-lived conifer species. I found evidence for phylosymbiosis within this ancient plant lineage where there has been extensive opportunity for genetic divergence, indicating potential coevolution of microbes and host. I have shown that host genetic effects for the root microbiome persist at the intraspecies level within P. radiata. Furthermore, these influences are not limited to seedlings but were evident on the roots of physiologically mature trees growing in a more natural, uncontrolled environment. I also determined heritability of individual taxa within the bacterial and fungal root microbiomes, helping to formalise the association between tree genetic influences on root microbiomes to the individual taxa present. Thus, not only are there broad genetic influences for a core microbiome in P. radiata which extend to the overall microbiome community for fungi, but potentially many interacting genes associated with maintaining specific taxa.</p>