Phenotypic plasticity
Plant phenotype was modified by both the abiotic environment and the presence of the microbiome. Root length responded strongly to the abiotic environment (F3,21=80.09, p<0.001), increasing in length by 2.1x in low nutrient conditions, although this response was stronger in high light conditions (Fig. 3c). There was considerable variation in root length among genotypes (F7,128=12.06, p<0.001), which interacted with environmental condition (F21,128=3.47, p<0.001), indicating that the plastic response in phenotype to environmental conditions differed among genotypes (GxE). Systematically across all environmental conditions, roots were shorter when the microbiome was present (F1,7=52.45, p<0.001), (Fig. 3c).
Frond phenotype was also modified by the environmental condition. Fronds grown in low light conditions were visibly darker green in colour than those grown in high light (Fig. 3a). Frond area responded to environmental condition (F3,21=21.20, p<0.001) and was on average 1.1x times larger when grown in high nutrient conditions compared to low nutrient conditions (Fig 3b). There was considerable variation in frond area among genotypes (F7,128=19.44, p<0.001) although these all responded similarly to the environment, (no genotype x environment interaction) (F21,128=1.27, p>0.05). The presence of the microbiome resulted in systematically smaller fronds (F1,128=50.05, p<0.001) across all environmental treatments (Fig. 3b), and for all genotypes. The extent of this varied among genotypes resulting in a marginally significant microbiome x genotype interaction (F7,128=2.09, p<0.049). Furthermore, the GxE was mediated by the microbiome resulting in significant 3-way interactions (F21,128=2.19, p=0.004).