Microbes within plants are ubiquitous. The endorhizosphere, the root interior, contains a suite of bacteria that form a range of relationships with their host. They can enhance growth through the production of phytohormones, increase available nutrients (e.g. N fixation), and protect the plant against phytopathogens. The potential importance for bacteria in affecting host health make them an important area of study, especially with regard to the factors shaping their assembly within the root. The aim of this study was to assess the relative contribution of pH, the soil community, and plant host identity in controlling the interior root microbiome. To do this we collected roots and paired bulk soil samples across a heterogeneous alpine landscape near Niwot Ridge on the Front Range of Colorado. Roots were surface sterilized and both roots and soils were sequenced using Illumina MiSeq2000. We then used structural equation modelling (SEM) to examine the importance of host identity and the indirect versus direct effect of pH on the interior root microbiome structure, diversity, and richness. Furthermore, we examined a subset of bacteria that were categorized as dominant (defined as the overlap between the top 10% of bacterial families and families present in at least 90% of plots).
Results/Conclusions
The interior root microbiome exhibited variable host-specific control and an indirect influence of pH acting through the soil microbiome (SEM: P=0.21, X2= 3.16). This result suggests that pH has an important influence on the root microbiome of plants growing in those soils. Interestingly, when only examining dominant root bacterial families and those same families in the soil, plant host identity remained influential while pH and the soil community became non-significant predictors (SEM: P=0.73, X2= 0.63). This result suggests that under certain conditions host identity is more important than edaphic characteristics and the soil microbiome. When examining the diversity and richness of the root microbiome, neither pH, nor the soil microbiome, nor host identity were significant predictors. Overall, our findings demonstrate variable host-specific control of the interior root microbiome and an indirect influence of pH acting through the soil microbiome. However, when examining richness, diversity, and a subset of the dominant bacteria in the root microbiome, there is a shift in the factors influencing the interior root community.