The Root-Soil Microbiome: Unravelling the Other Half of the Hidden Half

Plants do not live in isolation but co-exist in nature with a vast array of microorganisms that collectively constitute the plant microbiome. This associated microbiome is integral to the ‘wider genome’ of the plant and contributes functionally to the plants ‘extended phenotype’. The below-ground root-soil microbiome in particular has major impact on plant health through interactions on growth and development, facilitation of nutrient uptake and host-plant tolerance to a wide range of biotic and abiotic stresses. Presently, there is widespread interest in capturing increased benefit from the root-soil microbiome. Recent studies have shown that the root microbiome is not stochastically assembled from the surrounding soil biota, but results from specific recruitment at the root-soil interface. Microbiome assemblage is both host species and soil dependent. We have also shown it to be responsive to root type and stage of development and to be strongly differentiated across different root compartments. The rhizosphere, rhizoplane (root surface) and endosphere (root internal region) thus contain distinct but reproducible communities. In contrast to the large effects due to soil type and plant presence, genotypic differences within a host species however have been found to have a relatively small, but sometimes defined influence on root microbiome structure. Whilst differences in microbiome are correlated with evolutionary distance across host plants, we have also shown clear differences between the domesticated modern bread wheats, landraces and wild relatives within the Triticeae. However, functional contribution of differences in microbiome structure on plant productivity remain to be established. Better connection between ‘descriptive genomics’ and ‘functional gene analysis’ is needed, including linkage to actual process rates that contribute to differences in plant growth. Understanding of spatial and temporal factors that operate under field conditions is also required. This may then allow deliberate selection of more beneficial microbiomes through either targeted management or specific selection of crop genotypes.