Fig. 8: Disentangling the genetic basis of rhizosphere microbiome assembly.

a The initial domestication, subsequent crop improvements, and introgression wild tomato traits to modern cultivars. b While domestication significantly decreased the allelic diversity of modern tomato cultivars, introgressions of allelic diversity from wild relatives has left a genomic signature. c Here we identify QTLs associated with changes in microbiome composition at both the community level, but also within individual populations (e.g., Streptomyces and Cellvibrio). We show that these QTL overlapping previously identified selective sweeps associated with domestication. d By identifying plant QTLs regions using population features of the microbiome (SNVs), it is possible to identify the reciprocal functional adaptations that may link plant and microbe (represented by capital and lower-case letters respectively). These functions may interact directly, or indirectly via the environment. For example, related to water balance (I, i), we identified plant aquaporin and both plant/microbe trehalose metabolism. Selection for altered host water usage may alter the water balance in the soil and associated repercussions on microbiome structure. Similarly, numerous plant and microbial genes related to nutrient cycling (II, ii) involving iron, sulfur, vitamin, and phosphorus acquisition were identified. Plant signaling and hormone genes (III) identified in QTL regions included 1-aminocyclopropane-1-carboxylic acid oxidase, alpha-humulene/beta-caryophyllene synthase, and a p450 involved to coumarin synthesis. Furthermore, plant cell wall metabolism (IV, iv) including expansins, extensins, pectinesterase were linked to microbial genes involved in plant cell wall plant polysaccharides catabolism, cellobiohydrolase glycosyl hydrolases, xylose, sarcosine oxidase, L-arabinofuranosidase, fructose import, a cellulase/esterase, and xyloglucan metabolism. Finally, genes related to exudation and possible cross feeding (V, v) included plant genes such as aluminum-activated malate transporter, polyamine, glutamine, and acetolactate synthetase, and microbial functions related to malate, mannonate, polyamine, and acetolactate metabolism. Created with BioRender.com.