Tomato Genotype Modulates Selection and Responses to Root Microbiota

Abstract

Using microbial inoculants to enhance plant health is promising for crop improvement. However, for success, knowledge of how different cultivars within a crop species select and respond to the root microbiome is critical. The aims of this study were to (i) determine the contribution of tomato genotype to the tomato root bacterial microbiome and (ii) investigate whether closely related tomato genotypes differ in their selection of and response to root endophytes. We used 16S ribosomal RNA amplicon sequencing to examine the root bacterial communities of six Solanum lycopersicum (domesticated tomato) and two S. pimpinellifolium (wild tomato) accessions. We found that, across accessions, both the root endosphere and rhizosphere were affected by genotype. Genotype accounted for 10% of the variation in root microbiota. Two bacterial families, Bacillaceae and Rhizobiaceae, were significantly enriched in the root endosphere in at least six of the eight tomato genotypes. To investigate whether closely related tomato genotypes differed in selection of these endosphere-enriched taxa, we profiled the root endosphere of 20 recombinant inbred lines (RILs) derived from two of the genotypes. The abundance of Bacillaceae and Rhizobiaceae isolates varied quantitatively in the root endosphere of the RILs. Inoculation of 16 RILs with a Bacillaceae isolate identified from the root endosphere of field-grown tomato showed that RIL responses, in terms of shoot and root growth, varied from less than 5% growth enhancement to more than 40%. Our data show that tomato genotypes have distinct but overlapping root bacterial microbiomes and respond differently to specific bacterial endophytes.