Tomato Rhiz`omics: Unravelling the Below-Ground Dialogue between Plant Roots and Soil Bacteria

The rhizosphere microbial community affects the host physiology, and vice versa. However, the intricate processes, i.e., environmental and host molecular factors combined, that shape the microbiome of the rhizosphere are still greatly unknown. Here, two approaches were used in order to correlate the two major components of the tomato rhizosphere: the tomato root and the soil bacterial diversity. First, we assessed the genetic factors that affect the rhizosphere bacterial composition in a set of 76 introgression lines (ILs) of Solanum lycopersicum carrying only a single chromosome segment from the wild species Solanum pennellii (LA0716). For that tomato population, a core microbiome was defined based on 16S rRNA amplicon sequencing, consisting of 154 abundant OTUs that changed quantitatively across most ILs. Testing of these OTUs’ abundances for cosegregation, 4 host quantitative trait loci (QTL) show significant linkage with relative abundances of specific bacterial OTU. These QTL affect bacterial OTU by increasing its abundance, either controlling an individual OTU or various OTUs spanning a diverse taxonomic range. In addition, in order to understand how the root exudation influences the tomato rhizosphere microbiota, tomato roots were challenged with soil microbial communities established using a dilution-to-extinction approach. The metabolic patterns, analyzed by LC-MS and GC-MS, of tomato roots and exudates are tailored by soil microbial diversity and composition. The metabolic changes of host plants in response to soil microbial diversity might also affect the rhizosphere microbial ecology.