Phylogenetic Divergence and Domestication Jointly Shape the Tomato Root Microbiome

Area of Science:

• Plant-microbe interactions
• Microbiome research
• Crop genetics

Background:

• Crop domestication often reduces genetic diversity, impacting resilience.
• Domestication can alter root-associated microbiomes, offering opportunities for crop improvement.
• Understanding these microbiome shifts is crucial for harnessing beneficial microbes.

Purpose of the Study:

• To compare rhizosphere and endosphere bacterial communities in cultivated tomato and its wild relatives.
• To investigate the impact of domestication on tomato root microbiome structure and function.
• To identify microbial traits in wild relatives that could enhance cultivated tomato resilience.

Main Methods:

• Multi-region 16S rRNA sequencing was used to analyze bacterial communities.
• Cultivated tomato (Solanum lycopersicum cv. Moneymaker) and six wild relatives were sampled.
• Bacterial community structure, diversity, and differential abundance were analyzed.

Main Results:

• Rhizosphere bacterial community structure was broadly conserved but ordered by host phylogeny.
• Specific bacterial groups were differentially recruited by different tomato genotypes.
• Endosphere analysis revealed reduced bacterial families in wild accessions and enrichment of certain families in wild species.

Conclusions:

• Domestication exerted a modest effect on tomato root microbiomes.
• Wild tomato relatives harbor unique microbial association traits.
• These traits offer potential for microbiome-informed breeding to enhance cultivated tomato resilience.