Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Ben O. Oyserman (), Stalin Sarango Flores, Thom Griffioen, Xinya Pan, Elmar Wijk, Lotte Pronk, Wouter Lokhorst, Azkia Nurfikari, Joseph N. Paulson, Mercedeh Movassagh, Nejc Stopnisek, Anne Kupczok, Viviane Cordovez, Víctor J. Carrión, Wilco Ligterink, Basten L. Snoek, Marnix H. Medema and Jos M. Raaijmakers ()
Additional contact information
Ben O. Oyserman: Netherlands Institute of Ecology
Stalin Sarango Flores: Netherlands Institute of Ecology
Thom Griffioen: Netherlands Institute of Ecology
Xinya Pan: Netherlands Institute of Ecology
Elmar Wijk: Wageningen University
Lotte Pronk: Wageningen University
Wouter Lokhorst: Netherlands Institute of Ecology
Azkia Nurfikari: Netherlands Institute of Ecology
Joseph N. Paulson: Genentech, Inc. South San Francisco
Mercedeh Movassagh: Harvard T.H. Chan School of Public Health
Nejc Stopnisek: Netherlands Institute of Ecology
Anne Kupczok: Wageningen University
Viviane Cordovez: Netherlands Institute of Ecology
Víctor J. Carrión: Netherlands Institute of Ecology
Wilco Ligterink: Wageningen University
Basten L. Snoek: Utrecht University
Marnix H. Medema: Wageningen University
Jos M. Raaijmakers: Netherlands Institute of Ecology

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating ‘microbiomics’ and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.

Date: 2022
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DOI: 10.1038/s41467-022-30849-9

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