Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.
Ben O Oyserman, Stalin Sarango Flores, Thom Griffioen, Xinya Pan, Elmar van der Wijk, Lotte Pronk, Wouter Lokhorst, Azkia Nurfikari, Joseph N Paulson, Mercedeh Movassagh, Nejc Stopnisek, Anne Kupczok, Viviane Cordovez, V��ctor J Carri��n, Wilco Ligterink, Basten L Snoek, Marnix H Medema, Jos M Raaijmakers
Author Information
Ben O Oyserman: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. benoyserman@gmail.com. ORCID
Stalin Sarango Flores: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
Thom Griffioen: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. ORCID
Xinya Pan: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
Elmar van der Wijk: Bioinformatics Group, Wageningen University, Wageningen, The Netherlands. ORCID
Lotte Pronk: Bioinformatics Group, Wageningen University, Wageningen, The Netherlands. ORCID
Wouter Lokhorst: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. ORCID
Azkia Nurfikari: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. ORCID
Joseph N Paulson: Department of Data Sciences, Genentech, Inc. South San Francisco, South San Francisco, CA, USA. ORCID
Mercedeh Movassagh: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Nejc Stopnisek: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. ORCID
Anne Kupczok: Bioinformatics Group, Wageningen University, Wageningen, The Netherlands. ORCID
Viviane Cordovez: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
V��ctor J Carri��n: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. ORCID
Wilco Ligterink: Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands. ORCID
Basten L Snoek: Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands. ORCID
Marnix H Medema: Bioinformatics Group, Wageningen University, Wageningen, The Netherlands. ORCID
Jos M Raaijmakers: Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. j.raaijmakers@nioo.knaw.nl. ORCID
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.
References
Front Microbiol. 2016 Dec 07;7:1971
[PMID: 28003808]
