Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields.

Yulduzkhon Abdullaeva,Stefan Ratering,Massimiliano Cardinale,Sylvia Schnell,Binoy Ambika Manirajan,David Rosado-Porto

doi:10.3389/fpls.2021.806915

Yulduzkhon Abdullaeva, Stefan Ratering + Show 4 more

Open Access

https://doi.org/10.3389/fpls.2021.806915

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Abstract

The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank’s and seed-originated microbiome recruitment depend on both plants’ genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.

Highlights

Plant domestication significantly altered the plant’s physiological, morphological, and genetic characteristics
We identified 27612 bacterial amplicon sequence variants (ASVs) from 119 samples in total (34 rhizosphere, 36 bulk soil, 36 root, 9 seedbed, and 4 seed samples)
The endorhiza and rhizosphere bacterial and fungal microbiomes were more comparable to one another than the seed microbiome (Figures 1C,D), suggesting that the majority of the endorhiza microbiome are originated from the rhizosphere which is consistent with previous studies (Bulgarelli et al, 2012; Leff et al, 2017) whereas seed has a unique environment which has no direct contact with the soil (Hardoim et al, 2012)

Summary

Introduction

Plant domestication significantly altered the plant’s physiological, morphological, and genetic characteristics. There is limited knowledge on how the alterations of plant genotype during the domestication influenced the assembly process of the rhizosphere microbiome composition. The microbiome inhabiting plant habitats or compartments are known to influence plant health by creating intricate relationships with the host and can play important roles in plant survival (Santos-Medellín et al, 2017). One of the most important microbial habitats for plant health is the rhizosphere (Mendes et al, 2011). The dynamics of the seed-transmitted microbiome and plant characteristics that regulate microbial assembly and maintenance remain to be elucidated

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