Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces, and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.

Background: Plants-microbiome associations are the results of millions of years of co-evolution. Due to the accelerated plant evolution during domestication of crops and aided by cultivation in non-native highly managed soils, plant-microbe links created through co-evolution could have been lost. Therefore, we hypothesize that dramatic effects on the root-associated microbiome occurred during domestication of wheat.Results: To uncover domestication effects we analyzed root associated fungal and bacterial communities in a transect of wheat evolution including modern wheat cultivars, landraces, Triticum aestivum ssp. spelta and ancestors of wheat including T. turgidum ssp. dicoccum , T. monococcum ssp. monococcum and T. monococcum ssp. aegilopoides at three growth phases shortly after emergence of seedlings. We found that numbers of observed microbial taxa were highest in the landraces, which had been domesticated in low-input agricultural systems, and lowest in wheat ancestors that evolved in native soils. The root-associated microbial community of modern cultivars was significantly different from that of landraces and ancestors of wheat. Old wheat accessions enriched Acidobacteria and Actinobacteria , while modern cultivars enriched OTUs from Candidatus Saccharibacteria , Verrucomicrobia and Firmicutes . The fungal pathogens Fusarium , Neoascochyta and Microdochium were enriched in modern cultivars. The composition of root-associated microbial communities of modern wheat cultivars significantly followed patterns predicted by the neutral community assembly model. Our observations allowed us to suggest that a stronger selective pressure drives the root-associated microbiome of ancient wheat accessions than that of modern wheat cultivars.Conclusions: Here we demonstrate that the wheat root-associated microbiome has dramatically changed through a transect of evolution from wheat ancestors over landraces to modern cultivars. Colonization of roots of ancient accessions was slower than in modern cultivars, and the root-associated microbiome of ancient wheat accessions was driven by stronger selective pressure than that of the modern wheat cultivars. We identified several taxa including Acidobacteria and Actinobacteria enriched in old cultivars and fungal wheat pathogens that were enriched in modern cultivars.