Consistent associations with beneficial bacteria in the seed endosphere of barley (Hordeum vulgare L.)

The importance of the plant microbiome for the host fitness lead to the concept of “plant holobiont”. Seeds can work as reservoirs and vectors of beneficial microbes, which should be regarded as the most intimate partners of higher plants with the potential of connecting plant generations, thus creating stable “core–holobionts”. In this work, the endophytic microbiota of different barley seed samples, representing different cultivars, geographical sites and harvest years, was investigated by cultivation–dependent and –independent analysis, microscopy, functional plate assays, greenhouse assay and functional prediction. The aim of this study was to assess stability and functions of the barley seed endophytes. Low–abundant but stable bacterial species (including Pantoea, Paenibacillus and Pseudomonas species) were detected in the seed endosphere, able to massively colonize the root after seed germination and to promote barley growth. Here we demonstrated that the seeds of an important crop (barley) always harbour certain beneficial bacteria across boundaries of genetics, geography and time. Our discovery has tremendous implications for plant microbiome ecology, and opens new frameworks for research and application of bioinoculants in sustainable agriculture.