Soybean microbiome recovery after disruption is modulated by the seed and not the soil microbiome
Endophytic microbiome of healthy seeds forms a symbiotic relationship with their host. Seeds and environment are sources of microbes that colonise the developing plant, however, the influence of each remains unclear. Here, using irradiation combined with surface sterilisation to generate near-axenic seeds with disrupted and reduced microbiome, we contrasted colonisation potential of seed and soil microbiome. We hypothesised that the seed microbiome would be the primary coloniser of the plant endophytic compartments. Our experimental design comprised four treatments, using soybean as a model plant: 1) nearly axenic seeds growing in a sterile environment, 2) non-axenic seeds inoculated with a microbial soil extract, 3) nearly axenic seeds inoculated with a microbial seed extract, and 4) nearly axenic seeds inoculated with a microbial soil extract. After 14 days of growth, plants were harvested, and DNA was extracted from the shoot, roots, rhizosphere, and subjected to 16S rRNA gene amplicon sequencing, qPCR quantification of the total community and functional genes involved in the N-cycle. Community dynamics were similar for most treatments within their respective compartments, except for the soil treatment, where rhizosphere and root microbiome differed from other treatments, suggesting that the soil microbiome colonises the belowground compartment efficiently only when the seed microbiome is severely disrupted. For the shoot, all treatments resembled the seed microbiome treatment, suggesting that the seed-borne bacteria colonise the aboveground compartment preferentially. Our results highlight the primacy of the seed microbiome over the soils during early colonisation, putting seed microbes as potential candidates of microbiome engineering efforts.