Seed Surface Sterilization Can Alter Root Microbiomes, Increase Endophyte Diversity and Enhance Plant Growth

With the goal of bioprospecting for growth-promoting endophytes that could become yield-enhancing inoculants in maize agriculture, we isolated 129 endophytic bacteria from 22 wild plants growing in a nature preserve and an urban park in Cali, Colombia. These strains were put through a bioassay with surface-sterilized seeds of perennial ryegrass (Lolium perenne) grown in sealed tubes, and growth promotion assessed by measuring plant fresh weight. The top two strains Pseudomonas delhiensis and Serratia marcescens, along with five different subcultured root endophytic communities, were put into a secondary screen along with two uninoculated controls of untreated and surface-sterilized seed of both the turfgrass and a commercial maize hybrid. Impact on plant microbiomes was assessed using molecular fingerprinting and high-throughput sequencing. This second bioassay indicated that plant growth promotion was corelated not with inoculation but with seed surface sterilization which shifted root microbiomes, increased endophyte diversity and probably eliminated pathogens. Inoculating maize (but not ryegrass) seed with either pure bacteria or microbial communities was also able to shift the root microbiome. Because the majority of plant microbiome researchers employ seed surface sterilization as a method to standardize their experiments, they could be inadvertently studying unusual plant phenotypes and microbiomes; a possible reason why field trials correlate poorly with those of lab tests.