Connecting the Lab and the Field: Genome Analysis of Phyllobacterium and Rhizobium Strains and Field Performance on Two Vegetable Crops

The legume nodules are a rich source not only of rhizobia but also of endophytic bacteria exhibiting plant growth-promoting mechanisms with potential as plant biostimulants. In this work we analyzed the genomes of Phyllobacterium endophyticum PEPV15 and Rhizobium laguerreae PEPV16 strains, both isolated from Phaseolus vulgaris nodules. In silico analysis showed that the genomes of these two strains contain genes related to N-acyl-homoserine lactone (AHL) and cellulose biosynthesis, involved in quorum sensing and biofilm formation, which are essential for plant colonization. Several genes involved in plant growth promotion such as those related to phosphate solubilization, indole acetic acid production, siderophore biosynthesis and nitrogen fixation were also located in both genomes. When strains PEPV15 and PEPV16 were inoculated in lettuce and carrot in field assays, we found that both significantly increased the yield of lettuce shoots and carrot roots by more than 20% and 10%, respectively. The results of this work confirmed that the genome mining of genes involved in plant colonization and growth promotion is a good strategy for predicting the potential of bacterial strains as crops inoculants, opening new horizons for the selection of bacterial strains with which to design new, effective bacteria-based plant biostimulants.

Automated summary

The genomes of endophytic bacteria isolated from legume nodules contain genes related to quorum sensing, biofilm formation, and plant growth promotion. Inoculation of these strains in lettuce and carrot increased crop yield by more than 20% and 10% respectively, confirming their potential as plant biostimulants. Genome mining of genes involved in plant colonization and growth promotion is a promising strategy for selecting effective bacterial strains for crops inoculation.