NCM 2021: Revealing the whole genome of olive antagonistic xylem-inhabiting bacteria, to fight vascular plant pathogens in olive trees

‘Olive xylem sap is colonized by specific microbial communities’ that are adapted to negative pressure, low oxygen concentration, and low mineral and nutrient content. They produce biotic and abiotic factors that could be used as biocontrol agents to protect against xylem-inhabiting pathogens, such as Verticillium dahliae and Xylella fastidiosa, which can kill whole plants. Manuel collected bacterial cultures from healthy olive trees, using two different methods to extract xylem. After culturing, 108 xylem bacterial strains were collected. In addition, defoliating (D) and non-defoliating (ND) strains of Verticillium dahlia which infect olive and a strain which infects tomato were isolated. A high-throughput fungal-bacterial interaction screen was performed using different media: control and xylem sap, and it was found that the culture media affects the bacterial-fungal interaction. The relative growth index (RGI) recorded any reduction or increase in fungal biomass after culturing with the xylem bacterial strains. Manuel found that the bacterial strains had different effects on pathogen growth: they could promote, restrict, or have a neutral effect, depending on the strain of V. dahlia. Bacterial strains with the greatest effect on pathogen growth were selected and their whole genomes were sequenced using nanopore technology. Genome annotation using RASTk identified one strain of Methylobacterium with the highest number of coding sequences (10,393) and a Microbacterium with the lowest number (3,523). Manuel analysed two Methylbacterium: one which restricted pathogen growth and one which increased growth, a Microbacterium, Rhizobium, and Sphingomonas and found that the bacterial strains both shared and had unique coding sequences: the unique sequences may ‘unravel the mechanisms behind the antagonistic activity of xylem-inhabiting organisms’.