The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion

Plant-associated microbe play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assay

Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere

Pseudomonas and Sphingomonas are among the most abundant bacterial genera in the phyllosphere of wild Arabidopsis thaliana. Relative to Pseudomonas, the ecology of Sphingomonas and its interaction with plants remains elusive, despite its global ubiquity and known representatives of plant-beneficial strains. We analyzed the genomic features of over 400 endophytic Sphingomonas isolates collected from A. thaliana and neighboring plants, revealing high intergenomic diversity compared to much more homogenous Pseudomonas populations on the same plants. Variation in plasmid complement and additional genomic features suggest high adaptability, and the widespread presence of protein secretion systems hints at frequent biotic interactions. While some of the isolates showed plant-protective properties, this was a rare trait. To begin to understand the bacterial populations at the investigated A. thaliana sites and the alternate hosts of these strains when A. thaliana becomes limiting, we employed amplicon sequencing and a novel bulk-culturing metagenomics approach on A. thaliana and neighboring plants, both in spring when A. thaliana was flowering and in late summer before the emergence of the A. thaliana winter cohort. Our data reveal that Sphingomonas and Pseudomonas strains from A. thaliana not only survive, but also thrive on other diverse local plant hosts, suggesting that leaf-to-leaf transmission from these biotic reservoirs may be a major source of microbes to the next generation