Pseudomonas taxonomic and functional microdiversity in the wheat rhizosphere is cultivar-dependent and links to disease resistance profile and root diameter

Abstract

Diversity within lower taxonomic units in microbial communities is a key trait, giving rise to important ecological functions. In the rhizosphere, these functions include disease suppression and pathogen inhibition. However, limited effort has been given to defining the importance of rhizosphere intragenus microdiversity, despite the increasing homogeneity of agricultural systems. Through an integrative approach combining culture-dependent and -independent methods, we generated a strain library of 373 pseudomonads, benchmarked to long-read 16S rRNA amplicon sequencing, from two modern winter wheat cultivars. Representative isolates were genome sequenced to provide a Pseudomonas pangenome of 112 genomes. The isolates were used to demonstrate cultivar-dependent taxonomic and functional microdiversity between two closely related winter wheat cultivars. A Fusarium-resistant cultivar demonstrated increased Pseudomonas taxonomic diversity but not biosynthetic diversity when compared to the susceptible cultivar, coinciding with a thinner root diameter of the resistant cultivar. We found enrichment of Pseudomonas isolates capable of antagonizing Fusarium as well as chitinase-encoding genes and pyoverdine gene clusters in the resistant cultivar. Across closely related Pseudomonas isolates from the two cultivars, there were differences in genomic content and biosynthetic gene clusters. Ultimately, we highlight the need for fine-scale analysis to uncover the hidden microdiversity within rhizosphere Pseudomonas.