Auxin Degradation By Variovorax Maintains Stereotypic Plant Root Development within the Complex Plant Microbiome

Plant-microbe and microbe-microbe interactions within the rhizosphere contribute both positively and negatively to plant physiology, health, and productivity. To test hypotheses about these interactions and define the bacterial genes responsible, we are using a synthetic community of 185 fully genome sequenced bacteria isolated from Arabidopsis roots. Through a large screening of Arabidopsis plants across various stress gradients (pH, temperature, phosphate, and salt), bacterial colonization patterns robust to these stresses were identified. Then through analysis of subset communities, the genus Variovorax was identified as being required to maintain stereotypic root development in these mixed bacterial communities. This ability was traced to Variovorax reverting the phenotypic effects of many root growth inhibition (RGI)-inducing bacteria by consuming indole-3-acetic acid (IAA), an auxin plant hormone produced by both plants and bacteria. Using a combination of comparative genomics, RNA-Seq, and screening of a gain-of-function plasmid library in E. coli, a single locus conserved in all sequenced Variovorax genomes, containing IAA degradation genes, was identified. Using bacterial genetics, this locus was deleted, confirming its role in stereotypic root development. This locus was also expressed in a closely related bacterium from the genus Acidovorax, conferring this strain with the ability to degrade IAA and partially revert IAA-induced plant phenotypes. Sub-cloning of genes from this locus have identified the essential genes for IAA degradation. Further, we are investigating the regulation of this locus through a MarR transcriptional regulator. Isothermal titration calorimetry has demonstrated this MarR binds to IAA and related auxins, as well as a promoter element upstream of the degradation genes. Crystal structures of the MarR regulator identified the IAA binding residues and mutation analysis confirms their role in IAA binding. Understanding the Variovorax genes required for auxin degradation, and their regulation through the MarR regulator, will enable more carful engineering of this locus in Variovorax or related bacteria. The ability to control auxin homeostasis and promote stereotypic root development through this mechanism is of interest for inclusion in biofertilizers and microbial probiotics in agricultural applications.

Reference

Finkel OM^†, Salas-González I^†, Castrillo G^†, Conway JM^†, Law TF, Teixeira PJPL, Wilson ED, Fitzpatrick CR, Jones CD, Dangl JL. 2020. A single bacterial genus maintains root development in a complex microbiome. bioRxiv:645655. Doi: 10.1101/645655 († These authors contributed equally to this work)