Mortierellaceae phylogenomics and tripartite plant-fungal-bacterial symbiosis of mortierella elongata

Microbial promotion of plant growth has great potential to improve agricultural yields and protect plants against pathogens and/or abiotic stresses. Soil fungi in Mortierellaceae are non-mycorrhizal plant associates that frequently harbor bacterial endosymbionts. My research focused on resolving the Mortierellaceae phylogeny and on characterizing the effect of Mortierella elongata and its bacterial symbionts on Arabidopsis thaliana growth and molecular functioning.Early efforts to classify Mortierellaceae were based on morphology, but phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. In this study, I applied two approaches: low coverage genome (LCG) sequencing and high-throughput targeted amplicon sequencing to generate multi-locus sequence data. I combined these datasets to generate a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic groups led to the definition of 14 genera, 7 of which are newly proposed.Mortierellaceae are broadly considered plant associates, but the underlying mechanisms of association are not well understood. In this study, I focused on the symbiosis between M. elongata, its endobacteria, and A. thaliana. I measured aerial plant growth and seed production and used transcriptomics to characterize differentially expressed plant genes (DEGs) while varying fungal treatments. M. elongata was shown to promote aerial plant growth and affect seed production independent of endobacteria. A. thaliana DEGs were related to hormone signaling, immune responses, root development, abiotic stress, and metabolism. These data suggest that the mechanism of plant-fungal symbiosis involves fungal manipulation and stimulation of the auxin, ethylene, and ROS response pathways. Future experiments are proposed that could test these hypotheses and further characterize the fungal side of this symbiosis.