Plant-Microbial Interactions Group

Plant microbiomes hold the amazing ability to influence plant development, fitness and health. This is a dynamic and complex ecosystem that includes bacteria, fungi, viruses. Resident viruses can be found in a myriad of bacterial strains, whereby they can modulate host metabolism, gene expression and phenotype. We have recently identified resident bacteriophages (viruses infecting bacteria) in the plant growth-promoting rhizobacterium (PGPR) Pseudomonas simiae WCS417. One suggested function of these phage genes is the modulation of their bacterial host to colonize plant roots, as with Arabidopsis thaliana. Using a coupled experimental and computational approach, we employ various omics technologies, strain engineering and experimental characterization methods, in addition to bioinformatics tools to elucidate phage function in this tripartite plant-bacterial-phage model system. We seek to expand beyond this model system by identifying phages and characterizing this multipartite phenomenon in additional plant and bacterial species of bioenergy importance.

We are using cutting-edge single-cell profiling methods, including single-cell RNA-seq, single-cell ATAC-seq, and spatial transcriptomics to profile the plant/environmental interface. We are using these methods to understand how plant cells respond to low nutrient conditions (low nitrogen or low phosphorus), and how cell identity impacts this response. We will eventually construct a bioenergy plant single-cell atlas comprising Sorghum, Switchgrass, and Brachypodium datasets. We recently profiled the association between the plant, Medicago truncatula and an arbuscular mycorrhizae, Rhizophagus irregularis using single-cell and spatial ‘omics methods. Here we were able to capture both plant and fungal expression patterns in root cross-sections.

• 10.1038/s41579-020-0381-4
• 10.1038/s41396-020-0637-z
• 10.1038/s41477-024-01666-3
• 10.1016/j.celrep.2023.112676
• 10.1016/j.devcel.2022.01.008
• 10.1038/s42003-021-02477-4
• 10.1038/s41477-021-00915-z
• 10.1073/pnas.1907500116
• 10.1016/j.celrep.2019.04.054
• 10.1371/journal.pbio.2002860

Postdocs:

• Margot Bezrutczyk (JGI Postdoc)
• Lamprinos Frantzeskakis (JGI Postdoc)

Interns:

• Katsuma Yonehara (Tokyo University)
• Dongfong Wang (Spelman University, VFP Program)
• Emerald Nash (UC Merced Intern)
• Tyrome Sweet (UC Merced Intern)
• Ruoxi Zhao (UC Merced Intern)
• Alex Pennacchio (Occidental College Intern)
• Cristian Espinosa (UC Merced Intern)
• Maria Mendoza (UC Merced Intern)
• Lorenzo Scaturchio (UC Merced Intern)
• Candace Cole (UC Merced Intern)
• Sabah Ul-Hasan (UC Merced Intern)
• Brenda Yu (UC Merced Intern)
• Keedrian Olmstead (UC Merced Intern)
• Sai Prahabkar (UC Merced Intern)