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Song, Siyu

University of British Columbia

Plant roots associate with a variety of soil-borne microbes, collectively known as the rhizosphere microbiome. Increasing evidence highlights the important roles of plant immune regulators in modulating the microbiome. However, the detailed plant genetic regulatory networks that shape the microbiome composition, and mechanisms by which plants tune their immune responses against microbiota, remain largely unexplored. In my thesis, I employed a reductionist Arabidopsis-Pseudomonas fluorescens WCS365 mono-association model to facilitate both forward and reverse genetic approaches and identified two novel plant microbiome regulators. Studies in Chapter 2 identified Arabidopsis phytosulfokine receptor 1 (pskr1) mutants displaying autoimmunity and reduced rhizosphere bacterial growth with normally growth-promoting P. fluorescens WCS365. Microbiome analysis by 16S ribosomal RNA (rRNA) sequencing and colonization assays with taxonomically diverse synthetic community (SynCom) strains showed PSKR1 shifts the rhizosphere microbiome composition by predominately regulating Pseudomonas abundance. RNAseq analysis and genetic epistasis experiments revealed that PSKR1 mediates this specific interaction via suppressing salicylic acid (SA) signaling. Finally, using a transgenic reporter, I found that P. fluorescens induces PSKR1 expression in roots, suggesting P. fluorescens might manipulate plant signaling to promote its colonization. Chapter 3 describes the identification of an Arabidopsis leucine-rich repeat extensin 1/ leucine-rich repeat extensin 2 (lrx1/2) mutant with enriched rhizosphere P. fluorescens in natural soil, similar to previously described FERONIA (FER) loss-of-function mutants. Microbiome sequencing revealed similarly altered microbiome composition for lrx1/2 and fer-4 mutants relative to wildtype plants. Building on the previously described role of FER in shaping the microbiome under varying phosphate availability, we further investigated these mutants under natural and supplemented phosphate levels. We found that while the fer-4 mutant displayed significant phosphate-dependent microbiome changes, the altered microbiome in lrx1/2 was insensitive to phosphate ability. These data indicate that FER and LRX1/2 may work together in response to low phosphate to shape the rhizosphere microbiome, but may function through distinct pathways under phosphate-sufficient conditions. Collectively, studies in this dissertation describe novel plant genetic mechanisms involved in regulating the rhizosphere microbiome and expand our understanding of intricate plant-microbiome conversations.  

Text

2025-04-30

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/87989

Microbiology and Immunology

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/