Education:

• 2001-2005, B.Sc. in Agronomy, Anhui Agricultural University, China

• 2006-2014, Ph.D. in Crop Genetics and Breeding, Nanjing Agricultural University, China

Working experience:

• 2015-2019, Postdoctoral Research Fellow, Department of Plant Molecular Biology, University of Lausanne, Switzerland

• 2020-Present, Principal Investigator, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, China

Plant roots act as a pivotal hub for sensing and interacting with the soil environment, orchestrating plant growth, immune homeostasis, stress adaptation, and microbial assembly. Despite substantial progress driven by multi-omics approaches (e.g., ionomics, metabolomics, and metagenomics), our understanding of root-microbe interactions remains constrained by bulk-level analyses that average out cellular heterogeneity and lack the necessary spatial and temporal resolution. The profound spatiotemporal heterogeneity of root-microbe interactions makes it a major challenge for existing analytical methods to decipher the cellular and molecular mechanisms governing their dynamic regulation.

Our laboratory aims to dissect the spatiotemporal dynamics of root-microbe interactions at single-cell resolution. Integrating state-of-the-art live-cell imaging, single-cell and spatial omics, microbial genetics, and plant molecular biology, we investigate how diverse root cell types sense environmental signals, mount immune responses, recruit beneficial microbes, and defend against pathogen attack.

Our current research focuses on three major areas:

• Cellular mechanisms of root immunity, dissecting the spatiotemporal and cell-type-specific regulation of immune responses at single-cell resolution.

• Spatiotemporal dynamics of root-microbe interactions, unraveling how root developmental programs and metabolic signals drive microbial colonization patterns.

• Engineering of root-microbe interactions, designing precision strategies to enhance disease resistance, nutrient-use efficiency, and environmental adaptation in crop roots.

Our long-term goal is to establish predictive frameworks for engineering root systems and their associated microbiota, enabling the rational design of crops with enhanced resilience, productivity, and sustainability.

(1) We engineered high-resolution fluorescent reporters to monitor root immune dynamics at single-cell resolution, revealing a “cell damage-gated” mechanism that links microbial recognition to host cell integrity. In this paradigm, roots differentiate beneficial microbes from pathogens by activating localized antibacterial immunity only upon concurrent detection of microbial signals and cellular damage. This mechanism enables effective pathogen defense while maintaining tolerance toward commensal microbes (Zhou et al., 2020).

(2) We uncovered how plants activate localized immunity while maintaining root growth through the dual functions of the receptor-like kinase FERONIA (FER). Upon bacterial colonization, FER undergoes proteolytic cleavage, releasing its cytoplasmic domain for nuclear translocation to activate localized immune responses in root transition and elongation zones. In contrast, full-length FER remains plasma membrane-localized under non-challenging conditions to support growth. This work uncovers a molecular switch balancing root immunity and development (Chen et al., 2024).

(3) We proposed a conceptual framework that captures the spatiotemporal dynamics of root immunity and microbial colonization, highlighting the utility of single-cell and single-microbe profiling in dissecting cellular heterogeneity and microbial behaviors during root-microbe interactions (Tsai et al., 2023; Zhou et al., 2024).

(4) How plants shape the spatial organization of root microbiota through metabolic cues remains a fundamental question. We revealed that endodermal Casparian strips function as extracellular nutrient diffusion barriers to control bacterial colonization patterns. Vasculature-derived glutamine leakage acts as a key signal driving bacterial chemotaxis and proliferation, uncovering a previously unknown mechanism by which nutrient leakage shapes root microbiome assembly and maintains microbial homeostasis (Tsai et al., 2025).