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Updated: Feb 28, 2026

A Hydroponic Co-cultivation System for Simultaneous and Systematic Analysis of Plant/Microbe Molecular Interactions and Signaling

A Hydroponic Co-cultivation System for Simultaneous and Systematic Analysis of Plant/Microbe Molecular Interactions and Signaling

Published on: July 22, 2017

Integrating Single-Cell and Spatial Multi-Omics to Decode Plant-Microbe Interactions at Cellular Resolution.

Yaohua Li¹, Jared Vigil¹, Rajashree Pradhan¹

¹Division of Plant Science and Technology, College of Agriculture, Food and Natural Resources, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA.

|February 27, 2026

Summary

This summary is machine-generated.

Single-cell and spatial multi-omics reveal plant cell-type-specific interactions with microbes. This approach helps engineer crop-microbiome relationships for sustainable agriculture by understanding cellular communication.

Keywords:

holobiont microbiome multi-omics plant–microbe interactions single-cell RNA sequencing spatial transcriptomics

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Microfluidic Tools for Probing Fungal-Microbial Interactions at the Cellular Level

Microfluidic Tools for Probing Fungal-Microbial Interactions at the Cellular Level

Published on: June 23, 2022

Area of Science:

Plant biology
Microbiome research
Agricultural science

Background:

Understanding plant-microbe interactions at the cellular level is key for optimizing plant holobionts.
Traditional methods lack resolution for cell-type-specific microbial colonization and interactions.
Single-cell and spatial multi-omics offer new insights into plant cell identity and regulation.

Purpose of the Study:

To review single-cell discoveries in plant-microbe interactions across different tissues.
To discuss integrating multi-omics data for reconstructing interaction networks.
To highlight strategies for engineering crop-microbiome interactions for sustainable agriculture.

Main Methods:

Review of single-cell transcriptomics and spatial multi-omics studies.
Analysis of plant cell-type-specific microbial perception and immune responses.
Integration of transcriptomic, epigenomic, and spatial data.

Main Results:

Identification of plant cell-type-specific microbial perception, immune activation, and symbiotic differentiation.
Reconstruction of multilayered interaction networks connecting plant regulatory states with microbial niches.
Elucidation of inter-kingdom signaling mechanisms like ligand-receptor and metabolite exchange.

Conclusions:

Single-cell and spatial multi-omics are transforming the study of plant holobionts.
Integrating diverse omics data is crucial for a systems-level understanding of plant-microbe interactions.
Future research should focus on building a comprehensive cellular interactome for improved agricultural applications.