Visualising Plant-Microbiome interactions at single-cell resolution using PHYTOMap

*This is a poster for PPATH ECPP/BSPP 2026

Visualising Plant-Microbiome interactions at single-cell resolution using PHYTOMap

Siyu Song (1), Hsuan Pai (1), Karen Uchida (1), and Tatsuya Nobori (1)

¹The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom

Plants co-exist with diverse microbial communities whose effects on host fitness span a continuum from beneficial to pathogenic. These interactions are highly spatially organised and heterogeneous, yet conventional approaches often measure microbial distribution and host gene expression at the tissue level, obscuring the local cell-cell interactions through which plant-microbiome relationships are established and maintained.

Here, we present our ongoing efforts to expand PHYTOMap (Plant HYbridization-based Targeted Observation of gene expression Map), a multiplexed fluorescence in situ hybridisation-based platform for 3D spatial gene-expression mapping in whole-mount plant tissues, to simultaneously profile host transcriptional responses and microbial colonisation. We establish a dual-visualisation protocol that enables bacterial cells and plant transcripts to be imaged in the same sample while preserving Arabidopsis root architecture.

As a test case, we show that this approach enables the observation of distinct spatial colonisation patterns of Agrobacterium and Pseudomonas along Arabidopsis roots. Notably, co-detection reveals a spatial association between Pseudomonas colonisation and host cells expressing defence-associated genes, directly linking bacterial colonisation with local transcriptional responses of the host. We are further adapting this platform to investigate how environmental stresses and altered host signalling shape microbiome colonisation and cell state-specific gene expression patterns. Together, this work provides a powerful spatial framework for studying plant-microbiome interactions in intact plant tissues.