Fig. 2: SmT resolves the microbial profile and host transcriptome at microscopic resolution.

a, A Toluidine blue-stained bright-field image of a 14-µm thick longitudinal A. thaliana leaf section (left) and the fluorescent cDNA footprint (right) of the same section from the tissue optimization experiment. b, Left, fluorescence image of an intact A. thaliana leaf syringe-infiltrated (yellow square) with mCherry-tagged Pst DC3000 bacteria. Middle, a 14-µm thick longitudinal section from the same leaf was analyzed using a 50% poly-d(T), 25% P799 and 25% P902 array, revealing the spatial capture of Pst DC3000 16S rRNA molecules. Right, spatial distribution of PR1 gene expression in the same leaf section. Scale bars: 1 mm. c, Pearson correlation coefficient and the corresponding two-tailed significance test of bacterial 16S rRNA, eukaryotic 18S rRNA/ITS and A. thaliana molecules captured in leaf 1 with a multimodal array containing 10% poly-d(T), 45% 16S rRNA and 45% 18S rRNA/ITS probes and with 100% 16S rRNA or 18S rRNA/ITS and poly-d(T) arrays. In all correlations, P = 0. d, Bray–Curtis similarity for bacterial and fungal taxa captured on different arrays, organized by hierarchical clustering. e, Experimental validation of SmT by amplicon sequencing. f,g, Numbers of bacterial and archaeal taxa detected using the two methods in a representative sample of four leaves from two plants are compared qualitatively using a Venn diagram (f) and quantitatively using NMDS (g). NMDS, non-metric multidimensional scaling.