Fig. 3

Analyses of marker genes and proteins and functions of selected processes in aerial and root cells. a Northern blot analysis of selected RNAs with higher expression in aerial (AE) and in root (RT) samples, identified by RNA seq. VMA1, RDN18 and RDN25 are unregulated controls. b Levels of GFP-labeled proteins (expected to be more highly expressed in aerial or root samples based on the expression data) in 3-day-old colonies of respective BR-F derived strains (Additional file 2: Table S7). Vertical cross-sections of colonies were analyzed by 2PE-CM. Green, GFP fluorescence. c 2PE-CM of aerial and root cells of 3-day-old BR-F-Arg1p-GFP colonies (left). Western blot (WB) of Arg1p-GFP from aerial (AE) and root (RT) cells (right). In aerial cells, autophagy is active and cytosolic Arg1p-GFP is delivered to vacuoles (indicated by white arrows) (left) and degraded as indicated by free GFP in WB (right). d Model of localization of cells with aerial features (in green) and root features (in red) in 3-day-old colony biofilms based on the levels of GFP-labeled proteins in different colony areas as shown in B. Dotted white line indicates border between cells collected as aerial cells and root cells (upper panel). One feature of this model is a spatial overlap between cells with root features and cells embedded in ECM and between cells with aerial features and ECM-free cells, as described in [3]; ECM is indicated by yellow color in the lower panel of the scheme (reprinted from [3])