Spatial transcriptome unveils the heterogeneity between subpopulations of Bacillus subtilis surface-associated communities

Bacillus subtilis has been extensively used as a model for molecular studies on biofilm formation. These studies encompassed the development of complex macro-colonies on agar, the formation of pellicles at the air-liquid interface, and lately the formation of submerged architectural biofilms at the solid-liquid interface. Beside similarities, these multicellular communities also display considerable heterogeneity at the structural, chemical and biological levels. Here we use RNA-seq to analyze nine different spatio-physiological conditions, including the three biofilm populations (colony, pellicle, and submerged). From shaken planktonic cultures, the exponential (EX) and the stationary (ST) phase were collected. The stationary phase cultures were used to inoculate static liquid cultures and semi-solid agar plates, which were incubated for 24 hours. From the static liquid culture, three localized compartments were collected separately: the pellicle (PL) formed at the air-liquid interface, the submerged biofilm (SB) formed on the solid-liquid interface, and the free detached cells (DC) between these two compartments were collected separately. From the semi-solid agar plate, four localized compartments were collected separately: the mother colony (MC), corresponding to the inoculation site from which the swarm has developed as a mature macrocolony; the base (BS) of the dendrites in the early biofilm form; the dendrites (DT), a monolayer of cells ready to form later the biofilm; and the tips (TP) formed of motile and highly dividing cells. the base (BS) of the dendrites in the early biofilm form; the dendrites (DT), a monolayer of cells ready to form later the biofilm; and the tips (TP) formed of motile and highly dividing cells. For each compartment, three independent samples were taken as biological replicates and subjected to transcriptome analysis (RNA-Seq).