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). Overall design: 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).