Differential gene expression in planktonic and sessile cell populations of Clostridium (Ruminiclostridium) thermocellum and their contributions to cellulose bioconversion

Clostridium thermocellum employs cell-bound cellulosomes as its primary enzymatic toolset for cellulose and hemicellulose breakdown. Cellulosome binding to cellulosic substrates and, by extension, the bacterium’s adherence to cellulose surfaces is required for efficient hydrolysis. The adherent bacteria (i.e., sessile or biofilm cells) may freely revert to the non-adherent form (i.e., planktonic cells) through generation of offspring cells or due to microenvironment constraints such as limited surface area. The two cell populations co-exist, are interdependent and have different contributions to the bioconversion of carbon substrates. We developed a novel bioreactor design to culture and rapidly harvest sessile and planktonic cell populations for omics studies. Distinct physiological changes within the different cell populations were identified through RNA-seq analyses, and 1,958 genes had a minimum of two-fold differential expression. Results suggest that sessile populations are metabolically active and fit for rapid proliferation while planktonic populations turn on persistence and survival mechanisms. This is unlike classic biofilms that are long-lasting slow-growing persistent communities. We illustrate the changes in the central carbon metabolism (from cellulose to dead-end metabolites), nutrient transport across membranes, expression of cellulosomal genes, activation of important biosynthetic pathways, oxidative stress, sporulation, flagellar motility and chemotaxis. For example, the MsrA (peptide methionine sulfoxide reductase) gene - a primary mechanism against oxidative stress - was more than fifteen-fold overexpressed in planktonic cells. Understanding these cellular responses will help the genetic engineering of the species for use in large scale conversion of cellulosic materials to liquid fuels.