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Background   Clostridium (Ruminiclostridium) thermocellum  is a model fermentative anaerobic thermophile being studied and engineered for consolidated bioprocessing of lignocellulosic feedstocks into fuels and chemicals. Engineering efforts have resulted in significant improvements in ethanol yields and titers although further advances are required to make the bacterium industry-ready. For instance, fermentations at lower pH could enable co-culturing with microbes that have lower pH optima, augment productivity, and reduce buffering cost.  C. thermocellum  is typically grown at neutral pH, and little is known about its pH limits or pH homeostasis mechanisms. To better understand  C. thermocellum  pH homeostasis we grew strain LL1210 ( C. thermocellum  DSM1313  Δhpt ΔhydG Δldh Δpfl Δpta - ack ), currently the highest ethanol producing strain of  C. thermocellum , at different pH values in chemostat culture and applied systems biology tools.    Results   Clostridium thermocellum  LL1210 was found to be growth-limited below pH 6.24 at a dilution rate of 0.1 h −1 . F 1 F 0 -ATPase gene expression was upregulated while many ATP-utilizing enzymes and pathways were downregulated at pH 6.24. These included most flagella biosynthesis genes, genes for chemotaxis, and other motility-related genes (> 50) as well as sulfate transport and reduction, nitrate transport and nitrogen fixation, and fatty acid biosynthesis genes. Clustering and enrichment of differentially expressed genes at pH values 6.48, pH 6.24 and pH 6.12 (washout conditions) compared to pH 6.98 showed inverse differential expression patterns between the F 1 F 0 -ATPase and genes for other ATP-utilizing enzymes. At and below pH 6.24, amino acids including glutamate and valine; long-chain fatty acids, their iso-counterparts and glycerol conjugates; glycolysis intermediates 3-phosphoglycerate, glucose 6-phosphate, and glucose accumulated intracellularly. Glutamate was 267 times more abundant in cells at pH 6.24 compared to pH 6.98, and intercellular concentration reached 1.8 μmol/g pellet at pH 5.80 (stopped flow).    Conclusions   Clostridium thermocellum  LL1210 can grow under slightly acidic conditions, similar to limits reported for other strains. This foundational study provides a detailed characterization of a relatively acid-intolerant bacterium and provides genetic targets for strain improvement. Future studies should examine adding gene functions used by more acid-tolerant bacteria for improved pH homeostasis at acidic pH values.    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1095-y) contains supplementary material, which is available to authorized users.

Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics