Faster growth enhances low carbon fuels and commodity chemcial production through gas fermentation

Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Acetogens are particularly attractive biocatalysts but effects of the key physiological parameter – specific growth rate (μ) – on acetogen metabolism and the gas fermentation bioprocess have not been established yet. Here, we investigate the μ-dependent bioprocess performance of the model-acetogen Clostridium autoethanogenum in CO and syngas (CO+CO2+H2) grown chemostat cultures and assess systems-level metabolic responses using gas analysis, metabolomics, transcriptomics, and metabolic modelling. We were able to obtain steady-states up to μ ~2.8 day-1 (~0.12 h-1) and show that faster growth supports both higher yields and productivities for reduced by-products ethanol and 2,3-butanediol. Transcriptomics data revealed differential expression of 1,337 genes with increasing μ and suggest that C. autoethanogenum uses transcriptional regulation to a large extent for facilitating faster growth. Metabolic modelling showed significantly increased fluxes for faster growing cells that were, however, not accompanied by gene expression changes in key catabolic pathways for CO and H2 metabolism. Cells thus seem to maintain sufficient “baseline” gene expression to rapidly respond to CO and H2 availability without delays to kick-start metabolism. Our work advances understanding of transcriptional regulation in acetogens and shows that faster growth of the biocatalyst improves the gas fermentation bioprocess. RNA sequencing of CO-grown or syngas-grown Clostridium autoethanogenum chemostat cultures at three specific growth rates; 20 samples in total with various number of biological replicate samples

气体发酵（Gas fermentation）可实现无化石碳的可持续燃料与化学品生产，同时可利用产气微生物对气态及固态废弃物进行资源化回收。生物工艺开发、生物催化剂代谢的系统级分析以及细胞工厂工程技术的进步，正推动该商业化技术的大规模部署。产乙酸菌（Acetogens）是一类极具应用潜力的生物催化剂，但关键生理参数——比生长速率（specific growth rate, μ）对产乙酸菌代谢及气体发酵工艺的影响尚未得到明确阐释。本研究以模式产乙酸菌自体乙醇梭菌（Clostridium autoethanogenum）为研究对象，在以CO及合成气（syngas，CO+CO₂+H₂）为碳源的恒化培养体系中，探究其比生长速率依赖的工艺性能，并通过气体分析、代谢组学（metabolomics）、转录组学（transcriptomics）及代谢建模（metabolic modelling）手段开展系统级代谢响应分析。本研究成功获得了比生长速率最高达~2.8 d⁻¹（~0.12 h⁻¹）的稳态培养体系，结果显示更快的生长速率可同时提升还原型副产物乙醇与2,3-丁二醇的产率及生产强度。转录组学数据分析显示，随着比生长速率提升，共有1337个基因呈现差异表达，提示自体乙醇梭菌主要通过转录调控机制实现快速生长。代谢建模结果表明，快速生长的细胞代谢通量显著提升，但CO及H₂代谢关键分解代谢途径的基因表达并未发生显著变化。由此推测，该菌株可维持足够的“基线”基因表达水平，从而能够快速响应CO与H₂的可利用性，无延迟地启动代谢过程。本研究加深了对产乙酸菌转录调控机制的理解，并证实提升生物催化剂的生长速率可优化气体发酵工艺。本数据集包含以CO或合成气为碳源培养的自体乙醇梭菌恒化培养物的转录组测序数据，共涵盖3个比生长速率条件，总计20个样本，包含不同数量的生物学重复样本。