Automated bioreactor sampling – process trigger sampling for enhancing microbial strain engineering and characterization

We have integrated a Flownamics® Seg-Flow® 4800 Automated On-line Sampling System with an Eppendorf DASGIP® Parallel Bioreactor System using the platform-independent Object Linking and Embedding for Process Control (OPC) communication protocol. The bidirectional communication we established between the Eppendorf and Flownamics equipment enabled us to implement remote-controlled, automated process trigger sampling as a vital part of our yeast strain fitness studies and engineering workflow. By implementing this functionality in our experiments, we were better able to time sample collection at moments critical to our systems biology approach to studying yeast fitness for improved industrial fermentation. Our analysis of the samples collected by this automated process trigger sampling method was used to generate a genetic blueprint for an engineered yeast strain with superior fitness during fermentation. In the example presented here, we investigated fitness during the fermentation of Miscanthus plant hydrolysate under continuous culture conditions. We executed on our genetic design and characterized our engineered yeast strain, again making use of the bidirectional communication between the Eppendorf and Flownamics equipment to simplify our organization of data. Ultimately, this characterization demonstrates that our engineered strain is more fit relative to both the lab and the industrial yeast strains on which our strain design was based. In conclusion, integration of the on-line sampling system with the bioreactor system facilitated our engineering and screening processes with the objective of improving yeast strain fitness and, consequently, bioethanol productivity.