A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter

For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization. Further, a recursive algorithm for on-line growth rate estimation has been implemented. The employed Kalman filtering approach based on a very general state model retains the flexibility of the used control type and can be easily adapted to other bioreactor designs. Within several minutes it can converge to robust, accurate growth rate estimates. This is particularly useful for directed evolution experiments or studies on metabolic challenges, as it allows direct monitoring of the population fitness.

[1]  Geraldine Naughton,et al.  Multilevel Approach of a 1-Year Program of Dietary and Exercise Interventions on Bone Mineral Content and Density in Metabolic Syndrome – the RESOLVE Randomized Controlled Trial , 2015, PloS one.

[2]  Maitreya J. Dunham,et al.  Design and Use of Multiplexed Chemostat Arrays , 2013, Journal of visualized experiments : JoVE.

[3]  B. Görke,et al.  Carbon catabolite repression in bacteria: many ways to make the most out of nutrients , 2008, Nature Reviews Microbiology.

[4]  D. Metzgar,et al.  Development of a novel continuous culture device for experimental evolution of bacterial populations , 2007, Applied Microbiology and Biotechnology.

[5]  R. Hengge-aronis,et al.  Survival of hunger and stress: The role of rpoS in early stationary phase gene regulation in E. coli , 1993, Cell.

[6]  Sébastien Rodrigue,et al.  A Small-Volume, Low-Cost, and Versatile Continuous Culture Device , 2015, PloS one.

[7]  N. Fujita,et al.  Growth phase-dependent modification of RNA polymerase in Escherichia coli , 1991, Molecular and General Genetics MGG.

[8]  Eric Klavins,et al.  A Low Cost, Customizable Turbidostat for Use in Synthetic Circuit Characterization , 2014, ACS synthetic biology.

[9]  James D. Hamilton.  Time Series Analysis , 1994 .

[10]  J. Leigh,et al.  Nitrogen regulation in bacteria and archaea. , 2007, Annual review of microbiology.

[11]  Gavin Sherlock,et al.  Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1. , 2012, FEMS yeast research.

[12]  R. E. Kalman,et al.  A New Approach to Linear Filtering and Prediction Problems , 2002 .

[13]  T. Hwa,et al.  Growth Rate-Dependent Global Effects on Gene Expression in Bacteria , 2009, Cell.

[14]  Remy Chait,et al.  Evolutionary paths to antibiotic resistance under dynamically sustained drug selection , 2011, Nature Genetics.

[15]  Metabolic changes underlying the higher accumulation of glutathione in Saccharomyces cerevisiae mutants , 2011, Applied Microbiology and Biotechnology.

[16]  David Gresham,et al.  The enduring utility of continuous culturing in experimental evolution. , 2014, Genomics.

[17]  W. Bennett.  Measurement of manganese amelioration of cadmium toxicity inChlorella pyrenoidosa using turbidostat culture , 1990, Archives of environmental contamination and toxicology.

[18]  E. Blumwald,et al.  Salt adaptation of the cyanobacterium synechococcus 6311 growing in a continuous culture (turbidostat). , 1984, Plant physiology.

[19]  David R. Liu,et al.  A System for the Continuous Directed Evolution of Biomolecules , 2011, Nature.