Cultivation

The aim of the cultivation was to characterize the carbon dioxide fixation in E. coli by an appropriate process. For this approach we wanted to establish a fermentation process, where E. coli is growing first under aeration to obtain aerobic growth conditions to determine the carbon dioxide fixation of the RuBisCo and the Carboxysome afterwrds under this condition, as well as conditions were oxygen is limited, but still aeration takes place. Besides we wanted to ensure that an effective carbon dioxide fixation would be measured. Therefore we gased in additional carbon dioxide, resulting in an 10 fold hihger atmospheric concentraction of 0,312 %. Besides there were no experience described in litarature how much carbon dioxide can be used by a hetereotrophic bacteria like E. coli. To determine even the slightest change in the carbon dioxide balance a the very sensitive Qubit Analyzer was used for the carbon dioxide fixation...
Besides the complex equilibrium of carbon dioxide (CO₂) and bicarbonate (HCO₃^-) as shwon in Figure 1 have to be considered. One aspect is that the higher concentration of carbon dioxide is inhibiting hte bacterial growth by stressing the cell to maintain the intracelluar pH value and decreasing the pH optimum of its enzymes when the cell is not able to regulate the pH anymore. A higher concentration of carbon dioxide (CO₂) is archieved by excess pressure, a higher stirrer speed or lower pH value. This parameter are also optimal for an efficient oxygen supply of the cell, but the problem is that carbon dioxide is better soulable than oxygen in water so that it must be evaluate how much carbon dioxde the cell tolerate and how much oxygen is dispensble for the implemtation of the process.

Figure 1: Carbonate equilibrium. For an optimal process a consideration of how much carbon dioxide can be tolerated by the cell is needed.

For the design of an appropiate process for the measurement of CO2 fixation the system shown in Figure 2 was established. In this system the reactor is gased in with a mixure of carbon dioxe, in a total amount of 0,312% and air. The flow rate was set up and verified to 334,26 ml/min.
Because there are no reported experience how much carbon dioxide can be used by an organism which is normaly not able to use carbon dioxde, but produce it, the very sensitive Qubit Analyzer was used for the quantification of carbon dioxide. But because of its sensitivty the exhaust gas of the reactor needs to be diluted, to avoid an overload of the Qubit Analyzer. This is realized by another gas mixure with air, so that only 4% of the exhaust gas of the reactor are analyzed in the Qubit Analyzer. But as shown in the final cultivation process the measurement is still very sensitive and the calibration was also possible without some fluctations due to the reduced amount of analyzer.
To obtain an constant flow to the Qubit Analyzer and excess pressure of the reacotr is neccessary, and also a pump must be established between the displacer of the 4% of the exhaust gas and the reacotr avoiding tailback of the püressure into the reactor and unstable growth conditions. The same problem occurs afterwards when the flow rate needs to be limited for the Qubitr Analyzer to 150 ml/min, while for the gas mixure higher flow rates need to bee perfomred. Therefore gas outlet was established to avoid a second tailback. Apart the cool traps are used for dehydration of the exhaust gas, because the measurement of carbon dioxide within the Qubit Analyzer is performed within infra red detection and therefore dry gas are needed. Additional to the cooling traps Mixure of carbon dioxde and air of the exhaust gas because the Qubit analyzer is too sensitive.
Avoiding tailback by additional pump -> pulsing Figure 4

Figure 2: Schematic construction of the reactor for the measurement of carbon dioxide fixation in the hetereotrophic bacteria E. coli.

Figure 3: Calibration 10% of the exhaust gas (no pulsing). Higher concentration of the fermentation could not be recorded with this high portion of exhaust gas from the reactor.

Figure 4: Calibration 4%, which where used for establishment of the final process and the calibration in Figure 5.

Figure5x: Calibration by linear fit of the output signal of the qubit analyzer to determine the carbon dioxide fixation.

Equation to calculate the concentration of carbon dioxide from the output of the Qubit Analyzer
x = y - 1555,34754 / 4,10739
this needs to be estimated by the portion of exhaust gas from the reactor to quantify the amount of carbon dioxide precisely
Estimation an measurement shows the same result indicating the accuracy of the system!

Figure 6: Comparision of the calibration by the measured carbon dioxide using the Qubit Analyzer and calculation from the measured flow rates of the system.

Long time process optimization were perfomred to find appropiate conditions for the cultivation, where there is first an efficient supply with oxygen and limitation of oxygen afterwads so that the carbon dioxide fixation can be characterized and compared under both condtions ideally. For this approach we have identified an inocolum of OD₆₀₀ = 0.03 as ideal, ensuring a longer time under aerobic growth conditions. A pH-value of 7,1 allowing relative weak fluctations in the carbon dioxide signal, compared to lower pH values as one aspect. And reducing the additional salt load in comparision to higher pH values as the other aspect. Beside the excess pressure was kept by 0,1 mbar to obtain enough pressure for the displacer of the exhaust gas and avoiding to much pressure for a higher solubility of carbon dioxide resulting in a longer lag-phase because of the intracellular stress. The stirrer spedd of 600 rpm was turned out to be usable for aerobic conditions, resulting also in oxygen limitations after some time. But a faster oxygen limitation is probably diserable and can be archiev simple be the reducing of the stirrer speed. Apart the gas entry of carbon dioxide and oxygen was kept constante in all experiments 334,26 ml/min to obtain stable conditions of the gas mixure as the gas entry can be affected by other parameters like the stirrer speed or the excess pressure. Furthermore the temperature of 37 °C was never changed to obtain optimal growth conditions of E. coli.
After the development of the cultivation process for the measurement of carbon dioxde fiaxtion in a hetereotrophic bacteria, the process shown in Figure 7 shows the desired requirements for the quantification, as there is first a phase of full oxygen supply, which dreases in the exponentiell phase with the bacterial growth to end up in the desired oxygen limitation! With this system a quantification of the carbon dioxide fixation of a organism that is normal not able to use carbon dioxide as a substrate in quantitative amounts should be able up to now!

Figure 7: Successfull cultivation process for the measurement of carbon dioxide.

References

Sage, Rowan F. „Variation in the K(cat) of Rubisco in C(3) and C(4) Plants and Some Implications for Photosynthetic Performance at High and Low Temperature“. Journal of Experimental Botany 53, no. 369 (2002): 609–20.
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