Compare microbial communities in extremely well-defined conditions

About the Parallel Cultivation Platform

The Parallel Cultivation Platform consists of multiple bioreactor units. Its flexible arrangement allows for cultivation and investigation of most chemotrophic and phototrophic microbial communities in extremely well-defined conditions

Delft University of Technology
chemotrophic, phototrophic, redox conditions

Freqently asked questions

This platform is specifically suitable for investigating the impact of dynamic process conditions on the functional and molecular development of microbial communities. In fact, dynamic process conditions are typical for many natural and man-made ecosystems, such as day-night cycles, seasonal variations and variable substrate supply rates. However, to date, they remain largely unexplored in microbial ecology.

The flexible arrangement of analytical equipment enables the investigation of virtually all redox conditions of interest in microbial ecology, ranging from aerobic to strictly anaerobic conditions. Please see the figure and technical details below for a schematic overview of a potential experimental set-up.

The platform consists of 40 temperature-controlled stirred bioreactor units that can be operated at 0.5 to 2.0 liter liquid volume. These bioreactors are equipped with an extensive set of on- and off-line analytical facilities. Further, we distuinguish a standard and an intensive experimental set-up. Please consult the technical details below for more info.


Schematic figure of experimental set-up of reactors in the Parallel Cultivation Platform at TUD.
Detailed overview of the experimental set-up of reactors in the Parallel Cultivation Platform at TUD. The different components of the set-up are described in the text. This is shown to exemplify the conceptual set-up of the different reactor types included in UNLOCK.

Additional platform benefits

In this platform, supply of both gaseous and liquid substrates and removal of effluent is conducted with computer-controlled systems. Herewith, we can impose a wide variation of feeding regimes to the system (see figure). Moreover, the combination of detailed on-line measurements with a dynamic feeding regime provides an unprecedented high resolution of functional system information. This makes it specifically suitable for dynamic process modelling and analysis. Evidently, this does not mean that bioreactors cannot be operated as chemostat or Sequencing Batch Reactor. However, we have repeatedly demonstrated that inclusion of (periodic) dynamics in operation results in superior systems characterization and process identification (Johnson el al., 2009; Kleerebezem & van Loosdrecht, 2008).

Another specific feature included in the experimental set-up, is the ability to uncouple the liquid and solid (biomass) retention time in the process. This is done through a distinct channel for removal of the mixed fermentation broth and liquid effluent removal via an ultrafiltration membrane. User-friendly data interpretation software is under development that allows for direct analysis and inter-reactor comparison of all data generated in the experiments.

Experimental units

There are two types of experimental units that are different in terms of the intensity of process analysis and experimental aims:

  • The standard experimental set-up (30 units) is equipped with on-line analytical equipment. This includes Liquid electrode measurements for pH, Dissolved Oxygen (DO) concentration, Oxidation Reduction Potential (ORP), and ion specific electrode measurements (ISE, not shown in figure). Off-gas analysis after drying of the gas is conducted with a multi-channel Mass Spectrometer (MS). This low-maintenance set-up is specifically suitable for medium to long-term experiments (1 to 12 months). Further, the set-up allows the identification of the functional development of a microbial community in well-defined conditions over many generations. When working with non-defined microbial communities these experiments typically concern microbial competition and succession studies. For defined communities on the other hand, these systems are specifically suitable for directed evolution studies. On-line analysis of crucial process variables allow for direct identification of major changes in functional process properties, whicht may indicate potential extra analyses. 

  • The intensive experimental set-up (10 units, extra analytical facilities shown in green in figure) is equipped with an ultrafiltration sampling unit. It allows continuous supply of solid-free fermentation broth for periodic sampling and on-line analysis by High Pressure Liquid Chromatrography (HPLC), Gas Chromatography (GC), and Ion Chromatography (IC). Liquid samples are available for off-line analysis through a wide range of methods, e.g. ICP-MS, LC-MS, GC-MS. This intensive experimental setup is more suitable for short-term experiments (1 to 10 weeks). The aim could be to assess the effect of a specific process variable (e.g. pH, temperature, influent composition) on the functional and molecular development of a specific microbial community. A high-intensity experiment provides a high-resolution comparative analysis of the response of the system to the change imposed.

Integration with other platforms

The Parallel Cultivation Platform at Delft University of Technology has direct links with the other platforms of UNLOCK in Wageningen. For instance, the Biodiscovery Platform can provide defined synthetic communities to be analyzed. Vice versa, sample processing platform of the Biodiscovery Platform facilitates a wide range of molecular analyses of samples from the Parallel Cultivation Platform. In this way, the link between functional and molecular system properties can be investigated, which is of crucial importance for this field of research. Additionally, the cloud-based FAIR Data Platform facilitates storage and accessibility of both functional and molecular data obtained in the experiments conducted at the Parallel Cultivation Platform.