Single-cell computational analysis of light harvesting in a flat-panel photo-bioreactor

A custom 3D printed paddlewheel improves growth in flat panel photobioreactor

One of the main challenges with using flat panel photobioreactors for algal growth is uneven mixing and settling of cells in corners, especially when bubbling is the only method used for mixing. In order to improve mixing in our flat panel reactor, we designed a custom paddlewheel. Paddlewheels are frequently used in outdoor algae raceway ponds to improve mixing and we are taking advantage of the same principle for mixing in the reactor. The paddlewheel is easily integrated into our PSI FMT150 1-L flat panel photobioreactor and is printed on a 3D printer using high temperature poly lactic acid (HT-PLA). With the inclusion of an annealing step, the paddlewheel is autoclavable. Addition of the paddlewheel in the reactor minimized cell settling and improved algal growth, as evidenced by a nearly 40% increase in oxygen production rates. Nutrient dispersion and utilization in the culture was also improved as evidenced by a corresponding 38% decrease in CO2 concentration. The paddlewheel device presented here is a cost-effective method for improving algal growth in a flat panel photobioreactor.

Asymmetric survival in single-cell lineages of cyanobacteria in response to photodamage

Oxygenic photosynthesis is driven by the coupled action of the light-dependent pigment-protein complexes, photosystem I and II, located within the internal thylakoid membrane system. However, photosystem II is known to be prone to photooxidative damage. Thus, photosynthetic organisms have evolved a repair cycle to continuously replace the damaged proteins in photosystem II. However, it has remained difficult to deconvolute the damage and repair processes using traditional ensemble approaches. Here, we demonstrate an automated approach using time-lapse fluorescence microscopy and computational image analysis to study the dynamics and effects of photodamage in single cells at subcellular resolution in cyanobacteria. By growing cells in a two-dimensional layer, we avoid shading effects, thereby generating uniform and reproducible growth conditions. Using this platform, we analyzed the growth and physiology of multiple strains simultaneously under defined photoinhibitory conditions stimulated by UV-A light. Our results reveal an asymmetric cellular response to photodamage between sibling cells and the generation of an elusive subcellular structure, here named a 'photoendosome,' derived from the thylakoid which could indicate the presence of a previously unknown photoprotective mechanism. We anticipate these results to be a starting point for further studies to better understand photodamage and repair at the single-cell level.

Optogenetic control of beta-carotene bioproduction in yeast across multiple lab-scales

Optogenetics arises as a valuable tool to precisely control genetic circuits in microbial cell factories. Light control holds the promise of optimizing bioproduction methods and maximizing yields, but its implementation at different steps of the strain development process and at different culture scales remains challenging. In this study, we aim to control beta-carotene bioproduction using optogenetics in Saccharomyces cerevisiae and investigate how its performance translates across culture scales. We built four lab-scale illumination devices, each handling different culture volumes, and each having specific illumination characteristics and cultivating conditions. We evaluated optogenetic activation and beta-carotene production across devices and optimized them both independently. Then, we combined optogenetic induction and beta-carotene production to make a light-inducible beta-carotene producer strain. This was achieved by placing the transcription of the bifunctional lycopene cyclase/phytoene synthase CrtYB under the control of the pC120 optogenetic promoter regulated by the EL222-VP16 light-activated transcription factor, while other carotenogenic enzymes (CrtI, CrtE, tHMG) were expressed constitutively. We show that illumination, culture volume and shaking impact differently optogenetic activation and beta-carotene production across devices. This enabled us to determine the best culture conditions to maximize light-induced beta-carotene production in each of the devices. Our study exemplifies the stakes of scaling up optogenetics in devices of different lab scales and sheds light on the interplays and potential conflicts between optogenetic control and metabolic pathway efficiency. As a general principle, we propose that it is important to first optimize both components of the system independently, before combining them into optogenetic producing strains to avoid extensive troubleshooting. We anticipate that our results can help designing both strains and devices that could eventually lead to larger scale systems in an effort to bring optogenetics to the industrial scale.

Microbial lifelines in bioprocesses: From concept to application

Bioprocesses are scaled up for the production of large product quantities. With larger fermenter volumes, mixing becomes increasingly inefficient and environmental gradients get more prominent than in smaller scales. Environmental gradients have an impact on the microorganism's metabolism, which makes the prediction of large-scale performance difficult and can lead to scale-up failure. A promising approach for improved understanding and estimation of dynamics of microbial populations in large-scale bioprocesses is the analysis of microbial lifelines. The lifeline of a microbe in a bioprocess is the experience of environmental gradients from a cell's perspective, which can be described as a time series of position, environment and intracellular condition. Currently, lifelines are predominantly determined using models with computational fluid dynamics, but new technical developments in flow-following sensor particles and microfluidic single-cell cultivation open the door to a more interdisciplinary concept. We critically review the current concepts and challenges in lifeline determination and application of lifeline analysis, as well as strategies for the integration of these techniques into bioprocess development. Lifelines can contribute to a successful scale-up by guiding scale-down experiments and identifying strain engineering targets or bioreactor optimisations.

Modeling and Simulation of Photobioreactors with Computational Fluid Dynamics—A Comprehensive Review

Computational Fluid Dynamics (CFD) have been frequently applied to model the growth conditions in photobioreactors, which are affected in a complex way by multiple, interacting physical processes. We review common photobioreactor types and discuss the processes occurring therein as well as how these processes have been considered in previous CFD models. The analysis reveals that CFD models of photobioreactors do often not consider state-of-the-art modeling approaches. As a comprehensive photobioreactor model consists of several sub-models, we review the most relevant models for the simulation of fluid flows, light propagation, heat and mass transfer and growth kinetics as well as state-of-the-art models for turbulence and interphase forces, revealing their strength and deficiencies. In addition, we review the population balance equation, breakage and coalescence models and discretization methods since the predicted bubble size distribution critically depends on them. This comprehensive overview of the available models provides a unique toolbox for generating CFD models of photobioreactors. Directions future research should take are also discussed, mainly consisting of an extensive experimental validation of the single models for specific photobioreactor geometries, as well as more complete and sophisticated integrated models by virtue of the constant increase of the computational capacity.

Characterization of single-phase flow hydrodynamics in a Berty reactor using computational fluid dynamics (CFD)

This work studies the flow characteristics in a Berty reactor, a gradientless reactor for kinetic studies, using three-dimensional (3D) computational fluid dynamics (CFD), and a non-ideal continuous stirred tank reactor (CSTR) model.

How Do Operational and Design Parameters Effect Biomass Productivity in a Flat-Panel Photo-Bioreactor? A Computational Analysis

Optimal production of microalgae in photo-bioreactors (PBRs) largely depends on the amount of light intensity received by individual algal cells, which is affected by several operational and design factors. A key question is: which process parameters have the highest potential for the optimization of biomass productivity? This can be analyzed by simulating the complex interplay of PBR design, hydrodynamics, dynamic light exposure, and growth of algal cells. A workflow was established comprising the simulation of hydrodynamics in a flat-panel PBR using computational fluid dynamics, calculation of light irradiation inside the PBR, tracing the light exposure of individual cells over time, and calculation the algal growth and biomass productivity based on this light exposure. Different PBR designs leading to different flow profiles were compared, and operational parameters such as air inlet flowrate, microalgal concentration, and incident light intensity were varied to investigate their effect on PBR productivity. The design of internal structures and lighting had a significant effect on biomass productivity, whereas air inlet flowrate had a minimal effect. Microalgal concentration and incident light intensity controlled the amount of light intensity inside the PBR, thereby significantly affecting the overall productivity. For detailed quantitative insight into these dependencies, better parameterization of algal growth models is required.

Computational Analysis of Dynamic Light Exposure of Unicellular Algal Cells in a Flat-Panel Photobioreactor to Support Light-Induced CO2 Bioprocess Development

Cyanobacterial cell factories trace a vibrant pathway to climate change neutrality and sustainable development owing to their ability to turn carbon dioxide-rich waste into a broad portfolio of renewable compounds, which are deemed valuable in green chemistry cross-sectorial applications. Cell factory design requires to define the optimal operational and cultivation conditions. The paramount parameter in biomass cultivation in photobioreactors is the light intensity since it impacts cellular physiology and productivity. Our modeling framework provides a basis for the predictive control of light-limited, light-saturated, and light-inhibited growth of the Synechocystis sp. PCC 6803 model organism in a flat-panel photobioreactor. The model here presented couples computational fluid dynamics, light transmission, kinetic modeling, and the reconstruction of single cell trajectories in differently irradiated areas of the photobioreactor to relate key physiological parameters to the multi-faceted processes occurring in the cultivation environment. Furthermore, our analysis highlights the need for properly constraining the model with decisive qualitative and quantitative data related to light calibration and light measurements both at the inlet and outlet of the photobioreactor in order to boost the accuracy and extrapolation capabilities of the model.

A microfluidic photobioreactor for simultaneous observation and cultivation of single microalgal cells or cell aggregates

Microalgae are an ubiquitous and powerful driver of geochemical cycles which have formed Earth’s biosphere since early in the evolution. Lately, microalgal research has been strongly stimulated by economic potential expected in biofuels, wastewater treatment, and high-value products. Similar to bacteria and other microorganisms, most work so far has been performed on the level of suspensions which typically contain millions of algal cells per millilitre. The thus obtained macroscopic parameters average cells, which may be in various phases of their cell cycle or even, in the case of microbial consortia, cells of different species. This averaging may obscure essential features which may be needed for the correct understanding and interpretation of investigated processes. In contrast to these conventional macroscopic cultivation and measuring tools, microfluidic single-cell cultivation systems represent an excellent alternative to study individual cells or a small number of mutually interacting cells in a well-defined environment. A novel microfluidic photobioreactor was developed and successfully tested by the photoautotrophic cultivation of Chlorella sorokiniana. The reported microbioreactor facilitates automated long-term cultivation of algae with controlled temperature and with an illumination adjustable over a wide range of photon flux densities. Chemical composition of the medium in the microbioreactor can be stabilised or modulated rapidly to study the response of individual cells. Furthermore, the algae are cultivated in one focal plane and separate chambers, enabling single-cell level investigation of over 100 microcolonies in parallel. The developed platform can be used for systematic growth studies, medium screening, species interaction studies, and the thorough investigation of light-dependent growth kinetics.