A Microfluidic Platform for Long-Term Monitoring of Algae in a Dynamic Environment

Reliable cell retention of mammalian suspension cells in microfluidic cultivation chambers

Microfluidic cultivation, with its high level of environmental control and spatio-temporal resolution of cellular behavior, is a well-established tool in today's microfluidics. Yet, reliable retention of (randomly) motile cells inside designated cultivation compartments still represents a limitation, which prohibits systematic single-cell growth studies. To overcome this obstacle, current approaches rely on complex multilayer chips or on-chip valves, which makes their application for a broad community of users infeasible. Here, we present an easy-to-implement cell retention concept to withhold cells inside microfluidic cultivation chambers. By introducing a blocking structure into a cultivation chamber's entrance and nearly closing it, cells can be manually pushed into the chamber during loading procedures but are unable to leave it autonomously in subsequent long-term cultivation. CFD simulations as well as trace substance experiments confirm sufficient nutrient supply within the chamber. Through preventing recurring cell loss, growth data obtained from Chinese hamster ovary cultivation on colony level perfectly match data determined from single-cell data, which eventually allows reliable high throughput studies of single-cell growth. Due to its transferability to other chamber-based approaches, we strongly believe that our concept is also applicable for a broad range of cellular taxis studies or analyses of directed migration in basic or biomedical research.

Microalgae growth in ultra-thin steady-state continuous photobioreactors: assessing self-shading effects

To disclose the net effect of light on microalgal growth in photobioreactors, self-shading and mixing-induced light–dark cycles must be minimized and discerned from the transient phenomena of acclimation. In this work, we performed experiments of continuous microalgal cultivation in small-scale photobioreactors with different thicknesses (from 2 to 35 mm): working at a steady state allowed us to describe the effect of light after acclimation, while the geometry of the reactor was adjusted to find the threshold light path that can discriminate different phenomena. Experiments showed an increased inhibition under smaller culture light paths, suggesting a strong shading effect at thicknesses higher than 8 mm where mixing-induced light–dark cycles may occur. A Haldane-like model was applied and kinetic parameters retrieved, showing possible issues in the scalability of experimental results at different light paths if mixing-induced light–dark cycles are not considered. To further highlight the influence of mixing cycles, we proposed an analogy between small-scale operations with continuous light and PBR operations with pulsed light, with the computation of characteristic parameters from pulsed-light microalgae growth mathematical modeling.

Microfluidic chemostatic bioreactor for high-throughput screening and sustainable co-harvesting of biomass and biodiesel in microalgae

As a renewable and sustainable source for energy, environment, and biomedical applications, microalgae and microalgal biodiesel have attracted great attention. However, their applications are confined due to the cost-efficiency of microalgal mass production. One-step strategy and continuous culturing systems could be solutions. However, current studies for optimization throughout microalgae-based biofuel production pipelines are generally derived from the batch culture process. Better tools are needed to study algal growth kinetics in continuous systems. A microfluidic chemostatic bioreactor was presented here, providing low-bioadhesive cultivations for algae in a cooperative environment of gas, nutrition, and temperature (GNT) involved with high throughput. The chip was used to mimic the continuous culture environment of bioreactors. It allowed simultaneously studying of 8 × 8 different chemostatic conditions on algal growth and oil production in parallel on a 7 × 7 cm² footprint. On-chip experiments of batch and continuous cultures of Chlorella. sp. were performed to study growth and lipid accumulation under different nitrogen concentrations. The results demonstrated that microalgal cultures can be regulated to grow and accumulate lipids concurrently, thus enhancing lipid productivity in one step. The developed on-chip culturing condition screening, which was more suitable for continuous bioreactor, was achieved at a half shorter time, 64-times higher throughput, and less reagent consumption. It could be used to establish chemostat cultures in continuous bioreactors which can dramatically accelerate the development of renewable and sustainable algal for CO₂ fixation and biosynthesis and related systems for advanced sustainable energy, food, pharmacy, and agriculture with enormous social and ecological benefits.

A Low-Cost Microfluidic Method for Microplastics Identification: Towards Continuous Recognition

Plastic pollution has emerged as a growing concern worldwide. In particular, the most abundant plastic debris, microplastics, has necessitated the development of rapid and effective identification methods to track down the stages and evidence of the pollution. In this paper, we combine low-cost plastic staining technologies using Nile Red with the continuous feature offered by microfluidics to propose a low-cost 3D printed device for the identification of microplastics. It is observed that the microfluidic devices indicate comparable staining and identification performance compared to conventional Nile Red staining processes while offering the advantages of continuous recognition for long-term environmental monitoring. The results also show that concentration, temperature, and residency time possess strong effects on the identification performance. Finally, various microplastics have been applied to further demonstrate the effectiveness of the proposed devices. It is found that, among different types of microplastics, non-spherical microplastics show the maximal fluorescence level. Meanwhile, natural fibers indicate better staining quality when compared to synthetic ones.

Microfluidic Microalgae System: A Review

Microalgae that have recently captivated interest worldwide are a great source of renewable, sustainable and economical biofuels. The extensive potential application in the renewable energy, biopharmaceutical and nutraceutical industries have made them necessary resources for green energy. Microalgae can substitute liquid fossil fuels based on cost, renewability and environmental concern. Microfluidic-based systems outperform their competitors by executing many functions, such as sorting and analysing small volumes of samples (nanolitre to picolitre) with better sensitivities. In this review, we consider the developing uses of microfluidic technology on microalgal processes such as cell sorting, cultivation, harvesting and applications in biofuels and biosensing.

Multiphysics microfluidics for cell manipulation and separation: a review

Multiphysics microfluidics, which combines multiple functional physical processes in a microfluidics platform, is an emerging research area that has attracted increasing interest for diverse biomedical applications. Multiphysics microfluidics is expected to overcome the limitations of individual physical phenomena through combining their advantages. Furthermore, multiphysics microfluidics is superior for cell manipulation due to its high precision, better sensitivity, real-time tunability, and multi-target sorting capabilities. These exciting features motivate us to review this state-of-the-art field and reassess the feasibility of coupling multiple physical processes. To confine the scope of this paper, we mainly focus on five common forces in microfluidics: inertial lift, elastic, dielectrophoresis (DEP), magnetophoresis (MP), and acoustic forces. This review first explains the working mechanisms of single physical phenomena. Next, we classify multiphysics techniques in terms of cascaded connections and physical coupling, and we elaborate on combinations of designs and working mechanisms in systems reported in the literature to date. Finally, we discuss the possibility of combining multiple physical processes and associated design schemes and propose several promising future directions.

Recent advances of integrated microfluidic suspension cell culture system

Microfluidic devices with superior microscale fluid manipulation ability and large integration flexibility offer great advantages of high throughput, parallelisation and multifunctional automation. Such features have been extensively utilised to facilitate cell culture processes such as cell capturing and culturing under controllable and monitored conditions for cell-based assays. Incorporating functional components and microfabricated configurations offered different levels of fluid control and cell manipulation strategies to meet diverse culture demands. This review will discuss the advances of single-phase flow and droplet-based integrated microfluidic suspension cell culture systems and their applications for accelerated bioprocess development, high-throughput cell selection, drug screening and scientific research to insight cell biology. Challenges and future prospects for this dynamically developing field are also highlighted.

Microalgae Monitoring in Microscale Photobioreactors via Multivariate Image Analysis

Microscale photobioreactors for microalgae growth represent an interesting technology for fast data production and biomass characterization; however, the small scale poses severe monitoring challenges, as traditional methods cannot be used. Non-invasive techniques are therefore needed to quantify biomass concentration and other culture properties, for example, pigment composition. To this purpose, a soft sensing approach based on multivariate image regression is proposed to exploit RGB images and/or PAM-imaging chlorophyll fluorescence. Different PLS (Partial Least Squares) regression models are used to estimate: (a) biomass concentration from the features extracted by RGB indices and/or PAM-imaging chlorophyll fluorescence measurements; and (b) Chlorophyll a content per cell from the features extracted by RGB indices and biomass concentration measurements. Every single model is aimed at characterizing the microalgae culture at different light intensities during batch growth. Results show that the proposed monitoring approach is as accurate as traditional measurement approaches and may represent a promising methodology for fast and inexpensive monitoring of microscale photobioreactors.

Versatile Microfluidic Platform for Automated Live-Cell Hyperspectral Imaging Applied to Cold Climate Cyanobacterial Biofilms

Microfluidic bioanalytical platforms are driving discoveries from synthetic biology to the health sciences. In this work, we present a platform for in vivo live-cell imaging and automated species detection in mixed cyanobacterial biofilms from cold climate environments. Using a multimodal microscope with custom optics applied to a chip with six parallel growth channels, we monitored biofilm dynamics via continuous imaging at natural irradiance levels. Machine learning algorithms were applied to the collected hyperspectral images for automatic segmentation of mixed-species biofilms into individual species of cyanobacteria with similar filamentous morphology. The coupling of microfluidic technology with modern multimodal imaging and computer vision systems provides a versatile platform for the study of cause-and-effect scenarios of cyanobacterial biofilms, which are important elements of many ecosystems, including lakes and rivers of the polar regions.

Enhancement of microalgae growth using magnetic artificial cilia

Microalgae have shown great potential as a source of biofuels, food, and other bioproducts. More recently, microfluidic devices have been employed in microalgae-related studies. However, at small fluid volumes, the options for controlling flow conditions are more limited and mixing becomes largely reliant on diffusion. In this study, we fabricated magnetic artificial cilia (MAC) and implemented them in millimeter scale culture wells and conducted growth experiments with Scenedesmus subspicatus while actuating the MAC in a rotating magnetic field to create flow and mixing. In addition, surface of MAC was made hydrophilic using plasma treatment and its effect on growth was compared with untreated, hydrophobic MAC. The experiments showed that the growth was enhanced by ten and two times with hydrophobic and hydrophilic MAC, respectively, compared with control groups which contain no MAC. This technique can be used to investigate mixing and flow in small sample volumes, and the enhancement in growth can be beneficial for the throughput of screening studies. Moreover, the methods used for creating and controlling MAC can be easily adopted in labs without microfabrication infrastructures, and they can be mastered by people with little prior experience in microfluidics.

Microfluidic and mathematical modeling of aquatic microbial communities

Aquatic microbial communities contribute fundamentally to biogeochemical transformations in natural ecosystems, and disruption of these communities can lead to ecological disasters such as harmful algal blooms. Microbial communities are highly dynamic, and their composition and function are tightly controlled by the biophysical (e.g., light, fluid flow, and temperature) and biochemical (e.g., chemical gradients and cell concentration) parameters of the surrounding environment. Due to the large number of environmental factors involved, a systematic understanding of the microbial community-environment interactions is lacking. In this article, we show that microfluidic platforms present a unique opportunity to recreate well-defined environmental factors in a laboratory setting in a high throughput way, enabling quantitative studies of microbial communities that are amenable to theoretical modeling. The focus of this article is on aquatic microbial communities, but the microfluidic and mathematical models discussed here can be readily applied to investigate other microbiomes.

Microfluidics for microalgal biotechnology

Microalgae have expanded their roles as renewable and sustainable feedstocks for biofuel, smart nutrition, biopharmaceutical, cosmeceutical, biosensing, and space technologies. They accumulate valuable biochemical compounds from protein, carbohydrate, and lipid groups, including pigments and carotenoids. Microalgal biomass, which can be adopted for multivalorization under biorefinery settings, allows not only the production of various biofuels but also other value-added biotechnological products. However, state-of-the-art technologies are required to optimize yield, quality, and the economical aspects of both upstream and downstream processes. As such, the need to use microfluidic-based devices for both fundamental research and industrial applications of microalgae, arises due to their microscale sizes and dilute cultures. Microfluidics-based devices are superior to their competitors through their ability to perform multiple functions such as sorting and analyzing small amounts of samples (nanoliter to picoliter) with higher sensitivities. Here, we review emerging applications of microfluidic technologies on microalgal processes in cell sorting, cultivation, harvesting, and applications in biofuels, biosensing, drug delivery, and nutrition.

PhenoChip: A single-cell phenomic platform for high-throughput photophysiological analyses of microalgae

Photosynthetic microorganisms are key players in aquatic ecosystems with strong potential for bioenergy production, yet their systematic selection at the single-cell level for improved productivity or stress resilience ("phenotyping") has remained largely inaccessible. To facilitate the phenotyping of microalgae and cyanobacteria, we developed "PhenoChip," a platform for the multiparametric photophysiological characterization and selection of unicellular phenotypes under user-controlled physicochemical conditions. We used PhenoChip to expose single cells of the coral symbiont Symbiodinium to thermal and chemical treatments and monitor single-cell photophysiology via chlorophyll fluorometry. This revealed strain-specific thermal sensitivity thresholds and distinct pH optima for photosynthetic performance, and permitted the identification of single cells with elevated resilience toward rising temperature. Optical expulsion technology was used to collect single cells from PhenoChip, and their propagation revealed indications of transgenerational preservation of photosynthetic phenotypes. PhenoChip represents a versatile platform for the phenotyping of photosynthetic unicells relevant to biotechnology, ecotoxicology, and assisted evolution.

Dynamic Environmental Control in Microfluidic Single-Cell Cultivations: From Concepts to Applications

Microfluidic single-cell cultivation (MSCC) is an emerging field within fundamental as well as applied biology. During the last years, most MSCCs were performed at constant environmental conditions. Recently, MSCC at oscillating and dynamic environmental conditions has started to gain significant interest in the research community for the investigation of cellular behavior. Herein, an overview of this topic is given and microfluidic concepts that enable oscillating and dynamic control of environmental conditions with a focus on medium conditions are discussed, and their application in single-cell research for the cultivation of both mammalian and microbial cell systems is demonstrated. Furthermore, perspectives for performing MSCC at complex dynamic environmental profiles of single parameters and multiparameters (e.g., pH and O₂ ) in amplitude and time are discussed. The technical progress in this field provides completely new experimental approaches and lays the foundation for systematic analysis of cellular metabolism at fluctuating environments.

Mechanical regulation of photosynthesis in cyanobacteria

Photosynthetic organisms regulate their responses to many diverse stimuli in an effort to balance light harvesting with utilizable light energy for carbon fixation and growth (source-sink regulation). This balance is critical to prevent the formation of reactive oxygen species that can lead to cell death. However, investigating the molecular mechanisms that underlie the regulation of photosynthesis in cyanobacteria using ensemble-based measurements remains a challenge due to population heterogeneity. Here, to address this problem, we used long-term quantitative time-lapse fluorescence microscopy, transmission electron microscopy, mathematical modelling and genetic manipulation to visualize and analyse the growth and subcellular dynamics of individual wild-type and mutant cyanobacterial cells over multiple generations. We reveal that mechanical confinement of actively growing Synechococcus sp. PCC 7002 cells leads to the physical disassociation of phycobilisomes and energetic decoupling from the photosynthetic reaction centres. We suggest that the mechanical regulation of photosynthesis is a critical failsafe that prevents cell expansion when light and nutrients are plentiful, but when space is limiting. These results imply that cyanobacteria must convert a fraction of the available light energy into mechanical energy to overcome frictional forces in the environment, providing insight into the regulation of photosynthesis and how microorganisms navigate their physical environment.

The potential of quantitative models to improve microalgae photosynthetic efficiency

The massive increase in carbon dioxide concentration in the atmosphere driven by human activities is causing huge negative consequences and new sustainable sources of energy, food and materials are highly needed. Algae are unicellular photosynthetic microorganisms that can provide a highly strategic contribution to this challenge as alternative source of biomass to complement crops cultivation. Algae industrial cultures are commonly limited by light availability, and biomass accumulation is strongly dependent on their photon-to-biomass conversion efficiency. Investigation of algae photosynthetic metabolism is thus strategic for the generation of more efficient strains with higher productivity. Algae are cultivated at industrial scale in conditions highly different from the natural niches they adapted to and strains development efforts must fully consider the seminal influence on productivity of regulatory mechanism of photosynthesis as well as of cultivation parameters like cells concentration, light distribution in the culture, mixing, nutrients and carbon dioxide availability. In this review we will focus in particular on how mathematical models can account for the complex influence of all environmental parameters and can be exploited for development of improved algae strains.

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.

Microfluidic techniques for enhancing biofuel and biorefinery industry based on microalgae

This review presents a critical assessment of emerging microfluidic technologies for the application on biological productions of biofuels and other chemicals from microalgae. Comparisons of cell culture designs for the screening of microalgae strains and growth conditions are provided with three categories: mechanical traps, droplets, or microchambers. Emerging technologies for the in situ characterization of microalgae features and metabolites are also presented and evaluated. Biomass and secondary metabolite productivities obtained at microscale are compared with the values obtained at bulk scale to assess the feasibility of optimizing large-scale operations using microfluidic platforms. The recent studies in microsystems for microalgae pretreatment, fractionation and extraction of metabolites are also reviewed. Finally, comments toward future developments (high-pressure/-temperature process; solvent-resistant devices; omics analysis, including genome/epigenome, proteome, and metabolome; biofilm reactors) of microfluidic techniques for microalgae applications are provided.

Microfluidic technology for plankton research

Plankton produces numerous chemical compounds used in cosmetics and functional foods. They also play a key role in the carbon budget on the Earth. In a context of global change, it becomes important to understand the physiological response of these microorganisms to changing environmental conditions. Their adaptations and the response to specific environmental conditions are often restricted to a few active cells or individuals in large populations. Using analytical capabilities at the subnanoliter scale, microfluidic technology has also demonstrated a high potential in biological assays. Here, we review recent advances in microfluidic technologies to overcome the current challenges in high content analysis both at population and the single cell level.

An Automated Induction Microfluidics System for Synthetic Biology

The expression of a recombinant gene in a host organism through induction can be an extensively manual and labor-intensive procedure. Several methods have been developed to simplify the protocol, but none has fully replaced the traditional IPTG-based induction. To simplify this process, we describe the development of an autoinduction platform based on digital microfluidics. This system consists of a 600 nm LED and a light sensor to enable the real-time monitoring of  the optical density (OD) samples coordinated with the semicontinuous mixing of a bacterial culture. A hand-held device was designed as a microbioreactor to culture cells and to measure the OD of the bacterial culture. In addition, it serves as a platform for the analysis of regulated protein expression in E. coli without the requirement of standardized well-plates or pipetting-based platforms. Here, we report for the first time, a system that offers great convenience without the user to physically monitor the culture or to manually add inducer at specific times. We characterized our system by looking at several parameters (electrode designs, gap height, and growth rates) required for an autoinducible system. As a first step, we carried out an automated induction optimization assay using a RFP reporter gene to identify conditions suitable for our system. Next, we used our system to identify active thermophilic β-glucosidase enzymes that may be suitable candidates for biomass hydrolysis. Overall, we believe that this platform may be useful for synthetic biology applications that require regulating and analyzing expression of heterologous genes for strain optimization.

Review of Microfluidic Photobioreactor Technology for Metabolic Engineering and Synthetic Biology of Cyanobacteria and Microalgae

One goal of metabolic engineering and synthetic biology for cyanobacteria and microalgae is to engineer strains that can optimally produce biofuels and commodity chemicals. However, the current workflow is slow and labor intensive with respect to assembly of genetic parts and characterization of production yields because of the slow growth rates of these organisms. Here, we review recent progress in the microfluidic photobioreactors and identify opportunities and unmet needs in metabolic engineering and synthetic biology. Because of the unprecedented experimental resolution down to the single cell level, long-term real-time monitoring capability, and high throughput with low cost, microfluidic photobioreactor technology will be an indispensible tool to speed up the development process, advance fundamental knowledge, and realize the full potential of metabolic engineering and synthetic biology for cyanobacteria and microalgae.

Mechanically activated artificial cell by using microfluidics

All living organisms sense mechanical forces. Engineering mechanosensitive artificial cell through bottom-up in vitro reconstitution offers a way to understand how mixtures of macromolecules assemble and organize into a complex system that responds to forces. We use stable double emulsion droplets (aqueous/oil/aqueous) to prototype mechanosensitive artificial cells. In order to demonstrate mechanosensation in artificial cells, we develop a novel microfluidic device that is capable of trapping double emulsions into designated chambers, followed by compression and aspiration in a parallel manner. The microfluidic device is fabricated using multilayer soft lithography technology, and consists of a control layer and a deformable flow channel. Deflections of the PDMS membrane above the main microfluidic flow channels and trapping chamber array are independently regulated pneumatically by two sets of integrated microfluidic valves. We successfully compress and aspirate the double emulsions, which result in transient increase and permanent decrease in oil thickness, respectively. Finally, we demonstrate the influx of calcium ions as a response of our mechanically activated artificial cell through thinning of oil. The development of a microfluidic device to mechanically activate artificial cells creates new opportunities in force-activated synthetic biology.