Quantitative analysis of the chemotaxis of a green alga, Chlamydomonas reinhardtii, to bicarbonate using diffusion-based microfluidic device

COP5/HKR1 changes ciliary beat pattern and biases cell steering during chemotaxis in Chlamydomonas reinhardtii

This study investigates the control of ciliary beat patterns during ammonium chemotaxis in the model ciliate microalga Chlamydomonas reinhardtii. Screening the chemotaxis response of mutant strains with ciliary defects revealed that a strain lacking CAV2, the alpha subunit of the voltage-gated calcium channel, is deficient in ammonium chemotaxis. CAV2 regulates the switching of the ciliary beat pattern from the asymmetric to the symmetric waveform. Strains lacking COP5/HKR1 (chlamyopsin 5/histidine kinase rhodopsin 1) are also deficient in ammonium chemotaxis. Conversely, strains defective in phototaxis perform ammonium chemotaxis normally. Cell motility analysis revealed wild-type cells reduce the incidences of switching the ciliary beat pattern from the asymmetric to symmetric waveform when swimming up the ammonium gradient. In contrast, the COP5/HKR1 disrupted strain does not bias ciliary beat pattern switching in the gradient. This finding reveals that COP5/HKR1 plays a critical role in Chlamydomonas chemotaxis signaling transduction, similarly to animal chemotaxis. On the other hand, ciliary beat pattern switching induces randomized directional changes, analogous to run-and-tumble chemotaxis of bacteria and archaea. This study reveals that Chlamydomonas signaling transduction is similar to the eukaryotic mechanism, yet the cellular locomotion follows the bacteria and archaea mechanism.

Space, the final frontier: The spatial component of phytoplankton-bacterial interactions

Microscale interactions between marine phytoplankton and bacteria shape the microenvironment of individual cells, impacting their physiology and ultimately influencing global-scale biogeochemical processes like carbon and nutrient cycling. In dilute environments such as the ocean water column, metabolic exchange between microorganisms likely requires close proximity between partners. However, the biological strategies to achieve this physical proximity remain an understudied aspect of phytoplankton-bacterial associations. Understanding the mechanisms by which these microorganisms establish and sustain spatial relationships and the extent to which spatial proximity is necessary for interactions to occur, is critical to learning how spatial associations influence the ecology of phytoplankton and bacterial communities. Here, we provide an overview of current knowledge on the role of space in shaping interactions among ocean microorganisms, encompassing behavioural and metabolic evidence. We propose that characterising phytoplankton-bacterial interactions from a spatial perspective can contribute to a mechanistic understanding of the establishment and maintenance of these associations and, consequently, an enhanced ability to predict the impact of microscale processes on ecosystem-wide phenomena.

The younger flagellum sets the beat for Chlamydomonas reinhardtii

Eukaryotes swim with coordinated flagellar (ciliary) beating and steer by fine-tuning the coordination. The model organism for studying flagellate motility, Chlamydomonas reinhardtii, employs synchronous, breaststroke-like flagellar beating to swim, and it modulates the beating amplitudes differentially to steer. This strategy hinges on both inherent flagellar asymmetries (e.g. different response to chemical messengers) and such asymmetries being effectively coordinated in the synchronous beating. In C. reinhardtii, the synchrony of beating is known to be supported by a mechanical connection between flagella; however, how flagellar asymmetries persist in the synchrony remains elusive. For example, it has been speculated for decades that one flagellum leads the beating, as its dynamic properties (i.e. frequency, waveform, etc.) appear to be copied by the other one. In this study, we combine experiments, computations, and modeling efforts to elucidate the roles played by each flagellum in synchronous beating. With a non-invasive technique to selectively load each flagellum, we show that the coordinated beating essentially only responds to load exerted on the cis flagellum; and that such asymmetry in response derives from a unilateral coupling between the two flagella. Our results highlight a distinct role for each flagellum in coordination and have implication for biflagellates' tactic behaviors.

Chemotaxis of an elastic flagellated microrobot

Machine learning algorithms offer a tool to boost mobility and flexibility of a synthetic microswimmer, hence may help us design truly smart microrobots. In this work, we design a two-gait microrobot swimming in circular or helical trajectory. It utilizes the coupling between flagellum elasticity and resistive force to change the characteristics of swimming trajectory. Leveraging a deep reinforcement learning (DRL) approach, we show that the microrobot can self-learn chemotactic motion autonomously (without heuristics) using only several current and historical chemoattractant concentration and curvature information. The learned strategy is more efficient than a human-devised shortsighted strategy and can be further greatly improved in a stochastic environment. Furthermore, in the helical trajectory case, if additional heuristic information of direction is supplemented to evaluate the strategy during the learning process, then a highly efficient strategy can be discovered by the DRL. The microrobot can quickly align the helix vector to the gradient direction using just several smart sequential gait switchings. The success for the efficient strategies depends on how much historical information is provided and also the steering angle step size of the microrobot. Our results provide useful guidance for the design and smart maneuver of synthetic spermlike microswimmers.

Cells collectively migrate during ammonium chemotaxis in Chlamydomonas reinhardtii

The mechanisms governing chemotaxis in Chlamydomonas reinhardtii are largely unknown compared to those regulating phototaxis despite equal importance on the migratory response in the ciliated microalga. To study chemotaxis, we made a simple modification to a conventional Petri dish assay. Using the assay, a novel mechanism governing Chlamydomonas ammonium chemotaxis was revealed. First, we found that light exposure enhances the chemotactic response of wild-type Chlamydomonas strains, yet phototaxis-incompetent mutant strains, eye3-2 and ptx1, exhibit normal chemotaxis. This suggests that Chlamydomonas transduces the light signal pathway in chemotaxis differently from that in phototaxis. Second, we found that Chlamydomonas collectively migrate during chemotaxis but not phototaxis. Collective migration during chemotaxis is not clearly observed when the assay is conducted in the dark. Third, the Chlamydomonas strain CC-124 carrying agg1^-, the AGGREGATE1 gene (AGG1) null mutation, exhibited a more robust collective migratory response than strains carrying the wild-type AGG1 gene. The expression of a recombinant AGG1 protein in the CC-124 strain suppressed this collective migration during chemotaxis. Altogether, these findings suggest a unique mechanism; ammonium chemotaxis in Chlamydomonas is mainly driven by collective cell migration. Furthermore, it is proposed that collective migration is enhanced by light and suppressed by the AGG1 protein.

Improved Productivity of Astaxanthin from Photosensitive Haematococcus pluvialis Using Phototaxis Technology

Haematococcus pluvialis is a microalgae actively studied for the production of natural astaxanthin, which is a powerful antioxidant for human application. However, it is economically disadvantageous for commercialization owing to the low productivity of astaxanthin. This study reports an effective screening strategy using the negative phototaxis of the H. pluvialis to attain the mutants having high astaxanthin production. A polydimethylsiloxane (PDMS)-based microfluidic device irradiated with a specific light was developed to efficiently figure out the phototactic response of H. pluvialis. The partial photosynthesis deficient (PP) mutant (negative control) showed a 0.78-fold decreased cellular response to blue light compared to the wild type, demonstrating the positive relationship between the photosynthetic efficiency and the phototaxis. Based on this relationship, the Haematococcus mutants showing photosensitivity to blue light were selected from the 10,000 random mutant libraries. The M1 strain attained from the phototaxis-based screening showed 1.17-fold improved growth rate and 1.26-fold increases in astaxanthin production (55.12 ± 4.12 mg g⁻¹) in the 100 L photo-bioreactor compared to the wild type. This study provides an effective selection tool for industrial application of the H. pluvialis with improved astaxanthin productivity.

Augmented CO2 tolerance by expressing a single H+-pump enables microalgal valorization of industrial flue gas

Microalgae can accumulate various carbon-neutral products, but their real-world applications are hindered by their CO2 susceptibility. Herein, the transcriptomic changes in a model microalga, Chlamydomonas reinhardtii, in a high-CO2 milieu (20%) are evaluated. The primary toxicity mechanism consists of aberrantly low expression of plasma membrane H+-ATPases (PMAs) accompanied by intracellular acidification. Our results demonstrate that the expression of a universally expressible PMA in wild-type strains makes them capable of not only thriving in acidity levels that they usually cannot survive but also exhibiting 3.2-fold increased photoautotrophic production against high CO2 via maintenance of a higher cytoplasmic pH. A proof-of-concept experiment involving cultivation with toxic flue gas (13 vol% CO2, 20 ppm NOX, and 32 ppm SOX) shows that the production of CO2-based bioproducts by the strain is doubled compared with that by the wild-type, implying that this strategy potentially enables the microalgal valorization of CO2 in industrial exhaust.

The Transport Behavior of a Biflagellated Microswimmer before and after Cargo Loading

The changes in the transport behavior of a microswimmer before and after cargo loading are crucial to understanding and control of the motion of a biohybrid microbot. In this work, we show the change in swimming behavior of biflagellated microalgae Chlamydomonas reinhardtii picking up a 4.5 μm polystyrene microbead upon collision. The microswimmer changed from linear forward motion into helical motion upon the attachment of the cargo and swam with a decreased swimming velocity. We revealed the helical motion of the microswimmer upon cargo loading due to suppression of flagella by image analysis of magnified time-lapse images of C. reinhardtii with one microbead attached at the anterior end (between the flagella). Furthered suppression on the flagellum imposed by the loading of the second cargo has led to increased oscillation per displacement traveled and decreased swimming velocity. Moreover, the microswimmer with a microbead attached at the posterior end swam with swimming velocity close to free swimming microalgae and did not exhibit helical swimming behavior. The experimental results and analysis showed that the loading location of the cargo has a great influence over the swimming behavior of the microswimmer. Furthermore, the work balance calculation and mathematical analysis based on Lighthill's model are well consistent with our experimental findings.

Carbonate assisted lipid extraction and biodiesel production from wet microalgal biomass and recycling waste carbonate for CO2 supply in microalgae cultivation

High cost of microalgal biofuel is caused by all the steps in current technology, including cultivation, harvesting, lipid extraction, biofuel processing and wastewater and waste treatment. This study aims to systematically reduce these costs with one integrated process, in which carbonate is used for cell rupture, lipid extraction and biodiesel processing, and then recycled for CO₂ absorption and carbon supply for a new round of algae cultivation. To reach this goal, carbonate-heating treatment with N, N' - dibutylurea which can enhance cell disruption were used for cell-wall breaking of wet Neochloris oleoabundans (UTEX 1185) biomass. Lipid extraction was fulfilled with carbonate/ethanol aqueous two phase extraction method and residual carbonate with wastewater from bottom phase was recycled to absorb CO₂ to generate bicarbonate for algal cultivation with fresh medium. Taking into comprehensive consideration of cell disruption efficiency, partition coefficient, and lipid recovery, the condition of cell disruption and lipid extraction was set at 90 °C, 100 min reaction time, 1:7.5 DBU:H₂O (w/w) ratio, 1:3 Na₂CO₃:H₂O (w/w) ratio, and 9% (w/w_T) ethanol concentration. The results showed that carbonate-heating treatment of wet N. oleoabundans biomass resulted in up to 90.7% cell disruption efficiency. The lipid recovery rate in carbonate/ethanol system was up to 97.9%, and the final biodiesel production was 1.30 times of that with Soxhlet method. Utilization of the waste broth after CO₂ absorption with the content of 4% (v/v_T) in the medium for new batch of algae cultivation resulted in biomass concentration of 1.68 g/L. The corresponding total fatty acids production was 0.35 g/L, which was 1.63 fold of that with fresh medium. This study firstly proved the feasibility of using carbonate for lipid extraction and biodiesel production and recycle waste carbonate for carbon re-supply during algae cultivation.

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.

Advances in understanding the physiological role and locations of carbonic anhydrases in C3 plant cells

The review describes the structures of plant carbonic anhydrases (CAs), enzymes catalyzing the interconversion of inorganic carbon forms and belonging to different families, as well as the interaction of inhibitors and activators of CA activity with the active sites of CAs in representatives of these families. We outline the data that shed light on the location of CAs in green cells of C3 plants, algae and angiosperms, with the emphasis on the recently obtained data. The proven and proposed functions of CAs in these organisms are listed. The possibility of the involvement of several chloroplast CAs in acceleration of the conversion of bicarbonate to CO₂ and in supply of CO₂ for fixation by Rubisco is particularly considered. Special attention is paid to CAs in various parts of thylakoids and to discussion about current knowledge of their possible physiological roles. The review states that, despite the significant progress in application of the mutants with suppressed CAs synthesis, the approach based on the use of the inhibitors of CA activity in some cases remains quite effective. Combination of these two approaches, namely determining the effect of CA activity inhibitors in plants with certain knocked-out CA genes, turns out to be very useful for understanding the functions of other CAs.

The BBSome restricts entry of tagged carbonic anhydrase 6 into the cis-flagellum of Chlamydomonas reinhardtii

The two flagella of Chlamydomonas reinhardtii are of the same size and structure but display functional differences, which are critical for flagellar steering movements. However, biochemical differences between the two flagella have not been identified. Here, we show that fluorescence protein-tagged carbonic anhydrase 6 (CAH6-mNG) preferentially localizes to the trans-flagellum, which is organized by the older of the two flagella-bearing basal bodies. The uneven distribution of CAH6-mNG is established early during flagellar assembly and restored after photobleaching, suggesting that it is based on preferred entry or retention of CAH6-mNG in the trans-flagellum. Since CAH6-mNG moves mostly by diffusion, a role of intraflagellar transport (IFT) in establishing its asymmetric distribution is unlikely. Interestingly, CAH6-mNG is present in both flagella of the non-phototactic bardet-biedl syndrome 1 (bbs1) mutant revealing that the BBSome is involved in establishing CAH6-mNG flagellar asymmetry. Using dikaryon rescue experiments, we show that the de novo assembly of CAH6-mNG in flagella is considerably faster than the removal of ectopic CAH6-mNG from bbs flagella. Thus, different rates of flagellar entry of CAH6-mNG rather than its export from flagella is the likely basis for its asymmetric distribution. The data identify a novel role for the C. reinhardtii BBSome in preventing the entry of CAH6-mNG specifically into the cis-flagellum.

Insights on the Functions and Ecophysiological Relevance of the Diverse Carbonic Anhydrases in Microalgae

Carbonic anhydrases (CAs) exist in all kingdoms of life. They are metalloenzymes, often containing zinc, that catalyze the interconversion of bicarbonate and carbon dioxide-a ubiquitous reaction involved in a variety of cellular processes. So far, eight classes of apparently evolutionary unrelated CAs that are present in a large diversity of living organisms have been described. In this review, we focus on the diversity of CAs and their roles in photosynthetic microalgae. We describe their essential role in carbon dioxide-concentrating mechanisms and photosynthesis, their regulation, as well as their less studied roles in non-photosynthetic processes. We also discuss the presence in some microalgae, especially diatoms, of cambialistic CAs (i.e., CAs that can replace Zn by Co, Cd, or Fe) and, more recently, a CA that uses Mn as a metal cofactor, with potential ecological relevance in aquatic environments where trace metal concentrations are low. There has been a recent explosion of knowledge about this well-known enzyme with exciting future opportunities to answer outstanding questions using a range of different approaches.

Cilia-based peptidergic signaling

Peptide-based intercellular communication is a ubiquitous and ancient process that predates evolution of the nervous system. Cilia are essential signaling centers that both receive information from the environment and secrete bioactive extracellular vesicles (ectosomes). However, the nature of these secreted signals and their biological functions remain poorly understood. Here, we report the developmentally regulated release of the peptide amidating enzyme, peptidylglycine α-amidating monooxygenase (PAM), and the presence of peptidergic signaling machinery (including propeptide precursors, subtilisin-like prohormone convertases, amidated products, and receptors) in ciliary ectosomes from the green alga Chlamydomonas. One identified amidated PAM product serves as a chemoattractant for mating-type minus gametes but repels plus gametes. Thus, cilia provide a previously unappreciated route for the secretion of amidated signaling peptides. Our study in Chlamydomonas and the presence of PAM in mammalian cilia suggest that ciliary ectosome-mediated peptidergic signaling dates to the early eukaryotes and plays key roles in metazoan physiology.

Acidic cultivation of Haematococcus pluvialis for improved astaxanthin production in the presence of a lethal fungus

An acidic cultivation strategy was developed to prevent contamination of a lethal fungus Paraphysoderma sedebokerensis in Haematococcus pluvialis culture for astaxanthin production. Instead of generally used neutral pH, an acidic condition (pH 4) was applied to the cultivation, resulting in a significant inhibition of the fungal contamination. This could be ascribed to the acidity-associated denaturation of a surface protein of P. sedebokerensis, which plays an important role in recognition of H. pluvialis. Stress relief strategies including stepwise light irradiation and naturally occurring nitrogen deficiency were employed in the induction stage to minimize the reduction of astaxanthin production caused by acidic pH. Accordingly, an astaxanthin titer of 84.8 mg L^-1 was obtained, which is 141-fold of that from the completely contaminated culture and double of that without the stress relief methods. This strategy provides a persistent contamination control method that can be used for practical astaxanthin production by H. pluvialis.

Performance and potential appraisal of various microalgae as direct combustion fuel

Direct combustion of biomass is considered the most effective and simple means to contribute to CO₂ reduction. In this context, the life-cycle potential of microalgal solid fuel, which has been overlooked so far, was comprehensively scrutinized ranging from cultivation to direct combustion. According to the quantitative data, using the raw fuel was confirmed to offer great benefits over the conventional lipid-targeted microalgal fuel systems through exploiting all of the biomass' energy potential, thereby being able to significantly increase the energy yield from biomass. The solid fuel is shown to exhibit diverse positive aspects owing to its remarkable calorific value, productivity and CO₂ fixation ability. The combustion test reveals coal-microalgae co-combustion brings beneficial consequences on combustibility and environmental impacts with no notable thermal efficiency drop. This holistic appraisal shows microalgae patently possess high potential as a direct combustion fuel, even outperforming that of extensively used woody fuels.

Multiomics resolution of molecular events during a day in the life of Chlamydomonas

The unicellular green alga Chlamydomonas reinhardtii displays metabolic flexibility in response to a changing environment. We analyzed expression patterns of its three genomes in cells grown under light-dark cycles. Nearly 85% of transcribed genes show differential expression, with different sets of transcripts being up-regulated over the course of the day to coordinate cellular growth before undergoing cell division. Parallel measurements of select metabolites and pigments, physiological parameters, and a subset of proteins allow us to infer metabolic events and to evaluate the impact of the transcriptome on the proteome. Among the findings are the observations that Chlamydomonas exhibits lower respiratory activity at night compared with the day; multiple fermentation pathways, some oxygen-sensitive, are expressed at night in aerated cultures; we propose that the ferredoxin, FDX9, is potentially the electron donor to hydrogenases. The light stress-responsive genes PSBS, LHCSR1, and LHCSR3 show an acute response to lights-on at dawn under abrupt dark-to-light transitions, while LHCSR3 genes also exhibit a later, second burst in expression in the middle of the day dependent on light intensity. Each response to light (acute and sustained) can be selectively activated under specific conditions. Our expression dataset, complemented with coexpression networks and metabolite profiling, should constitute an excellent resource for the algal and plant communities.

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 Update on the Metabolic Roles of Carbonic Anhydrases in the Model Alga Chlamydomonas reinhardtii

Carbonic anhydrases (CAs) are metalloenzymes that are omnipresent in nature. CAs catalyze the basic reaction of the reversible hydration of CO₂ to HCO₃⁻ and H⁺ in all living organisms. Photosynthetic organisms contain six evolutionarily different classes of CAs, which are namely: α-CAs, β-CAs, γ-CAs, δ-CAs, ζ-CAs, and θ-CAs. Many of the photosynthetic organisms contain multiple isoforms of each CA family. The model alga Chlamydomonas reinhardtii contains 15 CAs belonging to three different CA gene families. Of these 15 CAs, three belong to the α-CA gene family; nine belong to the β-CA gene family; and three belong to the γ-CA gene family. The multiple copies of the CAs in each gene family may be due to gene duplications within the particular CA gene family. The CAs of Chlamydomonas reinhardtii are localized in different subcellular compartments of this unicellular alga. The presence of a large number of CAs and their diverse subcellular localization within a single cell suggests the importance of these enzymes in the metabolic and biochemical roles they perform in this unicellular alga. In the present review, we update the information on the molecular biology of all 15 CAs and their metabolic and biochemical roles in Chlamydomonas reinhardtii. We also present a hypothetical model showing the known functions of CAs and predicting the functions of CAs for which precise metabolic roles are yet to be discovered.

A Spatial Interactome Reveals the Protein Organization of the Algal CO2-Concentrating Mechanism

Approximately one-third of global CO2 fixation is performed by eukaryotic algae. Nearly all algae enhance their carbon assimilation by operating a CO2-concentrating mechanism (CCM) built around an organelle called the pyrenoid, whose protein composition is largely unknown. Here, we developed tools in the model alga Chlamydomonas reinhardtii to determine the localizations of 135 candidate CCM proteins and physical interactors of 38 of these proteins. Our data reveal the identity of 89 pyrenoid proteins, including Rubisco-interacting proteins, photosystem I assembly factor candidates, and inorganic carbon flux components. We identify three previously undescribed protein layers of the pyrenoid: a plate-like layer, a mesh layer, and a punctate layer. We find that the carbonic anhydrase CAH6 is in the flagella, not in the stroma that surrounds the pyrenoid as in current models. These results provide an overview of proteins operating in the eukaryotic algal CCM, a key process that drives global carbon fixation.