Best practices in the flow cytometry of microalgae

Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.

Unveiling the epigenetic landscape of plants using flow cytometry approach

Plants are sessile creatures that have to adapt constantly changing environmental circumstances. Plants are subjected to a range of abiotic stressors as a result of unpredictable climate change. Understanding how stress-responsive genes are regulated can help us better understand how plants can adapt to changing environmental conditions. Epigenetic markers that dynamically change in response to stimuli, such as DNA methylation and histone modifications are known to regulate gene expression. Individual cells or particles' physical and/or chemical properties can be measured using the method known as flow cytometry. It may therefore be used to evaluate changes in DNA methylation, histone modifications, and other epigenetic markers, making it a potent tool for researching epigenetics in plants. We explore the use of flow cytometry as a technique for examining epigenetic traits in this thorough discussion. The separation of cell nuclei and their subsequent labeling with fluorescent antibodies, offering information on the epigenetic mechanisms in plants when utilizing flow cytometry. We also go through the use of high-throughput data analysis methods to unravel the complex epigenetic processes occurring inside plant systems.

Best practices for instrument settings and raw data analysis in plant flow cytometry

Flow cytometry (FCM) is now the most widely used method to determine ploidy levels and genome size of plants. To get reliable estimates and allow reproducibility of measurements, the methodology should be standardized and follow the best practices in the field. In this article, we discuss instrument calibration and quality control and various instrument and acquisition settings (parameters, flow rate, number of events, scales, use of discriminators, peak positions). These settings must be decided before measurements because they determine the amount and quality of the data and thus influence all downstream analyses. We describe the two main approaches to raw data analysis (gating and histogram modeling), and we discuss their advantages and disadvantages. Finally, we provide a summary of best practice recommendations for data acquisition and raw data analysis in plant FCM.

Sub-lethal toxicity of five disinfection by-products on microalgae determined by flow cytometry - Lines of evidence for adverse outcome pathways

Standardised tests are often used to determine the ecotoxicity of chemicals and focus mainly on one or a few generic endpoints (e.g. mortality, growth), but information on the sub-cellular processes leading to these effects remain usually partial or missing. Flow cytometry (FCM) can be a practical tool to study the physiological responses of individual cells (such as microalgae) exposed to a stress via the use of fluorochromes and their morphology and natural autofluorescence. This work aimed to assess the effects of five chlorine-based disinfection by-products (DBPs) taken individually on growth and sub-cellular endpoints of the green microalgae Raphidocelis subcapitata. These five DBPs, characteristic of a chlorinated effluent, are the following monochloroacetic acid (MCAA), dichloroacetic acid (DCAA), trichloroacetic acid (TCAA), bromochloroacetic acid (BCAA) and 1,1-dichloropropan-2-one (1,1-DCP). Results showed that 1,1-DCP had the strongest effect on growth inhibition (EC50 = 1.8 mg.L-1), followed by MCAA, TCAA, BCAA and DCAA (EC50 of 10.1, 15.7, 27.3 and 64.5 mg.L-1 respectively). Neutral lipid content, reactive oxygen species (ROS) formation, red autofluorescence, green autofluorescence, size and intracellular complexity were significantly affected by the exposure to the five DBPs. Only mitochondrial membrane potential did not show any variation. Important cellular damages (>10%) were observed for only two of the chemicals (BCAA and 1,1-DCP) and were probably due to ROS formation. The most sensitive and informative sub-lethal parameter studied was metabolic activity (esterase activity), for which three types of response were observed. Combining all this information, an adverse outcome pathways framework was proposed to explain the effect of the targeted chemicals on R. subcapitata. Based on these results, both FCM sub-cellular analysis and conventional endpoint of algal toxicity were found to be complementary approaches.

Application of flow cytometry for rapid, high-throughput, multiparametric analysis of environmental microbiomes

Quantification of the abundance and understanding of the dynamics of the microbial communities is essential to establish a basis for microbiome characterization. The conventional techniques used for the quantification of microbes are complicated and time-consuming. With scientific advancement, many techniques evolved and came into account. Among them, flow cytometry is a robust, high-throughput technique through which microbial dynamics, morphology, microbial distribution, physiological characteristics, and many more attributes can be studied in a high-throughput manner with comparatively less time and resources. Flow cytometry, when combined with other omics-based methods, offers a rapid and efficient platform to analyze and understand the composition of microbiome at the cellular level. The microbial diversity observed through flow cytometry will not be equivalent to that obtained by sequencing methods, but this integrated approach holds great potential for high throughput characterization of microbiomes. Flow cytometry is regarded as an established characterization tool in haematology, oncology, immunology, and medical microbiology research; however, its application in environmental microbiology is yet to be explored. This comprehensive review aims to delve into the diverse environmental applications of flow cytometry across various domains, including but not limited to bioremediation, landfills, anaerobic digestion, industrial bioprocesses, water quality regulation, and soil quality regulation. By conducting an in-depth analysis, this article seeks to shed light on the potential benefits and challenges associated with the utilization of flow cytometry in addressing environmental concerns.

Reference standards for flow cytometric estimation of absolute nuclear DNA content in plants

The estimation of nuclear DNA content has been by far the most popular application of flow cytometry in plants. Because flow cytometry measures relative fluorescence intensities of nuclei stained by a DNA fluorochrome, ploidy determination, and estimation of the nuclear DNA content in absolute units both require comparison to a reference standard of known DNA content. This implies that the quality of the results obtained depends on the standard selection and use. Internal standardization, when the nuclei of an unknown sample and the reference standard are isolated, stained, and measured simultaneously, is mandatory for precise measurements. As DNA peaks representing G1 /G0 nuclei of the sample and standard appear on the same histogram of fluorescence intensity, the quotient of their position on the fluorescence intensity axis provides the quotient of DNA amounts. For the estimation of DNA amounts in absolute units, a number of well-established standards are now available to cover the range of known plant genome sizes. Since there are different standards in use, the standard and the genome size assigned to it has always to be reported. When none of the established standards fits, the introduction of a new standard species is needed. For this purpose, the regression line approach or simultaneous analysis of the candidate standard with several established standards should be prioritized. Moreover, the newly selected standard organism has to fulfill a number of requirements: it should be easy to identify and maintain, taxonomically unambiguous, globally available, with known genome size stability, lacking problematic metabolites, suitable for isolation of sufficient amounts of nuclei, and enabling measurements with low coefficients of variation of DNA peaks, hence suitable for the preparation of high quality samples.

Impact of High-Pressure Homogenization on the Cell Integrity of Tetradesmus obliquus and Seed Germination

Microalgae have almost unlimited applications due to their versatility and robustness to grow in different environmental conditions, their biodiversity and variety of valuable bioactive compounds. Wastewater can be used as a low-cost and readily available medium for microalgae, while the latter removes the pollutants to produce clean water. Nevertheless, since the most valuable metabolites are mainly located inside the microalga cell, their release implies rupturing the cell wall. In this study, Tetradesmus obliquus grown in 5% piggery effluent was disrupted using high-pressure homogenization (HPH). Effects of HPH pressure (100, 300, and 600 bar) and cycles (1, 2 and 3) were tested on the membrane integrity and evaluated using flow cytometry and microscopy. In addition, wheat seed germination trials were carried out using the biomass at different conditions. Increased HPH pressure or number of cycles led to more cell disruption (75% at 600 bar and 3 cycles). However, the highest increase in wheat germination and growth (40-45%) was observed at the lowest pressure (100 bar), where only 46% of the microalga cells were permeabilised, but not disrupted. Non-treated T. obliquus cultures also revealed an enhancing effect on root and shoot length (up to 40%). The filtrate of the initial culture also promoted shoot development compared to water (21%), reinforcing the full use of all the process fractions. Thus, piggery wastewater can be used to produce microalgae biomass, and mild HPH conditions can promote cell permeabilization to release sufficient amounts of bioactive compounds with the ability to enhance plant germination and growth, converting an economic and environmental concern into environmentally sustainable applications.

High-throughput screening for heterotrophic growth in microalgae using the Biolog Plate assay

Microalgae produce a broad range of organic compounds that are increasingly being recognised for their value in novel product production and biotechnological applications. Most microalgae are photoautotrophic, but some are capable of either mixotrophy or heterotrophy. Reported enhanced biomass yields or contrasting metabolite profiles compared to autotrophic growth improve the economics of large-scale production of microalgae, which currently limits industrial applications. Here, the potential of a high-throughput method for the rapid screening of microalgal metabolism was assessed against 95 different carbon sources, using the cost-effective Biolog plate. Of the 5 microalgae tested, Desmodesmus communis (30 carbon sources) and Chlorella vulgaris (19 carbon sources) had the highest number of positive responses to carbon sources, whereas Chlorella sorokiniana had the most negative (toxic) response to the various carbon sources (77 carbon sources). Comparison of Biolog plate results with traditional culture techniques showed good agreement. Species with a high number of positive responses on the Biolog plate exhibited the highest biomass yield under heterotrophic conditions, whilst those with low number of positive responses exhibited the highest biomass yield under autotrophic conditions, using traditional culturing techniques. While the use of these plates is limited to obtaining axenic lines of microalgal species, the method provided a high-throughput assessment of carbon source metabolism, without the expense of undertaking large, laborious traditional culturing assessments. Such high-throughput assessments can be regarded as useful tools for progressing species selection, metabolic capacity and optimal culture conditions for microalgal biotechnology applications.