Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Small cells with big photosynthetic productivities: biotechnological potential of the Picochlorum genus

The Picochlorum genus is a distinctive eukaryotic green-algal clade that is the focus of several current biotechnological studies. It is capable of extremely rapid growth rates and has exceptional tolerances to high salinity, intense light, and elevated temperatures. Importantly, it has robust stability and high-biomass productivities in outdoor field trials in seawater. These features have propelled Picochlorum into the spotlight as a promising model for both fundamental and biotechnological research. Recently, several genetic tools, including genome editing, were developed for these algae, enabling insights into Picochlorum photophysiology and algal transformations for expanded capabilities. Here, we survey the Picochlorum genus, its genetic toolbox, recently characterized transformants, and discuss the commercial potential of Picochlorum as a salt-water photoautotrophic biocatalyst.

Reclassification of Botryococcus braunii chemical races into separate species based on a comparative genomics analysis

The colonial green microalga Botryococcus braunii is well known for producing liquid hydrocarbons that can be utilized as biofuel feedstocks. B. braunii is taxonomically classified as a single species made up of three chemical races, A, B, and L, that are mainly distinguished by the hydrocarbons produced. We previously reported a B race draft nuclear genome, and here we report the draft nuclear genomes for the A and L races. A comparative genomic study of the three B. braunii races and 14 other algal species within Chlorophyta revealed significant differences in the genomes of each race of B. braunii. Phylogenomically, there was a clear divergence of the three races with the A race diverging earlier than both the B and L races, and the B and L races diverging from a later common ancestor not shared by the A race. DNA repeat content analysis suggested the B race had more repeat content than the A or L races. Orthogroup analysis revealed the B. braunii races displayed more gene orthogroup diversity than three closely related Chlamydomonas species, with nearly 24-36% of all genes in each B. braunii race being specific to each race. This analysis suggests the three races are distinct species based on sufficient differences in their respective genomes. We propose reclassification of the three chemical races to the following species names: Botryococcus alkenealis (A race), Botryococcus braunii (B race), and Botryococcus lycopadienor (L race).

Low-dose ionizing radiation generates a hormetic response to modify lipid metabolism in Chlorella sorokiniana

Algal biomass is a viable source of chemicals and metabolites for various energy, nutritional, medicinal and agricultural uses. While stresses have commonly been used to induce metabolite accumulation in microalgae in attempts to enhance high-value product yields, this is often very detrimental to growth. Therefore, understanding how to modify metabolism without deleterious consequences is highly beneficial. We demonstrate that low-doses (1-5 Gy) of ionizing radiation in the X-ray range induces a non-toxic, hormetic response in microalgae to promote metabolic activation. We identify specific radiation exposure parameters that give reproducible metabolic responses in Chlorella sorokiniana caused by transcriptional changes. This includes up-regulation of >30 lipid metabolism genes, such as genes encoding an acetyl-CoA carboxylase subunit, phosphatidic acid phosphatase, lysophosphatidic acid acyltransferase, and diacylglycerol acyltransferase. The outcome is an increased lipid yield in stationary phase cultures by 25% in just 24 hours, without any negative effects on cell viability or biomass.

Environmental fate of aquatic pollutants and their mitigation by phycoremediation for the clean and sustainable environment: A review

Emerging pollutants such as natural and manufactured chemicals, insecticides, pesticides, surfactants, and other biological agents such as personal care products, cosmetics, pharmaceuticals, and many industrial discharges hamper the aquatic environment. Nanomaterials and microplastics, among the categories of pollutants, can directly interfere with the marine ecosystem and translate into deleterious effects for humans and animals. They are either uncontrolled or poorly governed. Due to their known or suspected effects on human and environmental health, some chemicals are currently causing concern. The aquatic ecology is at risk from these toxins, which have spread worldwide. This review assesses the prevalence of emerging and hazardous pollutants that have effects on aquatic ecosystems and contaminated water bodies and their toxicity to non-target organisms. Microalgae are found to be a suitable source to remediate the above-mentioned risks. Microalgae based mitigation techniques are currently emerging approaches for all such contaminants, including the other categories that are discussed above. These studies describe the mechanism of phycoremediation, provide outrage factors that may significantly affect the efficiency of contaminants removal, and discuss the future directions and challenges of microalgal mediated remediations.

Nitrogen and phosphorus stress as a tool to induce lipid production in microalgae

Microalgae, capable of accumulating large amounts of lipids, are of great value for biodiesel production. The high cost of such production stimulates the search for cultivation conditions that ensure their highest productivity. Reducing the content of nitrogen and phosphorus in the culture medium is widely used to change the content and productivity of lipids in microalgae. Achieving the right balance between maximum growth and maximum lipid content and productivity is the primary goal of many experimental works to ensure cost-effective biodiesel production from microalgae. The content of nitrogen and phosphorus in nutrient media for algal cultivation after converted to nitrogen (-N) and phosphorus (-P) lies in an extensive range: from 0.007 g L- 1 to 0.417 g L- 1 and from 0.0003 g L- 1 to 0.227 g L- 1 and N:P ratio from 0.12:1 to 823.33:1. When studying nutritional stress in microalgae, no single approach is used to determine the experimental concentrations of nitrogen and phosphorus. This precludes the possibility of correct interpretation of the data and may lead to erroneous conclusions. This work results from the systematisation of information on using nitrogen and phosphorus restriction to increase the lipid productivity of microalgae of different taxonomic and ecological groups to identify future research directions. The results of 301 experiments were included in the analysis using the principal components method. The investigation considered various divisions and classes: Cyanobacteria, Rhodophyta, Dinophyta, Haptophyta, Cryptophyta, Heterokontophyta/Ochrophyta (Bacillariophyceae, Eustigmatophyceae, Xanthophyceae), Chlorophyta, and also the ratio N:P, the time of the experiment, the light intensity during cultivation. Based on the concentrations of nitrogen and phosphorus existing in various nutrient media, a general scheme for designating the supply of nutrient media for nitrogen (as NO3- or NH4+, N g L- 1) and phosphorus (as РO4-, P g L- 1) has been proposed: replete -N (˃0.4 g L- 1), moderate -N (0.4-0.2), moderate N-limitation (0.19-0.1), strong N-limitation (˂0.1), without nitrogen (0), replete -Р (˃0.2), moderate -P (0.2-0.02), moderate P-limitation (0.019-0.01), strong P-limitation (˂0.01), without phosphorus (0).

Comparative metabarcoding analysis of phytoplankton community composition and diversity in aquaculture water and the stomach contents of Tegillarca granosa during months of growth

Filter-feeder bivalves and phytoplankton are interdependent. Their interaction plays important role in estuarine and coastal ecosystem. The correlation between bivalve feeding and phytoplankton is highly species specificity and environment dependent. In the background of miniature and nondiatom trend of phytoplankton in coastal seawaters, how bivalve respond and how the response play roles in the phytoplankton community are poorly known. In the present study, by applying DNA metabarcoding approach based on plastid 23S rDNA, this question was addressed by comparing the phytoplankton composition in the seston and the stomach content of blood clam Tegillarca granosa sampled during the growth period from March to November 2020 in an experimental farm on tidal flat in Xiangshan Bay, East China Sea. The result showed that, a total of seven phyla, 55 genera and 73 species of phytoplankton were identified for all samples. Chlorophyta, Bacillariophyta, and Cyanobacteria were found to be three dominant phyla both in the stomach contents and seston. High diversity of pico-sized phytoplankton, which was easy overlooked by microscopy, was revealed both in seston and stomach contents. This result indicated that the clam was able to feed on the pico-sized algae. At the genus level, the most abundant genera were the pico-sized green alga Ostreococcus (6.12 %-67.88 %) in seston and Picochlorum (4.07 %-35.33 %) in the stomach contents. In addition, microalgae of high nutritional value showed trend of higher proportion in stomach contents than that in seston, especially in July and September when significant growth of T. granosa was observed during this period (the body size increased 155 %). Biodiversity of phytoplankton in the seston was totally higher than that in stomach content, however, the changes among the months showed respective trend. Especially in July when the biodiversity was the lowest in seston, that in the stomach content showed the highest. The results indicated that blood clam farming might influence the phytoplankton composition, including those of pico-sized level, although the particular species in seston were mainly correlating with the dominant environmental factors such as temperature, salinity, pH respectively. These results extend the understanding of roles that bivalve aquaculture may play in the changing of coastal phytoplankton community.

Advanced treatment of secondary effluent from wastewater treatment plant by a newly isolated microalga Desmodesmus sp. SNN1

Secondary effluents contain considerable amounts of nitrogen and phosphorous, which if dumped untreated can cause eutrophication of the receiving water bodies. Microalgae can remove these nutrients and other pollutants from the wastewater effluents and play an effective role in the secondary effluent treatment. In this study, six microalgae strains (SNN1, SNN2, SNN3, SNN4, SNS1, and SNS2) were isolated and screened from the water and mud of Yingxue Lake of Shandong Jianzhu University, and their efficiencies for the removal of COD, NH₄ ⁺-N, TN, and TP in the secondary effluent were assessed. By comparing the growth performances and nutrient removal ability of algal strains in domestic sewage, we found that SNN1 (identified and named as Desmodesmus sp. SNN1) has the highest efficiency for biomass accumulation and sewage purification. Hence, the algal strain SNN1 was selected for further screening and optimization experiments. The strain showed higher biomass yield and better nutrient removal rate when the pH of secondary effluent was 9.0 and the initial inoculum concentration (optical density at 680 nm) of algal strain was 0.4. After 12 days of treatment, the concentrations of COD, NH₄ ⁺-N, TN, and TP in the secondary effluent were 31.79, 0.008, 8.631, and 0.069 mg/L, respectively. Therefore, SNN1 with the removal rates of 52.69% (COD), 99.99% (NH₄ ⁺-N), 89.09% (TN), and 94.64% (TP) displayed its high potential in nutrient removal. In addition, it also yielded 5.30 mg/L of chlorophyll a and 168.33 mg/L of lipids. These results demonstrated that this strain exhibited an effective treatment capacity for secondary effluent and microalgal oil production. This study is helpful to provide a strategy for the resource utilization of secondary effluent and the conservation of freshwater resources required by microalgae culture.

Improving Microalgal Biomass Productivity Using Weather-Forecast-Informed Operations

The operation of microalgal cultivation systems, such as culture dilution associated with harvests, affects biomass productivity. However, the constantly changing incident light and ambient temperature in the outdoor environment make it difficult to determine the operational parameters that result in optimal biomass growth. To address this problem, we present a pond operation optimization tool that predicts biomass growth based on future weather conditions to identify the optimal dilution rate that maximizes biomass productivity. The concept was tested by comparing the biomass productivities of three dilution scenarios: standard batch cultivation (no dilution), fixed-rate dilution (harvest 60% of the culture every three days), and weather-forecast-informed dilution. In the weather-forecast-informed case, the culture was diluted daily, and the dilution ratio was optimized by the operation optimization tool according to the future 24 h weather condition. The results show that the weather-forecast-informed dilution improved the biomass productivity by 47% over the standard batch cultivation and 20% over the fixed-rate dilution case. These results demonstrate that the pond operation optimization tool could help pond operators to make decisions that maximize biomass growth in the field under ever-changing weather conditions.

A review on contemporary approaches in enhancing the innate lipid content of yeast cell

For the past few decades, industrialization has made a huge environmental hazard to the world with its waste. The approach of waste to wealth in the recent era has made many Eco-economical suggestions for the industries. The valuable products in biorefinery aspects of the eco-economical suggestions include; energy products, high-value drugs and novel materials. Bio-lipids are found to be the major influencing eco-economical products in the process. Production of bio-lipid from microbial sources has paved the way for future research on lipid-bioproducts. The yeast cell is a unique organism with a large unicellular structure capable of accumulating a high amount of lipids. It constitutes 90% of neutral lipids. Various strategies enhance the lipid profile of yeast cells: usage of oleaginous yeast, usage of low cost (or) alternative substrates, developing stress conditions in the growth medium, using genetically modified yeast, altering metabolic pathways of yeast and by using the symbiotic cultures of yeast with other microbes. The metabolic alterations of lipid pathways such as lipid biosynthesis, lipid elongation, lipid accumulation and lipid degradation have been a striking feature of research in lipid-based microbial work. The lipid-bioproducts have also made a strong footprint in the history of alternative energy products. It includes partial acyl glycerol, oleochemicals, phospholipids and biofuels. This report comprises the recent approaches carried out in the yeast cell for enhancing its lipid content. The limitations, challenges and future scope of individual strategies were also highlighted in this article.

Multi-objective tailored optimization deciphering carbon partitioning and metabolomic tuning in response to elevated CO2 levels, organic carbon and sparging period

Microalgae have garnered much contemplation as candidates to fix CO₂ into valuable compounds. Although microalgae have been studied to produce various metabolites, they have not yet proved successful for commercialization. Since, handling such problems practically requires satisfying multiple parameters simultaneously, we put forth a multi-parameter optimization strategy to manipulate the carbon metabolism of Scenedesmus sp. to improve biomass production and enhance CO₂ fixation to increase the production of fuel-related metabolites. The Box-Behnken design method was applied with CO₂ concentration, CO₂ sparging time and glucose concentration as independent variables; biomass and total fatty acid methyl ester (total FAME) content were analyzed as response variables. The strain is supplemented with both CO₂ and glucose with an aim to enhance carbon flux and rechannel it towards carbon fixation. As per the results obtained in this study, Scenedesmus sp. could effectively exploit high CO₂ concentration (15%) for longer duration under high concentration of glucose supplementation (9 g/L) producing a biomass of 635.24 ± 39.9 μg/mL with a high total fatty acid methyl ester (FAME) content of 71.29 ± 4.2 μg/mg, significant acetyl-CoA carboxylase enzyme activity and a favorable fatty acid profile: 35.8% palmitic acid, 10.5% linoleic acid and 30.6% linolenic acid. The carbohydrate content was maximum at 10% CO₂ sparged for the longest duration of 90 min under glucose concentration of 9 g/L. This study puts forth an optimal design that can provide evidence on comprehending the carbon assimilation mechanism to enhance production of biomass and biofuels and provide conditions to microalgal species to tolerate CO₂ rich flue gas.

Transcriptome and Metabolome Profiling of a Novel Isolate Chlorella sorokiniana G32 (Chlorophyta) Displaying Enhanced Starch Accumulation at High Growth Rate Under Mixotrophic Condition

Chlorella sorokiniana is one of the most productive microalgal species with a high potential for the production of biofuels and other high value-added molecules. Many studies have focused on its capability of mixotrophic growth using reduced organic carbon and growth pattern shift between autotrophic and mixotrophic conditions. In this study, we investigated growth patterns of a novel isolate, C. sorokiniana G32, under mixotrophic growth conditions supplemented with a low level (1.25 g L-1) and a high level (5 g L-1) of glucose. Physiological, transcriptomic (i.e., RNA-seq), and metabolomic (i.e., LC-MS/MS) methods were used. We showed that peak growth based on OD680nm absorbance is ∼4-fold higher with high glucose vs. low glucose supplementation. Photosynthetic efficiency (Fv/Fm) in G32 mixotrophic cultures with high or low glucose supplementation remains identical to that of G32 phototrophic growth. We also found that the conversion rate between absorbance-based cell density and cell dry weight with high glucose supplementation was lower than with low glucose. This suggests that more cell biomass is produced under high glucose treatment than with low glucose. The result was confirmed via sucrose density gradient centrifugation. It is likely that accumulation of high concentration of starch may account for this effect. Transcriptomic analysis of G32 cultures (i.e., via RNA-seq) in response to reciprocal change of glucose levels reveals that expression of a subset of differentially expressed genes (DEGs) is correlated with the amount of glucose supplementation. These DEGs are designated as glucose-specific responsive (GSR) genes. GSR genes are enriched for a number of energy metabolic pathways. Together with metabolomics data (i.e., LC-MS/MS), we show that under high-level supplementation, glucose is preferentially oxidized through an oxidative pentose phosphate pathway. Collectively, our results indicate the mechanism of regulation of glucose assimilation and energy metabolism in G32 under mixotrophic conditions with different levels of glucose supplementation revealed by transcriptomic and metabolomic analyses. We propose that C. sorokiniana G32 has the potential for the production of high value-added molecules.

Photosynthetic transients in Chlorella sorokiniana during phycoremediation of dairy wastewater under distinct light intensities

The present study is aimed to understand the photosynthetic transients of Chlorella sorokiniana SVMBIOEN2 during treatment of dairy wastewater under different light intensities (100, 150, and 200 µmol m^-2s^-1) in mixotrophic mode. Light intensities showed marked influence on photosystem behavior, lipid profile, and organic pollutant removal. Analysis of Chlorophyll a fluorescence transient including Fv/Fm, ETo/RC, TRo/RC, and Abs/RC showed better photosystem efficiency at 100 µmol m^-2s^-1 operations. OJIP curve fitting depicted a positive L-band at 150 µmol m^-2s^-1 indicating lower kinetic energy of photosystem II (PSII) reaction centres at high light intensities. Better photosynthetic activity at 100 µmol m^-2s^-1 operations resulted in good assimilation of biomass (2.3 g L^-1), carbohydrates (10.2 mg g^-1), and proteins (14 mg g^-1) with a significant reduction in chemical oxygen demand (85%). Phycoremediation of dairy wastewater accumulates predominantly monounsaturated fatty acids followed by polyunsaturated fatty acids showing the application of C. sorokiniana in nutraceutical and food industries.

Evaluation of microalgal strains and microalgal consortium for higher lipid productivity and rich fatty acid profile towards sustainable biodiesel production

This present study has attempted to screen four microalgal strainsChlorella vulgaris, Coelastrellasp.Scenedesmus dimorphusandChlorococcumsp. and consortium for biodiesel application.Coelastrella sp. was found to show marginally higher optical density of 1.13 on 19th day whereas C. vulgaris and S. dimorphus consortium showed 1.59 OD. Regarding the dry cell weight, S. dimorphus and Chlorella vulgaris was found to yield higher DCW at about 0.544 and 0.508 g/L, respectively. In outdoor pond raceway pond, C. vulgaris and S. dimorphus yielded 0.76-0.80 g/L while consortium showed 0.87 g/L biomass. In the case of lipid content, S. dimorphus, C. vulgaris and consortium accumulated 36.4, 35.5 and 39.2% lipids, respectively in lab, whereas in outdoor raceway pond it was 26.4, 32.3 and 34.5%, respectively. The fatty profile of Chlorella and Scenedesmus sp. showed linolelaidic acid, and cis-8,11,14-eicosatrienoic acid as prevalent fatty acids whereas the consortium has 53.5% oleic acid than other fatty acids.

16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera

Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.

Cell Washing and Solution Exchange in Droplet Microfluidic Systems

Water-in-oil emulsion droplet microfluidic systems have been extensively developed, and currently, almost all cell handling steps can be conducted in this format. An exception is the cell washing and solution exchange step, which is commonly utilized in many conventional cell assays. This paper presents an in-droplet cell washing and solution exchange technology that utilizes dielectrophoretic (DEP) force to move all cells to one side of a droplet, followed by asymmetrical splitting of the droplet to obtain a small daughter droplet that contains all or most of the cells, and then finally merges this cell-concentrated droplet with a new droplet that contains the desired solution. These sequential droplet manipulation steps were integrated into a single platform, where up to 88% of the original solution in the droplet could be exchanged with the new solution while keeping cell loss to less than 5%. Two application examples were demonstrated using the developed technology. In the first example, green microalga Chlamydomonas reinhardtii cells were manipulated using negative DEP force to exchange the regular culture medium with a nitrogen-limited medium to induce lipid production. In the second example, Salmonella enterica cells were manipulated using positive DEP force to replace fluorescent dye that models fluorescent cell stains that contribute to high background noise in fluorescence-based droplet content detection with fresh buffer solution, significantly improving the droplet content detection sensitivity. Since the cell washing step is one of the most frequently utilized steps in many cell biology assays, we expect that the developed technology can significantly broaden the type of assay that can be conducted in droplet microfluidic format.

Transcriptome-based analysis of the effects of salicylic acid and high light on lipid and astaxanthin accumulation in Haematococcus pluvialis

BACKGROUND

The unicellular alga Haematococcus pluvialis has achieved considerable interests for its capacity to accumulate large amounts of triacylglycerol and astaxanthin under various environmental stresses. To our knowledge, studies focusing on transcriptome research of H. pluvialis under exogenous hormones together with physical stresses are rare. In the present study, the change patterns at transcriptome level were analyzed to distinguish the multiple defensive systems of astaxanthin and fatty acid metabolism against exogenous salicylic acid and high light (SAHL) stresses.

RESULTS

Based on RNA-seq data, a total of 112,463 unigenes and 61,191 genes were annotated in six databases, including NR, KEGG, Swiss-Prot, PFAM, COG and GO. Analysis of differentially expressed genes (DEGs) in KEGG identified many transcripts that associated with the biosynthesis of primary and secondary metabolites, photosynthesis, and immune system responses. Furthermore, 705 unigenes predicted as putative transcription factors (TFs) were identified, and the most abundant TFs families were likely to be associated with the biosynthesis of astaxanthin and fatty acid in H. pluvialis upon exposure to SAHL stresses. Additionally, majority of the fifteen key genes involved in astaxanthin and fatty acid biosynthesis pathways presented the same expression pattern, resulting in increased accumulation of astaxanthin and fatty acids in single celled H. pluvialis, in which astaxanthin content increased from 0.56 ± 0.05 mg·L-1 at stage Control to 0.89 ± 0.12 mg·L-1 at stage SAHL_48. And positive correlations were observed among these studied genes by Pearson Correlation (PC) analysis, indicating the coordination between astaxanthin and fatty acid biosynthesis. In addition, protein-protein interaction (PPI) network analysis also demonstrated that this coordination might be at transcriptional level.

CONCLUSION

The results in this study provided valuable information to illustrate the molecular mechanisms of coordinate relations between astaxanthin and fatty acid biosynthesis. And salicylic acid might play a role in self-protection processes of cells, helping adaption of H. pluvialis to high light stress.

Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity

Eukaryotic organisms regulate the organization, structure, and accessibility of their genomes through chromatin remodeling that can be inherited as epigenetic modifications. These DNA and histone protein modifications are ultimately responsible for an organism's molecular adaptation to the environment, resulting in distinctive phenotypes. Epigenetic manipulation of algae holds yet untapped potential for the optimization of biofuel production and bioproduct formation; however, epigenetic machinery and modes-of-action have not been well characterized in algae. We sought to determine the extent to which the biofuel platform species Picochlorum soloecismus utilizes DNA methylation to regulate its genome. We found candidate genes with domains for DNA methylation in the P. soloecismus genome. Whole-genome bisulfite sequencing revealed DNA methylation in all three cytosine contexts (CpG, CHH, and CHG). While global DNA methylation is low overall (∼1.15%), it occurs in appreciable quantities (12.1%) in CpG dinucleotides in a bimodal distribution in all genomic contexts, though terminators contain the greatest number of CpG sites per kilobase. The P. soloecismus genome becomes hypomethylated during the growth cycle in response to nitrogen starvation. Algae cultures were treated daily across the growth cycle with 20 μM 5-aza-2'-deoxycytidine (5AZA) to inhibit propagation of DNA methylation in daughter cells. 5AZA treatment significantly increased optical density and forward and side scatter of cells across the growth cycle (16 days). This increase in cell size and complexity correlated with a significant increase (∼66%) in lipid accumulation. Site specific CpG DNA methylation was significantly altered with 5AZA treatment over the time course, though nitrogen starvation itself induced significant hypomethylation in CpG contexts. Genes involved in several biological processes, including fatty acid synthesis, had altered methylation ratios in response to 5AZA; we hypothesize that these changes are potentially responsible for the phenotype of early induction of carbon storage as lipids. This is the first report to utilize epigenetic manipulation strategies to alter algal physiology and phenotype. Collectively, these data suggest these strategies can be utilized to fine-tune metabolic responses, alter growth, and enhance environmental adaption of microalgae for desired outcomes.

Using flow cytometry and multistage machine learning to discover label-free signatures of algal lipid accumulation

Most applications of flow cytometry or cell sorting rely on the conjugation of fluorescent dyes to specific biomarkers. However, labeled biomarkers are not always available, they can be costly, and they may disrupt natural cell behavior. Label-free quantification based upon machine learning approaches could help correct these issues, but label replacement strategies can be very difficult to discover when applied labels or other modifications in measurements inadvertently modify intrinsic cell properties. Here we demonstrate a new, but simple approach based upon feature selection and linear regression analyses to integrate statistical information collected from both labeled and unlabeled cell populations and to identify models for accurate label-free single-cell quantification. We verify the method’s accuracy to predict lipid content in algal cells (Picochlorum soloecismus) during a nitrogen starvation and lipid accumulation time course. Our general approach is expected to improve label-free single-cell analysis for other organisms or pathways, where biomarkers are inconvenient, expensive, or disruptive to downstream cellular processes.

Genomic Analysis of Picochlorum Species Reveals How Microalgae May Adapt to Variable Environments

Understanding how microalgae adapt to rapidly changing environments is not only important to science but can help clarify the potential impact of climate change on the biology of primary producers. We sequenced and analyzed the nuclear genome of multiple Picochlorum isolates (Chlorophyta) to elucidate strategies of environmental adaptation. It was previously found that coordinated gene regulation is involved in adaptation to salinity stress, and here we show that gene gain and loss also play key roles in adaptation. We determined the extent of horizontal gene transfer (HGT) from prokaryotes and their role in the origin of novel functions in the Picochlorum clade. HGT is an ongoing and dynamic process in this algal clade with adaptation being driven by transfer, divergence, and loss. One HGT candidate that is differentially expressed under salinity stress is indolepyruvate decarboxylase that is involved in the production of a plant auxin that mediates bacteria-diatom symbiotic interactions. Large differences in levels of heterozygosity were found in diploid haplotypes among Picochlorum isolates. Biallelic divergence was pronounced in P. oklahomensis (salt plains environment) when compared with its closely related sister taxon Picochlorum SENEW3 (brackish water environment), suggesting a role of diverged alleles in response to environmental stress. Our results elucidate how microbial eukaryotes with limited gene inventories expand habitat range from mesophilic to halophilic through allelic diversity, and with minor but important contributions made by HGT. We also explore how the nature and quality of genome data may impact inference of nuclear ploidy.

Physiological Properties of Photoautotrophic Microalgae and Cyanobacteria Relevant to Industrial Biomass Production

Photoautotrophic mass culture of microalgae is currently under investigation for social implementation, since such organisms are anticipated to be resources of alternative fuels and materials for reducing global warming. Production scale-up of culture systems and economy balance are great barriers for practical usage. In order to develop new culture systems such as attachment on solid surfaces or biofilms, we investigated various characteristics of photosynthesis in Chlorella, not only in liquid but also on filter membranes. In aquatic cultures, the photosynthetic rate was almost the same as the specific exponential growth rate at over 32 °C, suggesting that highly efficient cell growth was achieved at that temperature. The algal cells could fix about 50 mmol carbons per mole photons, at cloudy-day-level light intensities, which result to produce 1.2 g dry cell weight in calculation. Moreover, Chlorella could grow on a membrane surface at almost the same rate as in liquid. Similar tolerance to water deficiency was observed in a cyanobacterium, Synechocystis, in which gene expression responded in 30 min after the stress. Such a tolerance was also observed in other species of microalgae and cyanobacteria in photosynthesis.

Molecular Genetic Tools and Emerging Synthetic Biology Strategies to Increase Cellular Oil Content in Chlamydomonas reinhardtii

Microalgae constitute a highly diverse group of eukaryotic and photosynthetic microorganisms that have developed extremely efficient systems for harvesting and transforming solar energy into energy-rich molecules such as lipids. Although microalgae are considered to be one of the most promising platforms for the sustainable production of liquid oil, the oil content of these organisms is naturally low, and algal oil production is currently not economically viable. Chlamydomonas reinhardtii (Chlamydomonas) is an established algal model due to its fast growth, high transformation efficiency, and well-understood physiology and to the availability of detailed genome information and versatile molecular tools for this organism. In this review, we summarize recent advances in the development of genetic manipulation tools for Chlamydomonas, from gene delivery methods to state-of-the-art genome-editing technologies and fluorescent dye-based high-throughput mutant screening approaches. Furthermore, we discuss practical strategies and toolkits that enhance transgene expression, such as choice of expression vector and background strain. We then provide examples of how advanced genetic tools have been used to increase oil content in Chlamydomonas. Collectively, the current literature indicates that microalgal oil content can be increased by overexpressing key enzymes that catalyze lipid biosynthesis, blocking lipid degradation, silencing metabolic pathways that compete with lipid biosynthesis and modulating redox state. The tools and knowledge generated through metabolic engineering studies should pave the way for developing a synthetic biological approach to enhance lipid productivity in microalgae.

Microalgae biochar-derived carbon dots and their application in heavy metal sensing in aqueous systems

This research seeks a coupled solution for managing the large amounts of biochar produced by microalgae biofuel production, and the necessity for novel, economic and accurate heavy metal sensing methods. Therefore, this study evaluated the transformation of microalgae biochar (MAB) into carbon dots (Cdots) and their subsequent application as heavy metal ion sensors in aqueous systems. The experimental phase included the transformation of MAB into microalgae biochar-derived carbon dots (MAB-Cdots), MAB-Cdot characterisation and the evaluation of the MAB-Cdots as transducers for the detection of four heavy metal ions (Pb²⁺, Cu²⁺, Cd²⁺, and Ni²⁺). MAB-Cdot fluorescence was stable over a wide range of pH and resistant to photo-bleaching, making them suitable as fluorescence probes. The MAB-Cdot fluorescence was quenched by all of the metal ions and displayed different quenching levels. Depending upon the ions involved, MAB-Cdots were used to detect the presence of heavy metal ions from concentrations of 0.012 μM up to 2 mM by measuring the reduction in fluorescence intensity. Neutral and slightly alkaline pHs were optimal for Cu²⁺ Ni²⁺ and Pb²⁺ heavy metal quenching. To quantify the concentration of the heavy metal ions, linear and logarithmic functions were used to model the MAB-Cdot fluorescence quenching. The sensing mechanism was determined to be reversible and purely collisional with some fluorophores less accessible than the others. This work demonstrated the ability to produce Cdots from microalgae biochar, examined their application as a transducer for detecting heavy metal ions in aqueous systems and paves the way for novel sensing systems using MAB-Cdots.

Production of lipid-containing algal-bacterial polyculture in wastewater and biomethanation of lipid extracted residues: Enhancing methane yield through hydrothermal pretreatment and relieving solvent toxicity through co-digestion

The feasibility of generating a lipid-containing algal-bacterial polyculture biomass in municipal primary wastewater and enhancing biomethanation of lipid-extracted algal residues (LEA) through hydrothermal pretreatment and co-digestion with sewage sludge (SS) was investigated. In high-rate algal ponds, the polyculture of native algal and bacteria species demonstrated a monthly average net and gross biomass productivity of 30 ± 3 and 36 ± 3 g_AFDW m^-2 day^-1 (summer season). The algal community was dominated by Micractinium sp. followed by Scenedesmus sp., Chlorella sp., pennate diatoms and Chlamydomonas sp. The polyculture metabolic activities resulted in average reductions of wastewater volatile suspended solids (VSS), carbonaceous soluble biochemical oxygen demand (csBOD₅) and total nitrogen (N_total) of 63 ± 18%, 98 ± 1% and 76 ± 21%, respectively. Harvested biomass contained nearly 23% lipid content and an extracted blend of fatty acid methyl esters satisfied the ASTM D6751 standard for biodiesel. Anaerobic digestion of lipid extracted algal residues (LEA) demonstrated long lag-phase in methane production of 17 days and ultimate methane yield of 296 ± 2 mL/gVS (or ~50% of theoretical), likely because to its limited biodegradability and toxicity due to presence of the residual solvent (hexane). Hydrothermal pretreatment increased the ultimate methane yield and production rate by 15-30% but did not mitigate solvent toxicity effects completely leading to less substantial improvement in energy output of 5-20% and diminished Net Energy Ratio (NER < 1). In contrast, co-digestion of LEA with sewage sludge (10% to 90% ratio) was found to minimize solvent toxicity and improve methane yield enhancing the energy output ~4-fold, compared to using LEA as a single substrate, and advancing NER to 4.2.

The lipid biochemistry of eukaryotic algae

Algal lipid metabolism fascinates both scientists and entrepreneurs due to the large diversity of fatty acyl structures that algae produce. Algae have therefore long been studied as sources of genes for novel fatty acids; and, due to their superior biomass productivity, algae are also considered a potential feedstock for biofuels. However, a major issue in a commercially viable "algal oil-to-biofuel" industry is the high production cost, because most algal species only produce large amounts of oils after being exposed to stress conditions. Recent studies have therefore focused on the identification of factors involved in TAG metabolism, on the subcellular organization of lipid pathways, and on interactions between organelles. This has been accompanied by the development of genetic/genomic and synthetic biological tools not only for the reference green alga Chlamydomonas reinhardtii but also for Nannochloropsis spp. and Phaeodactylum tricornutum. Advances in our understanding of enzymes and regulatory proteins of acyl lipid biosynthesis and turnover are described herein with a focus on carbon and energetic aspects. We also summarize how changes in environmental factors can impact lipid metabolism and describe present and potential industrial uses of algal lipids.

Down-Selection and Outdoor Evaluation of Novel, Halotolerant Algal Strains for Winter Cultivation

Algae offer promising feedstocks for the production of renewable fuel and chemical intermediates. However, poor outdoor winter cultivation capacity currently limits deployment potential. In this study, 300 distinct algal strains were screened in saline medium to determine their cultivation suitability during winter conditions in Mesa, Arizona. Three strains, from the genera Micractinium, Chlorella, and Scenedesmus, were chosen following laboratory evaluations and grown outdoors in 1000 L raceway ponds during the winter. Strains were down-selected based on doubling time, lipid and carbohydrate amount, final biomass accumulation capacity, cell size and phylogenetic diversity. Algal biomass productivity and compositional analysis for lipids and carbohydrates show successful outdoor deployment and cultivation under winter conditions for these strains. Outdoor harvest-yield biomass productivities ranged from 2.9 to 4.0 g/m2/day over an 18 days winter cultivation trial, with maximum productivities ranging from 4.0 to 6.5 g/m2/day, the highest productivities reported to date for algal winter strains grown in saline media in open raceway ponds. Peak fatty acid levels ranged from 9 to 26% percent of biomass, and peak carbohydrate levels ranged from 13 to 34% depending on the strain. Changes in the lipid and carbohydrate profile throughout outdoor growth are reported. This study demonstrates that algal strain screening under simulated outdoor environmental conditions in the laboratory enables identification of strains with robust biomass productivity and biofuel precursor composition. The strains isolated here represent promising winter deployment candidates for seasonal algal biomass production when using crop rotation strategies.

Advanced genetic tools enable synthetic biology in the oleaginous microalgae Nannochloropsis sp

Nannochloropsis is a genus of fast-growing microalgae that are regularly used for biotechnology applications. Nannochloropsis species have a high triacylglycerol content and their polar lipids are rich in the omega-3 long-chain polyunsaturated fatty acid, eicosapentaenoic acid. Placed in the heterokont lineage, the Nannochloropsis genus has a complex evolutionary history. Genome sequences are available for several species, and a number of transcriptomic datasets have been produced, making this genus a facile model for comparative genomics. There is a growing interest in Nannochloropsis species as models for the study of microalga lipid metabolism and as a chassis for synthetic biology. Recently, techniques for gene stacking, and targeted gene disruption and repression in the Nannochloropsis genus have been developed. These tools enable gene-specific, mechanistic studies and have already allowed the engineering of improved Nannochloropsis strains with superior growth, or greater bioproduction.

Quantum Yield and Fatty Acid Profile Variations With Nutritional Mode During Microalgae Cultivation

Microalgae are gaining commercial interests in the areas food, feed and biofuel sector. They have intrinsic ability to harness energy from sunlight and photosynthetically valorize CO2 into various bio-based products viz., triacylglycerols (TAGs), mono/poly-unsaturated fatty acids (MUFA, PUFA), pigments etc. Microalgae have adapted to grow in various nutritional environments due to their metabolic versatility and resilience. Strategic evaluation of newly isolated strain Chlorella sp. from a residential lake was performed. The strain was investigated by varying the nutritional modes to gain insights into biomass and fatty acids production. Maximum biomass (3.59 g/L) was observed in mixotrophic condition followed by heterotrophic (1.58 g/L) and autotrophic condition (0.59 g/L). The maximum lipid yield (670 mg/g DCW) was observed in mixotrophic condition whereas maximum total lipid content (36%) was observed in heterotrophic condition. Significant correlation was noticed between fluorescence parameters measured by OJIP and non-photochemical quenching (NPQ) with the function of nutritional mode variations. Autotrophic condition showed higher photosynthetic activity which was well correlated with high fluorescence intensity as represented by OJIP, NPQ1, and NPQ2 curves. Good balance of saturated fatty acids (SFA) and unsaturated fatty acids was observed in autotrophic mode, whereas polyunsaturated fatty acids (PUFA) and mono unsaturated fatty acid (MUFA) content were relatively higher in mixotrophic and heterotrophic conditions.

Low-phosphate-selected Auxenochlorella protothecoides redirects phosphate to essential pathways while producing more biomass

Despite the capacity to accumulate ~70% w/w of lipids, commercially produced unicellular green alga A. protothecoides may become compromised due to the high cost of phosphate fertilizers. To address this limitation A. protothecoides was selected for adaptation to conditions of 100× and 5× lower phosphate and peptone, respectively, compared to 'wild-type media'. The A. protothecoides showed initial signs of adaptation by 45-50 days, and steady state growth at ~100 days. The low phosphate (P)-adapted strain produced up to ~30% greater biomass, while total lipids (~10% w/w) remained about the same, compared to the wild-type strain. Metabolomic analyses indicated that the low P-adapted produced 3.3-fold more saturated palmitic acid (16:0) and 2.2-fold less linolenic acid (18:3), compared to the wild-type strain, resulting in an ~11% increase in caloric value, from 19.5kJ/g for the wild-type strain to 21.6kJ/g for the low P-adapted strain, due to the amounts and composition of certain saturated fatty acids, compared to the wild type strain. Biochemical changes in A. protothecoides adapted to lower phosphate conditions were assessed by comparative RNA-Seq analysis, which yielded 27,279 transcripts. Among them, 2,667 and 15 genes were significantly down- and up-regulated, at >999-fold and >3-fold (adjusted p-value <0.1), respectively. The expression of genes encoding proteins involved in cellular processes such as division, growth, and membrane biosynthesis, showed a trend toward down-regulation. At the genomic level, synonymous SNPs and Indels were observed primarily in coding regions, with the 40S ribosomal subunit gene harboring substantial SNPs. Overall, the adapted strain out-performed the wild-type strain by prioritizing the use of its limited phosphate supply for essential biological processes. The low P-adapted A. protothecoides is expected to be more economical to grow over the wild-type strain, based on overall greater productivity and caloric content, while importantly, also requiring 100-fold less phosphate.

Nuclear, Chloroplast, and Mitochondrial Genome Sequences of the Prospective Microalgal Biofuel Strain Picochlorum soloecismus

Picochlorum soloecismus is a halotolerant, fast-growing, and moderate-lipid-producing microalga that is being evaluated as a renewable feedstock for biofuel production. Herein, we report on an improved high-quality draft assembly and annotation for the nuclear, chloroplast, and mitochondrial genomes of P. soloecismus DOE 101.

Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species Scenedesmus obliquus Strain DOE0152z

The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

Algae to Economically Viable Low-Carbon-Footprint Oil

Algal oil as an alternative to fossil fuel has attracted attention since the 1940s, when it was discovered that many microalgae species can produce large amounts of lipids. Economics and energy security were the motivational factors for a spurt in algae research during the 1970s, 1990s, and early 2000s. Whenever crude prices declined, research on algae stopped. The scenario today is different. Even given low and volatile crude prices ($30-$50/barrel), interest in algae continues all over the world. Algae, with their cure-all characteristics, have the potential to provide sustainable solutions to problems in the energy-food-climate nexus. However, after years of effort, there are no signs of algae-to-biofuel technology being commercialized. This article critically reviews past work; summarizes the current status of the technology; and based on the lessons learned, provides a balanced perspective on a potential path toward commercialization of algae-to-oil technology.