Demonstration of the potential of Picochlorum soloecismus as a microalgal platform for the production of renewable fuels

Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis

Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.

Simultaneous CAS9 editing of cpSRP43, LHCA6, and LHCA7 in Picochlorum celeri lowers chlorophyll levels and improves biomass productivity

High cellular pigment levels in dense microalgal cultures contribute to excess light absorption. To improve photosynthetic yields in the marine microalga Picochlorum celeri, CAS9 gene editing was used to target the molecular chaperone cpSRP43. Depigmented strains (>50% lower chlorophyll) were generated, with proteomics showing attenuated levels of most light harvesting complex (LHC) proteins. Gene editing generated two types of cpSRP43 transformants with distinct lower pigment phenotypes: (i) a transformant (Δsrp43) with both cpSRP43 diploid alleles modified to encode non-functional polypeptides and (ii) a transformant (STR30309) with a 3 nt in-frame insertion in one allele at the CAS9 cut site (non-functional second allele), leading to expression of a modified cpSRP43. STR30309 has more chlorophyll than Δsrp43 but substantially less than wild type. To further decrease light absorption by photosystem I in STR30309, CAS9 editing was used to stack in disruptions of both LHCA6 and LHCA7 to generate STR30843, which has higher (5-24%) productivities relative to wild type in solar-simulating bioreactors. Maximal productivities required frequent partial harvests throughout the day. For STR30843, exemplary diel bioreactor yields of ~50 g m-2 day-1 were attained. Our results demonstrate diel productivity gains in P. celeri by lowering pigment levels.

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.

Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. "desiccata" (Trebouxiophyceae, Chlorophyta), formerly Chlorella desiccata, supported by a high-quality genome assembly

Microalgae are diverse, with many gaps remaining in phylogenetic and physiological understanding. Thus, studying new microalgae species increases our broader comprehension of biological diversity, and evaluation of new candidates as algal production platforms can lead to improved productivity under a variety of cultivation conditions. Chlorella is a genus of fast-growing species often isolated from freshwater habitats and cultivated as a source of nutritional supplements. However, the use of freshwater increases competition with other freshwater needs. We identified Chlorella desiccata to be worthy of further investigation as a potential algae production strain, due to its isolation from a marine environment and its promising growth and biochemical composition properties. Long-read genomic sequencing was conducted for C. desiccata UTEX 2526, resulting in a high-quality, near chromosome level, diploid genome with an assembly length of 21.55 Mbp in only 18 contigs. We also report complete circular mitochondrial and chloroplast genomes. Phylogenomic and phylogenetic analyses using nuclear, chloroplast, 18S rRNA, and actin sequences revealed that this species clades within strains currently identified as Nannochloris (Trebouxiophyceae, Chlorophyta), leading to its reclassification as Nannochloris sp. "desiccata" UTEX 2526. The mode of cell division for this species is autosporulation, differing from the type species N. bacillaris. As has occurred across multiple microalgae genera, there are repeated examples of Nannochloris species reclassification in the literature. This high-quality genome assembly and phylogenetic analysis of the potential algal production strain Nannochloris sp. "desiccata" UTEX 2526 provides an important reference and useful tool for further studying this region of the phylogenetic tree.

Influence of Carbon Sources on Biomass and Biomolecule Accumulation in Picochlorum sp. Cultured under the Mixotrophic Condition

The major downfalls of the microalgal biorefinery are low volume of high value product accumulation, low biomass productivity and high cultivation costs. Here, we aimed to improve the biomass productivity of the industrially relevant Picochlorum sp. BDUG 100241 strain. The growth of Picochlorum sp. BDUG 100241 was investigated under different cultivations conditions, including photoautotrophic (with light), mixotrophic (1% glucose, with light) and heterotrophic (1% glucose, without light). Among them, Picochlorum sp. BDUG100241 showed the highest growth in the mixotrophic condition. Under different (1%) carbon sources’ supplementation, including glucose, sodium acetate, glycerol, citric acid and methanol, Picochlorum sp. BDUG100241 growth was tested. Among them, sodium acetate was found to be most suitable carbon source for Picochlorum sp. BDUG 100241 growth, biomass (1.67 ± 0.18 g/L) and biomolecule productivity. From the different concentrations of sodium acetate (0, 2.5, 5.0, 7.5 and 10 g/L) tested, the maximum biomass production of 2.40 ± 0.20 g/L with the biomass productivity of 95 ± 5.00 mg/L/d was measured from 7.5 g/L in sodium acetate. The highest total lipid (53.50 ± 1.70%) and total carotenoids (0.75 ± 0.01 µg/mL) contents were observed at the concentration of 7.5 g/L and 5.0 g/L of sodium acetate as a carbon source, respectively. In conclusion, the mixotrophic growth condition containing 7.5 g/L of sodium acetate showed the maximum biomass yield and biomolecule accumulation compared to other organic carbon sources.

Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet

Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.

Phycoremediation of nitrogen and phosphate from wastewater using Picochlorum sp.: A tenable approach

The wastewater originates from different industrial, municipal, and agriculture processes and contains different nitrogen sources, for example, nitrate, ammonium, nitrite, and phosphate such as inorganic and organic sources. The discharge of high nitrate and phosphate to the ecosystem or nearby water bodies can cause eutrophication which disbalances the aquatic ecosystem. Furthermore, ingestion of these pollutants can cause severe toxicity and disease to humans and animals. Thus, from an environmental and social perspective, its treatment is essential with no negative impact on the ecosystem. Microalgae are fundamental, mixotrophic microorganisms that treat different wastewater and utilize nitrate and phosphate in the medium as a source of nutrients. Among them, Picochlorum sp., have the potential to remove nitrogen and phosphate from wastewater. The biomass produced by Picochlorum sp. can be a promising candidate as a sustainable feedstock for biofuel and bioproducts formation. Thus, the present review provides a brief knowledge and understanding about the concentration of nitrogen and phosphate in different wastewater, their negative impacts, and the uptake mechanism of microalgae. Furthermore, the review also provides an insight into Picochlorum sp., and the effects of different physiological and nutritional factors on their growth, wastewater treatment efficacy, and biomass for value-added products and biorefinery applications. In addition, the review is useful to understand the potential of Picochlorum sp. for a tenable wastewater treatment process.

Picochlorum celeri as a model system for robust outdoor algal growth in seawater

With fast growth rates, broad halotolerance and the ability to thrive at high temperatures, algae in the genus Picochlorum are emerging as promising biomass producers. Recently, we isolated a remarkably productive strain, Picochlorum celeri, that attains > 40 g m-2 day-1 productivities using simulated outdoor light. To test outdoor productivities, Picochlorum celeri was cultivated in 820 L raceway ponds at the Arizona Center for Algae Technology and Innovation. Picochlorum celeri demonstrated the highest outdoor biomass productivities reported to date at this testbed averaging ~ 31 g m-2 day-1 over four months with a monthly (August) high of ~ 36 g m-2 day-1. Several single day productivities were > 40 g m-2 day-1. Importantly for sustainability, Picochlorum celeri achieved these productivities in saline water ranging from seawater to 50 parts per thousand sea salts, without any biocides or pond crashes, for over 143 days. Lastly, we report robust genetic engineering tools for future strain improvements.

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.