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

Ectoine production through a marine methanotroph-microalgae culture allows complete biogas valorization

Methanotrophs have recently emerged as a promising platform for producing bio-based chemicals, like ectoine, from biogas, offering an economical alternative to glucose. However, most studies have focused solely on CH4 consumption, often overlooking the CO2, which is both produced by methanotrophs and present in biogas, despite its potential as a carbon source for microorganisms, such as microalgae. In this study, marine methanotrophic-microalgal cultures were enriched from environmental samples collected at the North Sea coast to explore ectoine production from both CH4 and CO2 in biogas. The sediment-derived culture exhibited the highest CH4 removal efficiency and CO2 uptake, and was selected for further experiments. The culture was primarily composed of Methylobacter marinus, Methylophaga marina, and the microalga Picochlorum oklahomensis. Gas consumption, growth, and ectoine production were evaluated under varying salinity levels and osmotic stress. The NaCl concentrations above 6% negatively impacted CH4 oxidation and inhibited ectoine synthesis, while osmotic shocks enhanced ectoine accumulation, with a maximum ectoine content of 51.3 mgectoine gVSS-1 at 4.5% NaCl. This study is the first to report ectoine production from methanotroph-microalgal cultures, showing its potential for biogas valorization into high-value bio-based chemicals, like ectoine, marking a significant step toward sustainable biogas utilization.

Exceptional Quantum Efficiency Powers Biomass Production in Halotolerant Algae Picochlorum sp.. PHOTOSYNTHESIS RESEARCH 2024;162:439-457. [PMID: 38329705 DOI: 10.1007/s11120-024-01075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The green algal genus Picochlorum is of biotechnological interest because of its robust response to multiple environmental stresses. We compared the metabolic performance of P. SE3 and P. oklahomense to diverse microbial phototrophs and observed exceptional performance of photosystem II (PSII) in light energy conversion in both Picochlorum species. The quantum yield (QY) for O2 evolution is the highest of any phototroph yet observed, 32% (20%) by P. SE3 (P. okl) when normalized to total PSII subunit PsbA (D1) protein, and 80% (75%) normalized per active PSII, respectively. Three factors contribute: (1) an efficient water oxidizing complex (WOC) with the fewest photochemical misses of any organism; (2) faster reoxidation of reduced (PQH2)B in P. SE3 than in P. okl. (period-2 Fourier amplitude); and (3) rapid reoxidation of the plastoquinol pool by downstream electron carriers (Cyt b6f/PETC) that regenerates PQ faster in P. SE3. This performance gain is achieved without significant residue changes around the QB site and thus points to a pull mechanism involving faster PQH2 reoxidation by Cyt b6f/PETC that offsets charge recombination. This high flux in P. SE3 may be explained by genomically encoded plastoquinol terminal oxidases 1 and 2, whereas P. oklahomense has neither. Our results suggest two distinct types of PSII centers exist, one specializing in linear electron flow and the other in PSII-cyclic electron flow. Several amino acids within D1 differ from those in the low-light-descended D1 sequences conserved in Viridiplantae, and more closely match those in cyanobacterial high-light D1 isoforms, including changes near tyrosine Yz and a water/proton channel near the WOC. These residue changes may contribute to the exceptional performance of Picochlorum at high-light intensities by increasing the water oxidation efficiency and the electron/proton flux through the PSII acceptors (QAQB).

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.

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.

Seasonal Variability of Photosynthetic Microbial Eukaryotes (<3 µm) in the Kara Sea Revealed by 18S rDNA Metabarcoding of Sediment Trap Fluxes

This survey is the first to explore the seasonal cycle of microbial eukaryote diversity (<3 µm) using the NGS method and a 10-month sediment trap (2018–2019). The long-term trap was deployed from September to June in the northwestern part of the Kara Sea. A water sample collected before the sediment trap was deployed and also analyzed. The taxonomic composition of microbial eukaryotes in the water sample significantly differed from sediment trap samples, characterized by a high abundance of Ciliophora reads and low abundance of Fungi while trap samples contained an order of magnitude less Ciliophora sequences and high contribution of Fungi. Photosynthetic eukaryotes (PEs) accounting for about 34% of total protists reads were assigned to five major divisions: Chlorophyta, Cryptophyta, Dinoflagellata, Haptophyta, and Ochrophyta. The domination of phototrophic algae was revealed in late autumn. Mamiellophyceae and Trebouxiophyceae were the predominant PEs in mostly all of the studied seasons. Micromonas polaris was constantly present throughout the September–June period in the PE community. The obtained results determine the seasonal dynamics of picoplankton in order to improve our understanding of their role in polar ecosystems.

Characterization of the gut microbes of greater wax moth (Galleria mellonella Linnaeus) shows presence of potential polymer degraders

Greater wax moth (GWM), Galleria mellonella (Lepidoptera: Pyralidae), is a highly destructive honey bee pest prevalent throughout the world. It is considered as a major factor to the alarming decline in honey bee population. GWM destroys active honey combs as it feeds on the beeswax and lays eggs in bee hives, and the primary food of their larva is beeswax. Beeswax is a polymer composed mainly of saturated and unsaturated, linear and complex monoesters, and hydrocarbons. The most frequent bond in beeswax is ethene (CH₂-CH₂) which is also found in the common plastic polyethylene. As wax-digestion is not a common animal character, we hypothesized about a possible role of GWM gut microflora in the process; which could possibly degrade polyethylene-like polymers as well. This study was aimed to identify the GWM gut microflora via culture-dependant approach. We characterized several bacterial species based on the culture characteristics, Gram-reaction, and various biochemical tests. Sequencing of 16S-rDNA revealed nine bacterial and one microalgal species from GWM gut. The bacterial species included Gram-positive Exiguobacterium aestuarii, Bacillus circulans, Microbacterium zaea, Microbacterium sp. and Enterococcus faecalis; Gram-negative Agrobacterium sp., Sphingomonas pseudosanguinis, Sphingobium yanoikuyae and Acinetobacter radioresistens; the microalgae was Picochlorum oklahomensis. Some of them have been previously reported to degrade polycyclic aromatic hydrocarbon, low-density polyethylene, and 2-methylphenanthrene. Meanwhile, the microalga, P. oklahomensis, was reported to steal bacterial genes to adapt with abiotic stresses. Further investigation is necessary to explore the precise details about polymer degrading capabilities of these microbes; nevertheless, this study builds a foundation for elaborate and advanced future research.

Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery

Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for nonmodel organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved proximal orthologous gene pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte–chlorophyte split, 1,000 Ma. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid, “sunscreen,” neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene. Mutants of the ArsJ-like transporter and phosphoglycerate kinase-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.

A Review of Algae-Based Produced Water Treatment for Biomass and Biofuel Production

Produced water (PW), the largest waste stream generated in oil and gas industries, has the potential to be a harmless product rather than being a waste. Biological processes using microorganisms have proven useful to remediate PW contaminated by petroleum hydrocarbons, complex organic chemicals, and solvents. In particular, the bioremediation of PW using algae is an eco-friendly and low-cost approach due to algae’s ability to utilize certain pollutants as nutrient sources. Therefore, the utilization of PW as an algal growth medium has a great potential to eliminate chemicals from the PW and minimize the large volumes of freshwater needed for cultivation. Although several reviews describing the bioremediation of PW have been published, to the best of our knowledge, no review has exclusively focused on the algae-based PW treatment. Therefore, the present review is dedicated to filling this gap by portraying the many different facets of the algae cultivation in PW. Several algal species that are known to thrive in a wide range of salinity and the critical steps for their cultivation in hypersaline PW have been identified. Overall, this comprehensive review highlights the PW bioremediation using algae and brings attention to utilizing PW to grow biomass that can be processed to generate biofuels and useful bioproducts.

Phased Diploid Genome Sequence for the Fast-Growing Microalga Picochlorum celeri

Picochlorum celeri is a fast-growing marine microalga with high biomass productivity. Here, we report the use of PacBio sequencing to assemble the phased diploid genome of P. celeri.

Electrical impedance as an indicator of microalgal cell health

Separating specific cell phenotypes from a heterotypic mixture is a critical step in many research projects. Traditional methods usually require a large sample volume and a complex preparation process that may alter cell property during the sorting process. Here we present the use of electrical impedance as an indicator of cell health and for identifying specific microalgal phenotypes. We developed a microfluidic platform for measuring electrical impedance at different frequencies using the bacterium-sized green alga Picochlorum SE3. The cells were cultured under different salinity conditions and sampled at four different time points. Our results demonstrate the utility of electrical impedance as an indicator of cell phenotype by providing results that are consistent with known changes in cell size and physiology. Outliers in the cell data distribution are particularly useful because they represent phenotypes that have the ability to maintain size and/or membrane ionic permeability under prolonged salt stress. This suggests that our device can be used to identify and sort desired (e.g., experimentally evolved, mutant) cell phenotypes based on their electrical impedance properties.

Development of a high-productivity, halophilic, thermotolerant microalga Picochlorum renovo

Microalgae are promising biocatalysts for applications in sustainable fuel, food, and chemical production. Here, we describe culture collection screening, down-selection, and development of a high-productivity, halophilic, thermotolerant microalga, Picochlorum renovo. This microalga displays a rapid growth rate and high diel biomass productivity (34 g m-2 day-1), with a composition well-suited for downstream processing. P. renovo exhibits broad salinity tolerance (growth at 107.5 g L-1 salinity) and thermotolerance (growth up to 40 °C), beneficial traits for outdoor cultivation. We report complete genome sequencing and analysis, and genetic tool development suitable for expression of transgenes inserted into the nuclear or chloroplast genomes. We further evaluate mechanisms of halotolerance via comparative transcriptomics, identifying novel genes differentially regulated in response to high salinity cultivation. These findings will enable basic science inquiries into control mechanisms governing Picochlorum biology and lay the foundation for development of a microalga with industrially relevant traits as a model photobiology platform.

The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.

Systems Biology of Cold Adaptation in the Polyextremophilic Red Alga Galdieria sulphuraria

Rapid fluctuation of environmental conditions can impose severe stress upon living organisms. Surviving such episodes of stress requires a rapid acclimation response, e.g., by transcriptional and post-transcriptional mechanisms. Persistent change of the environmental context, however, requires longer-term adaptation at the genetic level. Fast-growing unicellular aquatic eukaryotes enable analysis of adaptive responses at the genetic level in a laboratory setting. In this study, we applied continuous cold stress (28°C) to the thermoacidophile red alga G. sulphuraria, which is 14°C below its optimal growth temperature of 42°C. Cold stress was applied for more than 100 generations to identify components that are critical for conferring thermal adaptation. After cold exposure for more than 100 generations, the cold-adapted samples grew ∼30% faster than the starting population. Whole-genome sequencing revealed 757 variants located on 429 genes (6.1% of the transcriptome) encoding molecular functions involved in cell cycle regulation, gene regulation, signaling, morphogenesis, microtubule nucleation, and transmembrane transport. CpG islands located in the intergenic region accumulated a significant number of variants, which is likely a sign of epigenetic remodeling. We present 20 candidate genes and three putative cis-regulatory elements with various functions most affected by temperature. Our work shows that natural selection toward temperature tolerance is a complex systems biology problem that involves gradual reprogramming of an intricate gene network and deeply nested regulators.