New paradigm in diatom omics and genetic manipulation

Towards sustainable diatom biorefinery: Recent trends in cultivation and applications

Diatoms, with their complex cellular architecture, have been recognized as a source of limitless potential. These microbes are common in freshwater and marine habitats and are essential for primary production and carbon sequestration. They are excellent at utilizing nutrients, providing a sustainable method of treating wastewater while also producing biomass rich in beneficial substances like vitamins, carotenoids, polysaccharides, lipids, omega-3 fatty acids, pigments, and novel bioactive molecules. Additionally, they are highly efficient organisms that can be employed to monitor the environment by acting as trustworthy indicators of water quality. This comprehensive review explores the multifaceted applications of diatoms in a variety of fields, such as bioremediation, aquaculture, value-added products, and other applications. The review set out on a path towards greener, more sustainable methods amicable to both industry and the environment by utilizing theenormous diverse biotechnological potentials of diatoms.

Effect of Salinity on Reproduction and Fatty Acid Profile of the Microalga Nitzschia сf. thermaloides

The microalga Nitzschia cf. thermaloides was found in reservoirs of mud volcanoes in eastern Crimea. The species was observed to have a wide range of halotolerance and, in particular, to be capable of vegetative reproduction within a substrate salinity range of 0-110‰. The effect of salinity on the fatty acid (FA) profile was for the first time studied in N. cf. thermaloides. The quantitative and qualitative FA composition remained unchanged regardless of salinity, suggesting maintenance of a stable compacted membrane structure, which probably contributes to the species adaptation to salinity. Saturated FAs accounted for a major portion of total FAs, and the species was therefore assumed to provide a potentially valuable source of saturated FAs for biotechnology and an alternative raw material for biofuel.

Assessing radiation dosimetry for microorganisms in naturally radioactive mineral springs using GATE and Geant4-DNA Monte Carlo simulations

Mineral springs in Massif Central, France can be characterized by higher levels of natural radioactivity in comparison to the background. The biota in these waters is constantly under radiation exposure mainly from the α-emitters of the natural decay chains, with 226Ra in sediments ranging from 21 Bq/g to 43 Bq/g and 222Rn activity concentrations in water up to 4600 Bq/L. This study couples for the first time micro- and nanodosimetric approaches to radioecology by combining GATE and Geant4-DNA to assess the dose rates and DNA damages to microorganisms living in these naturally radioactive ecosystems. It focuses on unicellular eukaryotic microalgae (diatoms) which display an exceptional abundance of teratological forms in the most radioactive mineral springs in Auvergne. Using spherical geometries for the microorganisms and based on γ-spectrometric analyses, we evaluate the impact of the external exposure to 1000 Bq/L 222Rn dissolved in the water and 30 Bq/g 226Ra in the sediments. Our results show that the external dose rates for diatoms are significant (9.7 μGy/h) and comparable to the threshold (10 μGy/h) for the protection of the ecosystems suggested by the literature. In a first attempt of simulating the radiation induced DNA damage on this species, the rate of DNA Double Strand Breaks per day is estimated to 1.11E-04. Our study confirms the significant mutational pressure from natural radioactivity to which microbial biodiversity has been exposed since Earth origin in hydrothermal springs.

Evaluation of the antioxidative response of diatoms grown on emerging steroidal contaminants

With increasing anthropic activities, a myriad of typical contaminants from industries, hospitals, and municipal discharges have been found which fail to be categorized under regulatory standards and are hence considered contaminants of "emerging concern". Since these pollutants are not removed effectively even by the conventional treatment systems, they tend to inflict potential threats to both human and aquatic life. However, microalgae-mediated remediation strategies have recently gained worldwide importance owing to their role in carbon fixation, low operational cost, and production of high-value products. In this study, centric diatom Chaetoceros neogracilis was exposed to different concentrations of estradiol (E2)-induced synthetic media ranging from 0 to 2 mg L^-1, and its impact on the antioxidative system of algae was investigated. The results demonstrate that the nutrient stress caused a strong oxidative response elevating the superoxide dismutase (SOD) activity and malondialdehyde (MDA) content in the 2 mg L^-1 E2-treated diatom cultures. However, the specific activity of the H₂O₂ radical scavenging enzymes like catalase (CAT) was inhibited by the E2 treatment, while that of ascorbate peroxidase (APX) remained comparable to the control (0 mg L^-1 of E2). Thus, the study reveals the scope of diatoms as potential indicators of environmental stress even under the varying concentration of a single contaminant (E2).

Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy

Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic strategy. In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins, accounting for ~ 81% of the predicted protein-coding genes. Proteogenomic analysis identified 1235 novel genes, 975 revised genes, 104 splice variants and 234 single amino acid variants. Furthermore, our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions. These findings substantially improve the genome annotation of T. pseudonana and provide insights into new biological functions of diatoms. This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00161-y.

Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity

Microalgae have drawn much attention for their potential applications as a sustainable source for developing bioactive compounds, functional foods, feeds, and biofuels. Diatoms, as one major group of microalgae with high yields and strong adaptability to the environment, have shown advantages in developing photosynthetic cell factories to produce value-added compounds, including heterologous bioactive products. However, the commercialization of diatoms has encountered several obstacles that limit the potential mass production, such as the limitation of algal productivity and low photosynthetic efficiency. In recent years, systems and synthetic biology have dramatically improved the efficiency of diatom cell factories. In this review, we discussed first the genome sequencing and genome-scale metabolic models (GEMs) of diatoms. Then, approaches to optimizing photosynthetic efficiency are introduced with a focus on the enhancement of biomass productivity in diatoms. We also reviewed genome engineering technologies, including CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing to produce bioactive compounds in diatoms. Finally, we summarized the recent progress on the diatom cell factory for producing heterologous compounds through genome engineering to introduce foreign genes into host diatoms. This review also pinpointed the bottlenecks in algal engineering development and provided critical insights into the future direction of algal production.

Genetic and non-genetic tailoring of microalgae for the enhanced production of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) - A review

The myriad health benefits associated with eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) laid the path for their application in the functional foods and nutraceutical industries. Fish being primarily exploited for extraction of EPA and DHA are unsustainable sources; thus, oleaginous microalgae turn out to be an alternative sustainable source. This review paper aims to provide the recent developments in the context of enhancing EPA and DHA production by utilising non-genetic tailoring and genetic tailoring methods. We have also summarized the legislation, public perception, and possible risks associated with the usage of genetically modified microalgae focusing on EPA and DHA production.

Insights into the genetic and metabolic engineering approaches to enhance the competence of microalgae as biofuel resource: A review

Conventional fuel resources are overburden with speedy global energy demand which ensued the urgent need of alternate energy resources. Biofuel generation efficiency of microalgae is notable due to their comparatively rapid biomass production rate and high oil content. But, the employment of microalgae as biofuel resource is in infancy due to low productivity and high production cost. The issues can be addressed by employing engineered microalgal strains that would be able to efficiently generate enhanced levels of biomass with augmented lipid and/or carbohydrate content for proficient biofuel production. Genetic alterations and metabolic engineering of microalgal species might be helpful in developing high stress-tolerant strains with improved properties for biofuel generation. Various omics approaches appeared significant to upgrade the microalgal lipid production. Intervention of genetic and metabolic engineering approaches would facilitate the development of microalgae as a competent biofuel resource and inflate the economic commercialization of biofuels.

Impact of organic carbon acquisition on growth and functional biomolecule production in diatoms

Diatoms are unicellular photosynthetic protists which constitute one of the most successful microalgae contributing enormously to global primary productivity and nutrient cycles in marine and freshwater habitats. Though they possess the ability to biosynthesize high value compounds like eicosatetraenoic acid (EPA), fucoxanthin (Fx) and chrysolaminarin (Chrl) the major bottle neck in commercialization is their inability to attain high density growth. However, their unique potential of acquiring diverse carbon sources via varied mechanisms enables them to adapt and grow under phototrophic, mixotrophic as well as heterotrophic modes. Growth on organic carbon substrates promotes higher biomass, lipid, and carbohydrate productivity, which further triggers the yield of various biomolecules. Since, the current mass culture practices primarily employ open pond and tubular photobioreactors for phototrophic growth, they become cost intensive and economically non-viable. Therefore, in this review we attempt to explore and compare the mechanisms involved in organic carbon acquisition in diatoms and its implications on mixotrophic and heterotrophic growth and biomolecule production and validate how these strategies could pave a way for future exploration and establishment of sustainable diatom biorefineries for novel biomolecules.