Methodological review of genetic engineering approaches for non-model algae

Bioprospection of the Antarctic Diatoms Craspedostauros ineffabilis IMA082A and Craspedostauros zucchelli IMA088A

In extreme environments such as Antarctica, a diverse range of organisms, including diatoms, serve as essential reservoirs of distinctive bioactive compounds with significant implications in pharmaceutical, cosmeceutical, nutraceutical, and biotechnological fields. This is the case of the new species Craspedostauros ineffabilis IMA082A and Craspedostauros zucchellii IMA088A Trentin, Moschin, Lopes, Custódio and Moro (Bacillariophyta) that are here explored for the first time for possible biotechnological applications. For this purpose, a bioprospection approach was applied by preparing organic extracts (acetone and methanol) from freeze-dried biomass followed by the evaluation of their in vitro antioxidant properties and inhibitory activities on enzymes related with Alzheimer's disease (acetylcholinesterase: AChE, butyrylcholinesterase: BChE), Type 2 diabetes mellitus (T2DM, α-glucosidase, α-amylase), obesity (lipase) and hyperpigmentation (tyrosinase). Extracts were then profiled by ultra-high-performance liquid chromatography-mass spectrometry (UPLC-HR-MS/MS), while the fatty acid methyl ester (FAME) profiles were established by gas chromatography-mass spectrometry (GC-MS). Our results highlighted strong copper chelating activity of the acetone extract from C. ineffabilis and moderate to high inhibitory activities on AChE, BChE, α-amylase and lipase for extracts from both species. The results of the chemical analysis indicated polyunsaturated fatty acids (PUFA) and their derivatives as the possible compounds responsible for the observed activities. The FAME profile showed saturated fatty acids (SFA) as the main group and methyl palmitoleate (C16:1) as the predominant FAME in both species. Overall, our results suggest both Antarctic strains as potential sources of interesting molecules with industrial applications. Further studies aiming to investigate unidentified metabolites and to maximize growth yield and natural compound production are required.

Outlook on RNAi-Based Strategies for Controlling Culicoides Biting Midges

Culicoides are small biting midges with the capacity to transmit important livestock pathogens around much of the world, and their impacts on animal welfare are likely to expand. Hemorrhagic diseases resulting from Culicoides-vectored viruses, for example, can lead to millions of dollars in economic damages for producers. Chemical insecticides can reduce Culicoides abundance but may not suppress population numbers enough to prevent pathogen transmission. These insecticides can also cause negative effects on non-target organisms and ecosystems. RNA interference (RNAi) is a cellular regulatory mechanism that degrades mRNA and suppresses gene expression. Studies have examined the utility of this mechanism for insect pest control, and with it, have described the hurdles towards producing, optimizing, and applying these RNAi-based products. These methods hold promise for being highly specific and environmentally benign when compared to chemical insecticides and are more transient than engineering transgenic insects. Given the lack of available control options for Culicoides, RNAi-based products could be an option to treat large areas with minimal environmental impact. In this study, we describe the state of current Culicoides control methods, successes and hurdles towards using RNAi for pest control, and the necessary research required to bring an RNAi-based control method to fruition for Culicoides midges.

Algal mediated intervention for the retrieval of emerging pollutants from aqueous media

Water is a crucial elemental contributor for all sectors; however, the agricultural sector alone accounts for 70% of the world's total water withdrawal. The anthropogenic activity from various industries including agriculture, textiles, plastics, leather, and defence has resulted in the release of contaminants into water systems, resulting harm to the ecosystem and biotic community. Algae-based organic pollutant removal uses several methods, such as biosorption, bioaccumulation, biotransformation, and biodegradation. The adsorption of methylene blue by algal species Chlamydomonas sp. showed a maximum adsorption capacity of 2744.5 mg/g with 96.13% removal efficiency; on the other hand, Isochrysis galbana demonstrated a maximum of 707 µg/g nonylphenol accumulation in the cell with 77% removal efficiency indicating the potential of algal systems as efficient retrieval system for organic contaminants. This paper is a compilation of detailed information about biosorption, bioaccumulation, biotransformation, biodegradation, and their mechanism, along with the genetic alteration of algal biomass. Where the genetic engineering and mutations on algae can be advantageously utilized for the enhancement of removal efficiency without any secondary toxicity.

Diversity of algae and their biotechnological potential

This chapter will discuss the diversity of algae and show that the diversity is much greater than just obligately oxygenic photosynthetic algae and that it includes many mixotrophic and heterotrophic organisms that are more similar to the major groups of microorganisms. The photosynthetic groups are seen as part of the plant kingdom, whereas the non-photosynthetic groups are not related to plants at all. The organisation of algal groups has become complex and confusing - The chapter will address the problems within this area of eukaryotic taxonomy. The metabolic diversity of algae and the ability to genetically engineer algae are key components in developing the biotechnology of algae. As more researchers become interested in exploiting algae for a number of industrial products, it is important to understand the relationships between different groups of algae and the relationships of algae with the rest of the living world.

Advances in engineering algae for biofuel production

While algae demonstrate potential as a sustainable fuel source, low productivities limit the economic realization of algal biofuels. High-throughput strain engineering, omics-informed genome-scale modeling, and microbiome engineering are key technologies for enabling algal biofuels. High-throughput strain engineering efforts generate improved traits, including high biomass productivity and lipid content, in diverse algal species. Genome-scale models, constructed with the aid of omics data, provide insight into metabolic limitations and guide rational algal strain engineering efforts. As outdoor cultivation systems introduce exogenous organisms, microbiome engineering seeks to eliminate harmful organisms and introduce beneficial species. Optimizing algal biomass production and lipid content using these technologies may overcome the productivity barrier for the commercialization of algal biofuels.

Translating advances in microbial bioproduction to sustainable biotechnology

Advances in synthetic biology have radically changed our ability to rewire microorganisms and significantly improved the scalable production of a vast array of drop-in biopolymers and biofuels. The success of a drop-in bioproduct is contingent on market competition with petrochemical analogues and weighted upon relative economic and environmental metrics. While the quantification of comparative trade-offs is critical for accurate process-level decision making, the translation of industrial ecology to synthetic biology is often ambiguous and assessment accuracy has proven challenging. In this review, we explore strategies for evaluating industrial biotechnology through life cycle and techno-economic assessment, then contextualize how recent developments in synthetic biology have improved process viability by expanding feedstock availability and the productivity of microbes. By juxtaposing biological and industrial constraints, we highlight major obstacles between the disparate disciplines that hinder accurate process evaluation. The convergence of these disciplines is crucial in shifting towards carbon neutrality and a circular bioeconomy.

Harnessing the Algal Chloroplast for Heterologous Protein Production

Photosynthetic microbes are gaining increasing attention as heterologous hosts for the light-driven, low-cost production of high-value recombinant proteins. Recent advances in the manipulation of unicellular algal genomes offer the opportunity to establish engineered strains as safe and viable alternatives to conventional heterotrophic expression systems, including for their use in the feed, food, and biopharmaceutical industries. Due to the relatively small size of their genomes, algal chloroplasts are excellent targets for synthetic biology approaches, and are convenient subcellular sites for the compartmentalized accumulation and storage of products. Different classes of recombinant proteins, including enzymes and peptides with therapeutical applications, have been successfully expressed in the plastid of the model organism Chlamydomonas reinhardtii, and of a few other species, highlighting the emerging potential of transplastomic algal biotechnology. In this review, we provide a unified view on the state-of-the-art tools that are available to introduce protein-encoding transgenes in microalgal plastids, and discuss the main (bio)technological bottlenecks that still need to be addressed to develop robust and sustainable green cell biofactories.

Multifaceted strategies for economic production of microalgae Haematococcus pluvialis-derived astaxanthin via direct conversion of CO2

Owing to its strong antioxidant properties, astaxanthin has a high market price in the nutraceutical and pharmaceutical fields, and its demand is increasing. Furthermore, with an increase in the demand for green technology, astaxanthin production through direct CO₂ conversion using the autotrophic green microalga Haematococcus pluvialis as a bio-platform has received much attention. Large-scale outdoor cultivation of H. pluvialis using waste CO₂ sources and sunlight can secure sustainability and improve economic efficiency. However, low strain performance, reduced light utilization because of increased cell density, and inefficient transfer of gaseous CO₂ into liquid culture broth hinder its large-scale commercialization of astaxanthin. Herein, we presented a multifaceted strategy, including the development of high-efficiency strains, a culture system for astaxanthin accumulation, and astaxanthin extraction from biomass, for economically producing astaxanthin from H. pluvialis through direct CO₂ conversion. Future perspectives were presented by comparing and analyzing various previous studies conducted using the latest technology.

Algae-mediated antibiotic wastewater treatment: A critical review

The existence of continually increasing concentrations of antibiotics in the environment is a serious potential hazard due to their toxicity and persistence. Unfortunately, conventional treatment techniques, such as those utilized in wastewater treatment plants, are not efficient for the treatment of wastewater containing antibiotic. Recently, algae-based technologies have been found to be a sustainable and promising technique for antibiotic removal. Therefore, this review aims to provide a critical summary of algae-based technologies and their important role in antibiotic wastewater treatment. Algal removal mechanisms including bioadsorption, bioaccumulation, and biodegradation are discussed in detail, with using algae-bacteria consortia for antibiotic treatment, integration of algae with other microorganisms (fungi and multiple algal species), hybrid algae-based treatment and constructed wetlands, and the factors affecting algal antibiotic degradation comprehensively described and assessed. In addition, the use of algae as a precursor for the production of biochar is highlighted, along with the modification of biochar with other materials to improve its antibiotic removal capacity and hybrid algae-based treatment with advanced oxidation processes. Furthermore, recent novel approaches for enhancing antibiotic removal, such as the use of genetic engineering to enhance the antibiotic degradation capacity of algae and the integration of algal antibiotic removal with bioelectrochemical systems are discussed. Finally, some based on the critical review, key future research perspectives are proposed. Overall, this review systematically presents the current progress in algae-mediated antibiotic removal technologies, providing some novel insights for improved alleviation of antibiotic pollution in aquatic environments.

Stramenopile microalgae as "green biofactories" for recombinant protein production

Photoautotrophic microalgae have become intriguing hosts for recombinant protein production because they offer important advantages of both prokaryotic and eukaryotic expression systems. Advanced molecular tools have recently been established for the biotechnologically relevant group of stramenopile microalgae, particularly for several Nannochloropsis species and diatoms. Strategies for the selection of powerful genetic elements and for optimization of protein production have been reported. Much needed high-throughput techniques required for straight-forward identification and selection of the best expression constructs and transformants have become available and are discussed. The first recombinant proteins have already been produced successfully in stramenopile microalgae and include not only several subunit vaccines but also one antimicrobial peptide, a fish growth hormone, and an antibody. These research results offer interesting future applications in aquaculture and as biopharmaceuticals. In this review we highlight recent progress in genetic technology development for recombinant protein production in the most relevant Nannochloropsis species and diatoms. Diverse realistic biotechnological applications of these proteins are emphasized that have the potential to establish stramenopile algae as sustainable green factories for an economically competitive production of high-value biomolecules.

Challenges and Potential in Increasing Lutein Content in Microalgae

Research on enhancing lutein content in microalgae has made significant progress in recent years. However, strategies are needed to address the possible limitations of microalgae as practical lutein producers. The capacity of lutein sequestration may determine the upper limit of cellular lutein content. The preliminary estimation presented in this work suggests that the lutein sequestration capacity of the light-harvesting complex (LHC) of microalgae is most likely below 2% on the basis of dry cell weight (DCW). Due to its nature as a structural pigment, higher lutein content might interfere with the LHC in fulfilling photosynthetic functions. Storing lutein in a lipophilic environment is a mechanism for achieving high lutein content but several critical barriers must be overcome such as lutein degradation and access to lipid droplet to be stored through esterification. Understanding the mechanisms underlying lipid droplet biogenesis in chloroplasts, as well as carotenoid trafficking through chloroplast membranes and carotenoid esterification, may provide insight for new approaches to achieve high lutein contents in algae. In the meantime, building the machinery for esterification and sequestration of lutein and other hydroxyl-carotenoids in model microorganisms, such as yeast, with synthetic biology technology provides a promising option.

Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri

Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration occurred randomly at a single locus in the genome and mainly as a single copy. Thus, we confirmed the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci. Furthermore, we often observed variations in the vector sequence itself. From these observations, we speculate that a nonhomologous end-joining-like mechanism is employed during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in this ecologically important marine alga.