The fate of antibiotic resistance genes in wastewater containing microalgae treated by chlorination, ultra-violet, and Fenton reaction

Antibiotic resistance genes (ARGs) and bacteria (ARBs) in the effluent of wastewater treatment plants (WWTPs) are of utmost importance for the dissemination of ARGs in natural aquatic environments. Therefore, there is an urgent need for effective technologies to eliminate WWTP ARGs/ARBs and mitigate the associated risks posed by the discharged ARG in aquatic environments. To test the effective technology for eliminating ARGs/ARBs, we compared the removal of ARGs and ARBs by three different tertiary treatments, namely ultra-violet (UV) disinfection, chlorination disinfection, and Fenton oxidation. Then, the treated wastewater was co-cultured with Chlorella vulgaris (representative of aquatic biota) to investigate the fate of discharged ARGs into the aquatic environment. The results demonstrated that chlorination (at a chlorine concentration of 15 mg/L) and Fenton (at pH 2.73, with 0.005 mol/L Fe2+ and 0.0025 mol/L H2O2) treatment showed higher efficacy in ARG removal (1.8 - 4.17 logs) than UV treatment (15 min) (1.29 - 3.87 logs). Moreover, chlorine at 15 mg/L and Fenton treatment effectively suppressed ARB regeneration while UV treatment for 15 min could not. Regardless of treatments tested in this study, the input of treated wastewater to the Chlorella system increased the number of ARGs and mobile genetic elements (MGEs), indicating the potential risk of ARG dissemination associated with WWTP discharge. Among the wastewater-Chlorella co-culture systems, chlorination resulted in less of an increase in the number of ARGs and MGEs compared to Fenton and UV treatment. When comparing the wastewater systems to the co-culture systems, it was observed that Chlorella vulgaris reduced the number of ARGs and MGEs in chlorination and UV-treated wastewater; however, Chlorella vulgaris promoted ARG survival in Fenton-treated water, suggesting that aquatic microalgae might act as a barrier to ARG dissemination. Overall, chlorination treatment not only effectively removes ARGs and inhibits ARB regeneration but also shows a lower risk of ARG dissemination. Therefore, chlorination is recommended for practical application in controlling the spread of discharged ARGs from WWTP effluent in natural aquatic environments.

Zeaxanthin epoxidase 3 Knockout Mutants of the Model Diatom Phaeodactylum tricornutum Enable Commercial Production of the Bioactive Carotenoid Diatoxanthin

Carotenoids are pigments that have a range of functions in human health. The carotenoid diatoxanthin is suggested to have antioxidant, anti-inflammatory and chemo-preventive properties. Diatoxanthin is only produced by a few groups of microalgae, where it functions in photoprotection. Its large-scale production in microalgae is currently not feasible. In fact, rapid conversion into the inactive pigment diadinoxanthin is triggered when cells are removed from a high-intensity light source, which is the case during large-scale harvesting of microalgae biomass. Zeaxanthin epoxidase (ZEP) 2 and/or ZEP3 have been suggested to be responsible for the back-conversion of high-light accumulated diatoxanthin to diadinoxanthin in low-light in diatoms. Using CRISPR/Cas9 gene editing technology, we knocked out the ZEP2 and ZEP3 genes in the marine diatom Phaeodactylum tricornutum to investigate their role in the diadinoxanthin-diatoxanthin cycle and determine if one of the mutant strains could function as a diatoxanthin production line. Light-shift experiments proved that ZEP3 encodes the enzyme converting diatoxanthin to diadinoxanthin in low light. Loss of ZEP3 caused the high-light-accumulated diatoxanthin to be stable for several hours after the cultures had been returned to low light, suggesting that zep3 mutant strains could be suitable as commercial production lines of diatoxanthin.

Characterization of halotolerant microalga isolated from waterlogged habitats: Deciphering the biochemical profiling and unraveling the molecular identity

The primary objective of this study was to comprehensively explore the biochemical profile of the novel halotolerant microalgae strain, biogas laboratory scenedesmus (BGLRS), previously isolated from waterlogged regions in the southwest zone of Punjab, India. To achieve this, three distinct drying methods viz. freeze-drying, oven-drying, and shade-drying were employed and biochemical composition and antioxidant analyses on the microalgal biomass were conducted. Utilizing advanced analytical techniques, including high-performance liquid chromatography (HPLC), inductively coupled plasma-atomic emission spectroscopy (ICP-AES), and gas chromatography-mass spectroscopy (GC-MS) on freeze-dried biomass, its carbohydrate profile, micronutrient composition, and presence of bioactive compounds with potential therapeutic and nutraceutical significance were sought to unravel. Among the drying methods evaluated, freeze-drying exhibited the most promising experimental results, prompting its selection for further investigation. Notably, ICP-AES unveiled elevated concentrations of essential elements such as calcium, iron, magnesium, and phosphorus in BGLRS, with negligible traces of heavy metals, underscoring its safety for human consumption. GC-MS analysis further divulged the existence of numerous biologically active compounds, indicating potential applications in medical and nutraceutical fields. Through molecular identification using sequencing of the internal transcribed spacer (ITS) region, a close taxonomic resemblance between BGLRS and Scenedesmus sp. MKB was established, solidifying its unique position within the microalgal taxonomy. The deposition of ITS sequences into the NCBI GenBank, obtaining accession number MN796425, attests to the rigor and transparency of this research. Overall, these findings strongly suggest that microalgae BGLRS possesses high-quality biochemical attributes of significant therapeutic and nutraceutical importance.

A comparison of two gene regions for assessing community composition of eukaryotic marine microalgae from coastal ecosystems

Two gene regions commonly used to characterise the diversity of eukaryotic communities using metabarcoding are the 18S ribosomal DNA V4 and V9 gene regions. We assessed the effectiveness of these two regions for characterising diverisity of coastal eukaryotic microalgae communities (EMCs) from tropical and temperate sites. We binned amplicon sequence variants (ASVs) into the high level taxonomic groups: dinoflagellates, pennate diatoms, radial centric diatoms, polar centric diatoms, chlorophytes, haptophytes and 'other microalgae'. When V4 and V9 generated ASV abundances were compared, the V9 region generated a higher number of raw reads, captured more diversity from all high level taxonomic groups and was more closely aligned with the community composition determined using light microscopy. The V4 region did resolve more ASVs to a deeper taxonomic resolution within the dinoflagellates, but did not effectively resolve other major taxonomic divisions. When characterising these communities via metabarcoding, the use of multiple gene regions is recommended, but the V9 gene region can be used in isolation to provide high-level community biodiversity to reflect relative abundances within groups. This approach reduces the cost of sequencing multiple gene regions whilst still providing important baseline ecosystem function information.

Metabolic and physiological adaptations of microalgal growth-promoting bacterium Azospirillum brasilense growing under biogas atmosphere: a microarray-based transcriptome analysis

Using microalgal growth-promoting bacteria (MGPB) to improve the cultured microalga metabolism during biotechnological processes is one of the most promising strategies to enhance their benefits. Nonetheless, the culture condition effect used during the biotechnological process on MGPB growth and metabolism is key to ensure the expected positive bacterium growth and metabolism of microalgae. In this sense, the present research study investigated the effect of the synthetic biogas atmosphere (75% CH4-25% CO2) on metabolic and physiological adaptations of the MGPB Azospirillum brasilense by a microarray-based transcriptome approach. A total of 394 A. brasilense differentially expressed genes (DEGs) were found: 201 DEGs (34 upregulated and 167 downregulated) at 24 h and 193 DEGs (140 upregulated and 53 downregulated) under the same conditions at 72 h. The results showed a series of A. brasilense genes regulating processes that could be essential for its adaptation to the early stressful condition generated by biogas. Evidence of energy production is shown by nitrate/nitrite reduction and activation of the hypothetical first steps of hydrogenotrophic methanogenesis; signal molecule modulation is observed: indole-3-acetic acid (IAA), riboflavin, and vitamin B6, activation of Type VI secretion system responding to IAA exposure, as well as polyhydroxybutyrate (PHB) biosynthesis and accumulation. Moreover, an overexpression of ipdC, ribB, and phaC genes, encoding the key enzymes for the production of the signal molecule IAA, vitamin riboflavin, and PHB production of 2, 1.5 and 11 folds, respectively, was observed at the first 24 h of incubation under biogas atmosphere Overall, the ability of A. brasilense to metabolically adapt to a biogas atmosphere is demonstrated, which allows its implementation for generating biogas with high calorific values and the use of renewable energies through microalga biotechnologies.

The effect of PK gene overexpression on content and antioxidant properties of carotenoids in marine microalga Dunaliella parva

Dunaliella parva can extensively accumulate carotenoids, which is a promising raw material for carotenoids production. Carotenoids have important medicinal value. D. parva is an ideal organism for studying the mechanism of carotenoid synthesis. Our previous study identified a transcription factor DpAP2 which could regulate carotenoid synthesis in D. parva. In addition, DpAP2 could interact with three proteins with different activities (DNA binding transcription factor activity, protein kinase activity, and alpha-D-phosphohexomutase). To investigate the function of PK gene encoding interacting protein of DpAP2 with protein kinase activity in D. parva, PK gene was cloned into vector pBI221-GFP-UbiΩ-CAT and transformed into D. parva in this study. The results showed that overexpression of PK gene enhanced the contents of carotenoids, total sugars, proteins, and antioxidant activities of carotenoid extract such as superoxide radical scavenging activity, reducing power, hydroxyl radical scavenging activity in transgenic D. parva with overexpression of PK gene. This study explored the function of PK gene, and improved the medicinal value of D. parva.

Optimized transgene expression in the red alga Porphyridium purpureum and efficient recombinant protein secretion into the culture medium

Microalgae represent a promising but yet underexplored production platform for biotechnology. The vast majority of studies on recombinant protein expression in algae have been conducted in a single species, the green alga Chlamydomonas reinhardtii. However, due to epigenetic silencing, transgene expression in Chlamydomonas is often inefficient. Here we have investigated parameters that govern efficient transgene expression in the red microalga Porphyridium purpureum. Porphyridium is unique in that the introduced transformation vectors are episomally maintained as autonomously replicating plasmids in the nucleus. We show that full codon optimization to the preferred codon usage in the Porphyridium genome confers superior transgene expression, not only at the level of protein accumulation, but also at the level of mRNA accumulation, indicating that high translation rates increase mRNA stability. Our optimized expression constructs resulted in YFP accumulation to unprecedented levels of up to 5% of the total soluble protein. We also designed expression cassettes that target foreign proteins to the secretory pathway and lead to efficient protein secretion into the culture medium, thus simplifying recombinant protein harvest and purification. Our study paves the way to the exploration of red microalgae as expression hosts in molecular farming for recombinant proteins and metabolites.

Reconstruction of Long-Chain Polyunsaturated Acid Synthesis Pathways in Marine Red Microalga Porphyridium cruentum Using Lipidomics and Transcriptomics

The marine red microalga Porphyridium can simultaneously synthesize long-chain polyunsaturated fatty acids, including eicosapentaenoic acid (C20:5, EPA) and arachidonic acid (C20:4, ARA). However, the distribution and synthesis pathways of EPA and ARA in Porphyridium are not clearly understood. In this study, Porphyridium cruentum CCALA 415 was cultured in nitrogen-replete and nitrogen-limited conditions. Fatty acid content determination, transcriptomic, and lipidomic analyses were used to investigate the synthesis of ARA and EPA. The results show that membrane lipids were the main components of lipids, while storage lipids were present in a small proportion in CCALA 415. Nitrogen limitation enhanced the synthesis of storage lipids and ω6 fatty acids while inhibiting the synthesis of membrane lipids and ω3 fatty acids. A total of 217 glycerolipid molecular species were identified, and the most abundant species included monogalactosyldiglyceride (C16:0/C20:5) (MGDG) and phosphatidylcholine (C16:0/C20:4) (PC). ARA was mainly distributed in PC, and EPA was mainly distributed in MGDG. Among all the fatty acid desaturases (FADs), the expressions of Δ5FAD, Δ6FAD, Δ9FAD, and Δ12FAD were up-regulated, whereas those of Δ15FAD and Δ17FAD were down-regulated. Based on these results, only a small proportion of EPA was synthesized through the ω3 pathway, while the majority of EPA was synthesized through the ω6 pathway. ARA synthesized in the ER was likely shuttled into the chloroplast by DAG and was converted into EPA by Δ17FAD.

Synthetic biology in microalgae towards fucoxanthin production for pharmacy and nutraceuticals

Synthetic biology has emerged as a powerful tool for engineering biological systems to produce valuable compounds, including pharmaceuticals and nutraceuticals. Microalgae, in particular, offer a promising platform for the production of bioactive compounds due to their high productivity, low land and water requirements, and ability to perform photosynthesis. Fucoxanthin, a carotenoid pigment found predominantly in brown seaweeds and certain microalgae, has gained significant attention in recent years due to its numerous health benefits, such as antioxidation, antitumor effect and precaution osteoporosis. This review provides an overview of the principles and applications of synthetic biology in the microbial engineering of microalgae for enhanced fucoxanthin production. Firstly, the fucoxanthin bioavailability and metabolism in vivo was introduced for the beneficial roles, followed by the biological functions of anti-oxidant activity, anti-inflammatory activity, antiapoptotic role antidiabetic and antilipemic effects. Secondly, the cultivation condition and strategy were summarized for fucoxanthin improvement with low production costs. Thirdly, the genetic engineering of microalgae, including gene overexpression, knockdown and knockout strategies were discussed for further improving the fucoxanthin production. Then, synthetic biology tools of CRISPR-Cas9 genome editing, transcription activator-like effector nucleases as well as modular assembly and chassis engineering were proposed to precise modification of microalgal genomes to improve fucoxanthin production. Finally, challenges and future perspectives were discussed to realize the industrial production and development of functional foods of fucoxanthin from microalgae.

Exploring the dynamics of algae-associated microbiome during the scale-up process of Tetraselmis sp. microalgae: A metagenomics approach

Microalgae have become a key source of valuable compounds, promoting commercial scale applications. However, biological contamination is one of the most critical problems associated with large scale algal production, especially in open systems such as raceway ponds. The current research is the first to assess the effectiveness of open raceway ponds in maintaining a pure culture of Tetraselmis sp., starting from 20 L culture up to 10,000 L culture. Microbial profiling of each successive stage revealed lower abundance of eukaryotic organisms, whereas bacterial abundance increased notably resulting in a significant decrease in Tetraselmis sp. abundance. Furthermore, several bacteria with algae growth-promoting properties were found throughout the various culture stages including Balneola, Roseovarius, and Marinobacter. However, some algae-suppressive bacteria were evidenced at later stages such as Ulvibacter, Aestuariicoccus, and Defluviimonas. Overall, due to the increasing bacterial concentration, considerations limiting bacterial contamination need to be taken.

Toxicity of tigecycline on the freshwater microalga Scenedesmus obliquus: Photosynthetic and transcriptional responses

Tigecycline (TGC) is a new tetracycline antibiotic medication against multidrug-resistant bacteria. However, the toxicity of TGC to microalgae remains largely unknown. In this study, the toxicity of TGC on Scenedesmus obliquus was examined, focusing on changes in algal growth, photosynthetic activity, and transcriptome. According to an acute toxicity test, the IC10 and IC50 values were 0.72 mg/L and 4.15 mg/L, respectively. Analyses of photosynthetic efficiency and related parameters, such as light absorption, energy capture, and electron transport, identified a 35% perturbation in the IC50 group, while the IC10 group remained largely unaffected. Transcriptomic analysis showed that in the IC10 and IC50 treatment groups, there were 874 differentially expressed genes (DEGs) (220 upregulated and 654 downregulated) and 4289 DEGs (2660 upregulated and 1629 downregulated), respectively. Gene Ontology enrichment analysis showed that TGC treatment markedly affected photosynthesis, electron transport, and chloroplast functions. In the IC50 group, a clear upregulation of genes related to photosynthesis and chloroplast functions was observed, which could be an adaptive stress response. In the IC10 group, significant downregulation of DEGs involved in ribosomal pathways and peptide biosynthesis processes was observed. Kyoto Encyclopedia of Gene and Genomes enrichment analysis showed that treatment with TGC also disrupted energy production, protein synthesis, and metabolic processes in S. obliquus. Significant downregulation of key proteins related to Photosystem II was observed under the IC10 TGC treatment. Conversely, IC50 TGC treatment resulted in substantial upregulation across a broad array of photosystem-related proteins from both Photosystems II and I. IC10 and IC50 TGC treatments differentially influenced proteins involved in the photosynthetic electron transport process. This study emphasizes the potential risks of TGC pollution to microalgae, which contributes to a better understanding of the effects of antibiotic contamination in aquatic ecosystems.

DNA and RNA Stability of Marine Microalgae in Cold-Stored Sediments and Its Implications in Metabarcoding Analyses

The ever-increasing applications of metabarcoding analyses for environmental samples demand a well-designed assessment of the stability of DNA and RNA contained in cells that are deposited or buried in marine sediments. We thus conducted a qPCR quantification of the DNA and RNA in the vegetative cells of three microalgae entrapped in facsimile marine sediments and found that >90% of DNA and up to 99% of RNA for all microalgal species were degraded within 60 days at 4 °C. A further examination of the potential interference of the relic DNA of the vegetative cells with resting cyst detection in sediments was performed via a metabarcoding analysis in artificial marine sediments spiked with the vegetative cells of two Kareniaceae dinoflagellates and the resting cysts of another three dinoflagellates. The results demonstrated a dramatic decrease in the relative abundances of the two Kareniaceae dinoflagellates in 120 days, while those of the three resting cysts increased dramatically. Together, our results suggest that a positive detection of microalgae via metabarcoding analysis in DNA or RNA extracted from marine sediments strongly indicates the presence of intact or viable cysts or spores due to the rapid decay of relic DNA/RNA. This study provides a solid basis for the data interpretation of metabarcoding surveys, particularly in resting cyst detection.

Pioneering DNA assembling techniques and their applications in eukaryotic microalgae

Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well-known physiology, alongside the steady increase in genome-enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.

Epigenetic Regulation in Response to CO2 Fluctuation in Marine Microalga Nannochloropsis oceanica

Microalgae often undergo different CO2 experiment in their habitat. To adapt to low CO2, carbon concentrating mechanism (CCM) could be launched in majority of microalgae and CCM are regulated at RNA level are well known. However, epigenetic modifications and their potential regulation of the transcription of masked genes at the genome level in response to CO2 fluctuation remain unclear. Here epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that lysine butyrylation (Kbu) and histone H3K9m2 modifications were present in N. oceanica IMET1. Moreover, Kbu modification positively regulated gene expression. In response to CO2 fluctuation, there were 5,438 and 1,106 genes regulated by Kbu and H3K9m2 in Nannochloropsis, respectively. Gained or lost histone methylations were closely associated with activating or repressing gene expressions. Differential modifications were mainly enriched in carbon fixation, photorespiration, photosynthesis, and lipid metabolism etc. Massive genome-wide epigenetic reprogramming was observed after N. oceanica cells shifted from high CO2 to low CO2. Particularly, we firstly noted that the transcription of the key low CO2 responsive carbonic anhydrase (CA5), a key component involved in CCM stress signaling, was potentially regulated by bivalent Kbu-H3K9m2 modifications in microalgae. This study provides novel insights into the relationship between gene transcription and epigenetic modification in Nannochloropsis, which will lay foundation on genetic improvement of CCM at epigenetic level.

Overexpression of a MYB1 Transcription Factor Enhances Triacylglycerol and Starch Accumulation and Biomass Production in the Green Microalga Chlamydomonas reinhardtii

Microalgae are promising platforms for biofuel production. Transcription factors (TFs) are emerging as key regulators of lipid metabolism for biofuel production in microalgae. We previously identified a novel TF MYB1, which mediates lipid accumulation in the green microalga Chlamydomonas under nitrogen depletion. However, the function of MYB1 on lipid metabolism in microalgae under standard growth conditions remains poorly understood. Here, we examined the effects of MYB1 overexpression (MYB1-OE) on lipid metabolism and physiological changes in Chlamydomonas. Under standard growth conditions, MYB1-OE transformants accumulated 1.9 to 3.2-fold more triacylglycerols (TAGs) than that in the parental line (PL), and total fatty acids (FAs) also significantly increased. Moreover, saturated FA (C16:0) was enriched in TAGs and total FAs in MYB1-OE transformants. Notably, starch and protein content and biomass production also significantly increased in MYB1-OE transformants compared with that in PL. Furthermore, RT-qPCR results showed that the expressions of key genes involved in TAG, FA, and starch biosynthesis were upregulated. In addition, MYB1-OE transformants showed higher biomass production without a compromised cell growth rate and photosynthetic activity. Overall, our results indicate that MYB1 overexpression not only enhanced lipid content but also improved starch and protein content and biomass production under standard growth conditions. TF MYB1 engineering is a promising genetic engineering tool for biofuel production in microalgae.

Reconstruction of a Genome-Scale Metabolic Model of Scenedesmus obliquus and Its Application for Lipid Production under Three Trophic Modes

Green microalgae have emerged as beneficial feedstocks for biofuel production. A systems-level understanding of the biochemical network is needed to harness the microalgal metabolic capacity for bioproduction. Genome-scale metabolic modeling (GEM) showed immense potential in rational metabolic engineering, utilizing biochemical flux distribution analysis. Here, we report the first GEM for the green microalga, Scenedesmus obliquus (iAR632), a promising biodiesel feedstock with high lipid-storing capability. iAR632 comprises 1467 reactions, 734 metabolites, and 632 genes distributed among 7 compartments. The model was optimized under three different trophic modes of microalgal cultivation, i.e., autotrophy, mixotrophy, and heterotrophy. The robustness of the reconstructed network was confirmed by analyzing its sensitivity to the biomass components. Pathway-level flux profiles were analyzed, and significant flux space expansion was noticed majorly in reactions associated with lipid biosynthesis. In agreement with the experimental observation, iAR632 predicted about 3.8-fold increased biomass and almost 4-fold higher lipid under mixotrophy than the other trophic modes. Thus, the assessment of the condition-specific metabolic flux distribution of iAR632 suggested that mixotrophy is the preferred cultivation condition for improved microalgal growth and lipid production. Overall, the reconstructed GEM and subsequent analyses will provide a systematic framework for developing model-driven strategies to improve microalgal bioproduction.

Biosensors in microalgae: A roadmap for new opportunities in synthetic biology and biotechnology

Biosensors are powerful tools to investigate, phenotype, improve and prototype microbial strains, both in fundamental research and in industrial contexts. Genetic and biotechnological developments now allow the implementation of synthetic biology approaches to novel different classes of microbial hosts, for example photosynthetic microalgae, which offer unique opportunities. To date, biosensors have not yet been implemented in phototrophic eukaryotic microorganisms, leaving great potential for novel biological and technological advancements untapped. Here, starting from selected biosensor technologies that have successfully been implemented in heterotrophic organisms, we project and define a roadmap on how these could be applied to microalgae research. We highlight novel opportunities for the development of new biosensors, identify critical challenges, and finally provide a perspective on the impact of their eventual implementation to tackle research questions and bioengineering strategies. From studying metabolism at the single-cell level to genome-wide screen approaches, and assisted laboratory evolution experiments, biosensors will greatly impact the pace of progress in understanding and engineering microalgal metabolism. We envision how this could further advance the possibilities for unraveling their ecological role, evolutionary history and accelerate their domestication, to further drive them as resource-efficient production hosts.

Optimization of 4-aminobutyric acid feeding strategy and clustered regularly interspaced short palindromic repeats activation for enhanced value-added chemicals in halophilic Chlorella sorokiniana

Chlorella sorokiniana (CS) is a prominent microalga with vast potential as a biocarrier for carbon mitigation toward a green process. However, challenges remain in achieving high biomass levels and production rates. Therefore, a systematic feeding strategy using 4-aminobutyric acid (GABA) and CRISPR technology was applied to improve microalgal productivity. At first, GABA increased protein content by 1.4-fold, while intermittent supplementation during cultivation resulted in a 1.58-fold and 2.13-fold increase in biomass and pigment content, respectively. Under halophilic conditions, the optimal approach involved repeated feeding of 5 mM GABA at the initial and mid-log phases of growth, resulting in biomass, protein, and pigment levels of 6.74 g/L, 3.24 g/L, and 49.87 mg/L. CRISPRa mediated glutamate synthase and using monosodium glutamate (MSG) as a cheap precursor for GABA has effectively enhanced the biomass, protein, and lutein content, thus offers a cost-effective approach to commercialize high-valued chemical using algae towards a low-carbon paradigm.

Metabolic engineering and synthetic biology strategies for producing high-value natural pigments in Microalgae

Microalgae are microorganisms capable of producing bioactive compounds using photosynthesis. Microalgae contain a variety of high value-added natural pigments such as carotenoids, phycobilins, and chlorophylls. These pigments play an important role in many areas such as food, pharmaceuticals, and cosmetics. Natural pigments have a health value that is unmatched by synthetic pigments. However, the current commercial production of natural pigments from microalgae is not able to meet the growing market demand. The use of metabolic engineering and synthetic biological strategies to improve the production performance of microalgal cell factories is essential to promote the large-scale production of high-value pigments from microalgae. This paper reviews the health and economic values, the applications, and the synthesis pathways of microalgal pigments. Overall, this review aims to highlight the latest research progress in metabolic engineering and synthetic biology in constructing engineered strains of microalgae with high-value pigments and the application of CRISPR technology and multi-omics in this context. Finally, we conclude with a discussion on the bottlenecks and challenges of microalgal pigment production and their future development prospects.

Mapping harmful microalgal species by eDNA monitoring: A large-scale survey across the southwestern South China Sea

A large-scale sampling was undertaken during a research cruise across the South China Sea in August 2016, covering an area of about 100,000 km2 to investigate the molecular diversity and distributions of micro-eukaryotic protists, with a focus on the potentially harmful microalgal (HAB) species along the east coast of Peninsular Malaysia. Environmental DNAs from 30 stations were extracted and DNA metabarcoding targeting the V4 and V9 markers in the 18S rDNA was performed. Many protistan molecular units, including previously unreported HAB taxa, were discovered for the first time in the water. Our findings also revealed interesting spatial distribution patterns, with a marked signal of compositional turnover between latitudinal regimes of water masses, where dinophytes and diatom compositions were among the most strongly enhanced at the fronts, leading to distinct niches. Our results further confirmed the widespread distribution of HAB species, such as the toxigenic Alexandrium tamiyavaichii and Pseudo-nitzschia species, and the fish-killing Margalefidinium polykrikoides and Karlodinium veneficum. The molecular information obtained from this study provides an updated HAB species inventory and a toolset that could facilitate existing HAB monitoring schemes in the region to better inform management decisions.

Agrobacterium tumefaciens-Mediated Genetic Engineering of Green Microalgae, Chlorella vulgaris

Agrobacterium tumefaciens-mediated transformation (AMT) serves as a widely employed tool for manipulating plant genomes. However, A. tumefaciens exhibit the capacity for gene transfer to a diverse array of species. Numerous microalgae species lack well-established methods for reliably integrating genes of interest into their nuclear genome. To harness the potential benefits of microalgal biotechnology, simple and efficient genome manipulation tools are crucial. Herein, an optimized AMT protocol is presented for the industrial microalgae species Chlorella vulgaris, utilizing the reporter green fluorescent protein (mGFP5) and the antibiotic resistance marker for Hygromycin B. Mutants are selected through plating on Tris-Acetate-Phosphate (TAP) media containing Hygromycin B and cefotaxime. Expression of mGFP5 is quantified via fluorescence after over ten generations of subculturing, indicating the stable transformation of the T-DNA cassette. This protocol allows for the reliable generation of multiple transgenic C. vulgaris colonies in under two weeks, employing the commercially available pCAMBIA1302 plant expression vector.

Alkaline Phosphatase PhoD Mutation Induces Fatty Acid and Long-Chain Polyunsaturated Fatty Acid (LC-PUFA)-Bound Phospholipid Production in the Model Diatom Phaeodactylum tricornutum

With rapid growth and high lipid contents, microalgae have become promising environmentally friendly candidates for renewable biodiesel and health supplements in our era of global warming and energy depletion. Various pathways have been explored to enhance algal lipid production, especially gene editing. Previously, we found that the functional loss of PhoD-type alkaline phosphatase (AP), a phosphorus-stress indicator in phytoplankton, could lead to increased lipid contents in the model diatom Phaeodactylum tricornutum, but how the AP mutation may change lipid composition remains unexplored. This study addresses the gap in the research and investigates the effects of PhoD-type AP mutation on the lipid composition and metabolic regulation in P. tricornutum using transcriptomic and lipidomic analyses. We observed significantly modified lipid composition and elevated production of fatty acids, lysophosphatidylcholine, lysophosphatidylethanolamine, ceramide, phosphatidylinositol bisphosphate, and monogalactosylmonoacylglycerol after PhoD_45757 mutation. Meanwhile, genes involved in fatty acid biosynthesis were upregulated in mutant cells. Moreover, the mutant exhibited increased contents of ω-3 long-chain polyunsaturated fatty acid (LC-PUFA)-bound phospholipids, indicating that PhoD_45757 mutation could improve the potential bioavailability of PUFAs. Our findings indicate that AP mutation could influence cellular lipid synthesis and probably redirect carbon toward lipid production and further demonstrate that AP mutation is a promising approach for the development of high-value microalgal strains for biomedical and other applications.

A potential paradigm in CRISPR/Cas systems delivery: at the crossroad of microalgal gene editing and algal-mediated nanoparticles

Microalgae as the photosynthetic organisms offer enormous promise in a variety of industries, such as the generation of high-value byproducts, biofuels, pharmaceuticals, environmental remediation, and others. With the rapid advancement of gene editing technology, CRISPR/Cas system has evolved into an effective tool that revolutionised the genetic engineering of microalgae due to its robustness, high target specificity, and programmability. However, due to the lack of robust delivery system, the efficacy of gene editing is significantly impaired, limiting its application in microalgae. Nanomaterials have become a potential delivery platform for CRISPR/Cas systems due to their advantages of precise targeting, high stability, safety, and improved immune system. Notably, algal-mediated nanoparticles (AMNPs), especially the microalgae-derived nanoparticles, are appealing as a sustainable delivery platform because of their biocompatibility and low toxicity in a homologous relationship. In addition, living microalgae demonstrated effective and regulated distribution into specified areas as the biohybrid microrobots. This review extensively summarised the uses of CRISPR/Cas systems in microalgae and the recent developments of nanoparticle-based CRISPR/Cas delivery systems. A systematic description of the properties and uses of AMNPs, microalgae-derived nanoparticles, and microalgae microrobots has also been discussed. Finally, this review highlights the challenges and future research directions for the development of gene-edited microalgae.

Biodiversity of symbiotic microalgae associated with meiofaunal marine acoels in Southern Japan

Acoels in the family Convolutidae are commonly found with microalgal symbionts. Convolutids can host green algal Tetraselmis and dinoflagellates within the family Symbiodiniaceae and the genus Amphidinium. The diversity of these microalgae has not been well surveyed. In this study, we used PCR and culture techniques to demonstrate the biodiversity of Tetraselmis and dinoflagellates in symbiosis with meiofaunal acoels. Here, 66 acoels were collected from seven localities around Okinawa, Ishigaki, and Kochi, Japan. While convolutids were heavily represented in this sampling, some acoels formed a clade outside Convolutidae and are potentially a new family of acoels harboring symbiotic microalgae. From the acoels collected, a total of 32 Tetraselmis and 26 Symbiodiniaceae cultures were established. Molecular phylogenies were constructed from cultured material (and from total host DNA) using the 18S rRNA gene (Tetraselmis) and 28S rRNA gene (dinoflagellates). The majority of Tetraselmis sequences grouped within the T. astigmatica clade but strains closely related to T. convolutae, T. marina, and T. gracilis were also observed. This is the first report of Tetraselmis species, other than T. convolutae, naturally associating with acoels. For dinoflagellates, members of Cladocopium and Miliolidium were observed, but most Symbiodiniaceae sequences formed clusters within Symbiodinium, grouping with S. natans, or sister to S. tridacnidorum. Several new Symbiodinium sequences from this study may represent novel species. This is the first molecular record of Miliolidium and Symbiodinium from acoels. Microalgal strains from this study will provide a necessary framework for future taxonomic studies and research on symbiotic relationships between acoels and microalgae.

Isolation and Characterization of Thraustochytrium Trk-23 Producing Docosahexaenoic Acid from North Kalimantan, Indonesia

<b>Background and Objective:</b> The mangrove forest located in Tarakan Bay, North Kalimantan Province, Indonesia is geographically distant from human settlement and industrial activities. Thus, it remains unaffected by the presence of human-generated waste and industrial pollutants. This study aims to isolate and characterize the microalgae Thraustochytrids from this location, which can produce docosahexaenoic acid (DHA, C22:6, n-3). It is anticipated that these microalgae possess the potential for commercial production of DHA. <b>Materials and Methods:</b> The fallen leaf sample was collected from the mangrove forest, then isolated and purified by scratching technique until a single colony state. The pure isolate then be identified by 18S rDNA. The sequences were then analyzed for similarities using the Basic Local Alignment Search Tool (BLAST). The phylogenetic trees were carried out using the MEGA 6 program. The choice of phylogenetic trees was based on maximum likelihood. <b>Results:</b> The identification 18S rDNA gene, a strain namely Trk-23, was identified as <i>Thraustochytrium</i> sp. In the optimization of the cell growth of this strain, it was found that <i>Thraustochytrium</i> Trk-23 has maximum growth at 6.0% glucose, 1.0% yeast extract and 50% natural seawater, at a pH of 5.0 and a temperature of 30°C. The maximum lipid content is 6.0 g and the DHA proportion is 41.6% of the total fatty acid content with a DHA yield is 2.5 g L¹. <b>Conclusion:</b> Some places in North Kalimantan are still free from industrial pollution and rich with <i>Thraustochytrium</i> sp., which is why it can find <i>Thraustochytrium</i> Trk-23. Due to its potency, <i>Thraustochytrium</i> Trk-23 is the promising candidate microalgae strain for producing DHA commercially.

Quantitative Polymerase Chain Reaction for the estimation of toxigenic microalgae abundance in shellfish production waters

Certain species of marine microalgae produce potent biotoxins that pose a risk to human health if contaminated seafood is consumed, particularly filter feeding bivalve shellfish. In regions where this is likely to occur water and seafood produce are regularly monitored for the presence of harmful algal cells and their associated toxins, but the current approach is flawed by a lengthy delay before results are available to local authorities. Quantitative Polymerase Chain Reaction (qPCR) can be used to measure phytoplankton DNA sequences in a shorter timeframe, however it is not currently used in official testing practices. In this study, samples were collected almost weekly over six months from three sites within a known HAB hotspot, St Austell Bay in Cornwall, England. The abundance of algal cells in water was measured using microscopy and qPCR, and lipophilic toxins were quantified in mussel flesh using LC-MS/MS, focusing on the okadaic acid group. An increase in algal cell abundance occurred alongside an increase in the concentration of okadaic acid group toxins in mussel tissue at all three study sites, during September and October 2021. This event corresponded to an increase in the measured levels of Dinophysis accuminata DNA, measured using qPCR. In the following spring, the qPCR detected an increase in D. accuminata DNA levels in water samples, which was not detected by microscopy. Harmful algal species belonging to Alexandrium spp. and Pseudo-nitzschia spp. were also measured using qPCR, finding a similar increase in abundance in Autumn and Spring. The results are discussed with consideration of the potential merits and limitations of the qPCR technique versus conventional microscopy analysis, and its potential future role in phytoplankton surveillance under the Official Controls Regulations pertaining to shellfish.

Phenotypic Analysis and Molecular Characterization of Enlarged Cell Size Mutant in Nannochloropsis oceanica

The cell cycle is the fundamental cellular process of eukaryotes. Although cell-cycle-related genes have been identified in microalgae, their cell cycle progression differs from species to species. Cell enlargement in microalgae is an essential biological trait. At the same time, there are various causes of cell enlargement, such as environmental factors, especially gene mutations. In this study, we first determined the phenotypic and biochemical characteristics of a previously obtained enlarged-cell-size mutant of Nannochloropsis oceanica, which was designated ECS. Whole-genome sequencing analysis of the insertion sites of ECS indicated that the insertion fragment is integrated inside the 5'-UTR of U/P-type cyclin CYCU;1 and significantly decreases the gene expression of this cyclin. In addition, the transcriptome showed that CYCU;1 is a highly expressed cyclin. Furthermore, cell cycle analysis and RT-qPCR of cell-cycle-related genes showed that ECS maintains a high proportion of 4C cells and a low proportion of 1C cells, and the expression level of CYCU;1 in wild-type (WT) cells is significantly increased at the end of the light phase and the beginning of the dark phase. This means that CYCU;1 is involved in cell division in the dark phase. Our results explain the reason for the larger ECS size. Mutation of CYCU;1 leads to the failure of ECS to fully complete cell division in the dark phase, resulting in an enlargement of the cell size and a decrease in cell density, which is helpful to understand the function of CYCU;1 in the Nannochloropsis cell cycle.

Harnessing the advances of genetic engineering in microalgae for the production of cannabinoids

Cannabis is widely recognized as a medicinal plant owing to bioactive cannabinoids. However, it is still considered a narcotic plant, making it hard to be accessed. Since the biosynthetic pathway of cannabinoids is disclosed, biotechnological methods can be employed to produce cannabinoids in heterologous systems. This would pave the way toward biosynthesizing any cannabinoid compound of interest, especially minor substances that are less produced by a plant but have a high medicinal value. In this context, microalgae have attracted increasing scientific interest given their unique potential for biopharmaceutical production. In the present review, the current knowledge on cannabinoid production in different hosts is summarized and the biotechnological potential of microalgae as an emerging platform for synthetic production is put in perspective. A critical survey of genetic requirements and various transformation approaches are also discussed.

A chromosome-level genome assembly for the astaxanthin-producing microalga Haematococcus pluvialis

The green microalga Haematococcus pluvialis can synthesize high amounts of astaxanthin, which is a valuable antioxidant that has been utilized in human health, cosmetics, and aquaculture. To illustrate detailed molecular clues to astaxanthin yield, we performed PacBio HIFI along with Hi-C sequencing to construct an improved chromosome-level haplotypic genome assembly with 32 chromosomes and a genome size of 316.0 Mb. Its scaffold N50 (942.6 kb) and contig N50 (304.8 kb) have been upgraded remarkably from our previous genome draft, and a total of 32,416 protein-coding genes were predicted. We also established a high-evidence phylogenetic tree from seven representative algae species, with the main aim to calculate their divergence times and identify expanded/contracted gene families. We also characterized genome-wide localizations on chromosomes of some important genes such as five BKTs (encoding beta-carotene ketolases) that are putatively involved in astaxanthin production. In summary, we reported the first chromosome-scale map of H. pluvialis, which provides a valuable genetic resource for in-depth biomedical investigations on this momentous green alga and commercial astaxanthin bioproduction.

"DNA signaturing" database construction for Tetradesmus species identification and phylogenetic relationships of Scenedesmus-like green microalgae (Scenedesmaceae, Chlorophyta)

Species identification of Scenedesmus-like microalgae, comprising Desmodesmus, Tetradesmus, and Scenedesmus, has been challenging due to their high morphological and genetic similarity. After developing a DNA signaturing tool for Desmodesmus identification, we built a DNA signaturing database for Tetradesmus. The DNA signaturing tool contained species-specific nucleotide sequences of Tetradesmus species or strain groups with high similarity in ITS2 sequences. To construct DNA signaturing, we collected data on ITS2 sequences, aligned the sequences, organized the data by ITS2 sequence homology, and determined signature sequences according to hemi-compensatory base changes (hCBC)/CBC data from previous studies. Four Tetradesmus species and 11 strain groups had DNA signatures. The signature sequence of the genus Tetradesmus, TTA GAG GCT TAA GCA AGG ACCC, recognized 86% (157/183) of the collected Tetradesmus strains. Phylogenetic analysis of Scenedesmus-like species revealed that the Tetradesmus species were monophyletic and closely related to each other based on branch lengths. Desmodesmus was suggested to split into two subgenera due to their genetic and morphological distinction. Scenedesmus must be analyzed along with other genera of the Scenedesmaceae family to determine their genetic relationships. Importantly, DNA signaturing was integrated into a database for identifying Scenedesmus-like species through BLAST.

Environmental and nuclear influences on microalgal chloroplast gene expression

Microalgal chloroplasts, such as those of the model organism Chlamydomonas reinhardtii, are emerging as a new platform to produce recombinant proteins, including industrial enzymes, diagnostics, as well as animal and human therapeutics. Improving transgene expression and final recombinant protein yields, at laboratory and industrial scales, require optimization of both environmental and cellular factors. Most studies on C. reinhardtii have focused on optimization of cellular factors. Here, we review the regulatory influences of environmental factors, including light (cycle time, intensity, and quality), carbon source (CO2 and organic), and temperature. In particular, we summarize their influence via the redox state, cis-elements, and trans-factors on biomass and recombinant protein production to support the advancement of emerging large-scale light-driven biotechnology applications.

Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii

Microalgae hold enormous potential to provide a safe and sustainable source of high-value compounds, acting as carbon-fixing biofactories that could help to mitigate rapidly progressing climate change. Bioengineering microalgal strains will be key to optimizing and modifying their metabolic outputs, and to render them competitive with established industrial biotechnology hosts, such as bacteria or yeast. To achieve this, precise and tuneable control over transgene expression will be essential, which would require the development and rational design of synthetic promoters as a key strategy. Among green microalgae, Chlamydomonas reinhardtii represents the reference species for bioengineering and synthetic biology; however, the repertoire of functional synthetic promoters for this species, and for microalgae generally, is limited in comparison to other commercial chassis, emphasizing the need to expand the current microalgal gene expression toolbox. Here, we discuss state-of-the-art promoter analyses, and highlight areas of research required to advance synthetic promoter development in C. reinhardtii. In particular, we exemplify high-throughput studies performed in other model systems that could be applicable to microalgae, and propose novel approaches to interrogating algal promoters. We lastly outline the major limitations hindering microalgal promoter development, while providing novel suggestions and perspectives for how to overcome them.

Comparative study of multiple approaches for identifying cultivable microalgae population diversity from freshwater samples

The vast diversity of microalgae imposes the challenge of identifying them through the most common and economical identification method, morphological identification, or through using the more recent molecular-level identification tools. Here we report an approach combining enrichment and metagenomic molecular techniques to enhance microalgae identification and identify microalgae diversity from environmental water samples. From this perspective, we aimed to identify the most suitable culturing media and molecular approach (using different primer sets and reference databases) for detecting microalgae diversity. Using this approach, we have analyzed three water samples collected from the River Nile on several enrichment media. A total of 37 microalgae were identified morphologically to the genus level. While sequencing the three-primer sets (16S rRNA V1-V3 and V4-V5 and 18S rRNA V4 region) and aligning them to three reference databases (GG, SILVA, and PR2), a total of 87 microalgae were identified to the genus level. The highest eukaryotic microalgae diversity was identified using the 18S rRNA V4 region and alignment to the SILVA database (43 genera). The two 16S rRNA regions sequenced added to the eukaryotic microalgae identification, 26 eukaryotic microalgae. Cyanobacteria were identified through the two sequenced 16S rRNA regions. Alignment to the SILVA database served to identify 14 cyanobacteria to the genera level, followed by Greengenes, 11 cyanobacteria genera. Our multiple-media, primer, and reference database approach revealed a high microalgae diversity that would have been overlooked if a single approach had been used over the other.

Buffered loofah supported Microalgae-Bacteria symbiotic (MBS) system for enhanced nitrogen removal from rare earth element tailings (REEs) wastewater: Performance and functional gene analysis

Rare earth element tailings (REEs) wastewater, which has the characteristics of high ammonia nitrogen (NH₄⁺-N) and low COD. It can cause eutrophication and biotoxicity in water which is produced in high volumes, requiring treatment before final disposal. Microalgae-Bacteria symbiotic (MBS) system can be applied in REEs wastewater, but its low extent of nitrogen removal and instability limit its application. By adding biodegradable carrier as both carbon source and carrier, the system can be stabilized and the efficiency can be improved. In this work, the extent of NH₄⁺-N removal reached 100% within 24 h in a MBS system after adding loofah under optimal conditions, and the removal rate reached 127.6 mg NH₄⁺-N·L^-1·d^-1. In addition, the carbon release from loofah in 3 d reached 408.7 mg/L, which could be used as a carbon source to support denitrification. During 90 d of operation of the MBS system loaded with loofah, the effluent NH₄⁺-N was less than 15 mg/L. At phylum level, Proteobacteria were dominant which accounted for 78.2%. Functional gene analysis showed that enhancement of microalgae assimilation was the main factor affecting NH₄⁺-N removal. This work expands our understanding of the enhanced role of carbon-based carriers in the denitrification of REEs wastewater.

Genome engineering via gene editing technologies in microalgae

CRISPR-Cas has revolutionized genetic modification with its comparative simplicity and accuracy, and it can be used even at the genomic level. Microalgae are excellent feedstocks for biofuels and nutraceuticals because they contain high levels of fatty acids, carotenoids, and other metabolites; however, genome engineering for microalgae is not yet as developed as for other model organisms. Microalgal engineering at the genetic and metabolic levels is relatively well established, and a few genomic resources are available. Their genomic information was used for a "safe harbor" site for stable transgene expression in microalgae. This review proposes further genome engineering schemes including the construction of sgRNA libraries, pan-genomic and epigenomic resources, and mini-genomes, which can together be developed into synthetic biology for carbon-based engineering in microalgae. Acetyl-CoA is at the center of carbon metabolic pathways and is further reviewed for the production of molecules including terpenoids in microalgae.

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

Nanoparticles and antibiotics stress proliferated antibiotic resistance genes in microalgae-bacteria symbiotic systems

The comprehensive effect of exogenous pollutants on the dispersal and abundance of antibiotic-resistance genes (ARGs) in the phycosphere, bacterial community and algae-bacteria interaction remains poorly understood. We investigated community structure and abundance of ARGs in free-living (FL) and particle-attached (PA) bacteria in the phycosphere under nanoparticles (silver nanoparticles (AgNPs) and hematite nanoparticles (HemNPs)) and antibiotics (tetracycline and sulfadiazine) stress using high-throughput sequencing and real-time quantitative PCR. Meanwhile, the intrinsic connection of algae-bacteria interaction was explored by transcriptome and metabolome. The results showed that the relative abundance of sulfonamide and tetracycline ARGs in PA and FL bacteria increased 103-129 % and 112-134 %, respectively, under combined stress of nanoparticles and antibiotics. Antibiotics have a greater effect on ARGs than nanoparticles at environmentally relevant concentrations. Proteobacteria, Firmicutes, and Bacteroidetes, as the primary potential hosts of ARGs, were the dominant phyla. Lifestyle, i.e., PA and FL, significantly determined the abundance of ARGs and bacterial communities. Moreover, algae can provide bacteria with nutrients (carbohydrates and amino acids), and can also produce antibacterial substances (fatty acids). This algal-bacterial interaction may indirectly affect the distribution and abundance of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in microalgae-bacteria symbiotic systems.

Clustered regularly interspaced short palindromic repeats (CRISPR) technology and genetic engineering strategies for microalgae towards carbon neutrality: A critical review

Carbon dioxide is the major greenhouse gas and regards as the critical issue of global warming and climate changes. The inconspicuous microalgae are responsible for 40% of carbon fixation among all photosynthetic plants along with a higher photosynthetic efficiency and convert the carbon into lipids, protein, pigments, and bioactive compounds. Genetic approach and metabolic engineering are applied to accelerate the growth rate and biomass of microalgae, hence achieve the mission of carbon neutrality. Meanwhile, CRISPR/Cas9 is efficiently to enhance the productivity of high-value compounds in microalgae for it is easier operation, more affordable and is able to regulate multiple genes simultaneously. The genetic engineering strategies provide the multidisciplinary concept to evolute and increase the CO₂ fixation rate through Calvin-Benson-Bassham cycle. Therefore, the technologies, bioinformatics tools, systematic engineering approaches for carbon neutrality and circular economy are summarized and leading one step closer to the decarbonization society in this review.

Mitochondria and chloroplasts function in microalgae energy production

Microalgae are organisms that have the ability to perform photosynthesis, capturing CO₂ from the atmosphere to produce different metabolites such as vitamins, sugars, lipids, among others, many of them with different biotechnological applications. Recently, these microorganisms have been widely studied due to their possible use to obtain clean energy. It has been postulated that the growth of microalgae and the production of high-energy metabolites depend on the correct function of cellular organelles such as mitochondria and chloroplasts. Thus, the development of different genetic tools to improve the function of these organelles is of high scientific and technological interest. In this paper we review the recent advances in microalgae engineering and the role of cellular organelles in order to increase cell productivity and biomass.

Use of next generation sequencing and bioinformatics for profiling freshwater eukaryotic microalgae in a novel peatland integrated multi-trophic aquaculture (IMTA) system: Case study from the Republic of Ireland

Development of integrated multi-trophic aquaculture (IMTA) systems constitutes a step change in the sustainable production of freshwater fish to meet emerging needs for high-protein foods globally. Recently, there has been a paradigm shift away from harvesting peat as a fuel towards the development of wettable peatland innovation (termed 'paludiculture'), such as aquaculture. Such eco-innovations support carbon sequestration and align with a balanced environmental approach to protecting biodiversity. This novel peatland-based IMTA process in the Irish midlands relies upon natural microalgae for waste treatment, recirculation and water quality where there is no use of pesticides or antibiotics. This novel IMTA system is powered with a wind turbine and the process has 'organic status'; moreover, it does not discharge aquaculture effluent to receiving water. However, there is a significant lack of understanding as to diversity of microalgae in this 'paludiculture'-based IMTA processes. This constitutes the first case study to use conventional microscopy combined with next-generation sequencing and bioinformatics to profile microalgae occurring in this novel IMTA system from pooled samples over a 12 month period in 2020. Conventional microscopy combined with classic identification revealed twenty genera of algae; with Chlorophyta and Charophyta being the most common present. However, algal DNA isolation, 16 s sequencing and bioinformatics revealed a combined total of 982 species from 341 genera across nine phyla from the same IMTA system, which emphasized a significant underestimation in the number and diversity of beneficial or potentially harmful algae in the IMTA-microbiome. These new methods also yield rich data that can be used by digital technologies to transform future monitoring and performance of the IMTA system for sustainability. The findings of this study align with many sustainability development goals of the United Nations including no poverty, zero hunger, good health and well-being, responsible consumption and production, climate change, and life below water.

Sustainable algal biorefineries: capitalizing on many benefits of GABA

We provide physiological and metabolic insights into the complex role of γ-aminobutyric acid (GABA) in fine-tuning algal metabolism to improve productivity. Genetic engineering strategies to improve algal GABA biosynthesis are also discussed. Our aim is to provide an understanding of how GABA can be used for cost-competitive algae-based biofuels and bioproducts.

CO2 bio-mitigation using genetically modified algae and biofuel production towards a carbon net-zero society

CO₂ sequestration carried by biological methodologies shows enhanced potential and has the advantage that biomass produced from the captured CO₂ can be used for different applications. Bio-mitigation of carbons through a micro-algal system addresses a promising and feasible option. This review mostly focused on the role of algae, particular mechanisms, bioreactors in algae cultivation, and genetically modified algae in CO₂ fixation and energy generation systems. A combination of CO₂ bio-mitigation and biofuel production might deliver an extremely promising alternative to current CO₂ mitigation systems. Bio mitigation in which the excess carbon is captured and bio fixation which the carbon is captured by algae or autotrophs and used for producing biofuel. This review revealed that steps for biofuel production from algae include factors affecting, harvesting techniques, oil extraction and transesterification. This review helps environmentalists and researchers to assess the effect of algae-based biorefinery on the green environment.

Temperature stress in psychrophilic green microalgae: Minireview

Photosynthetic algae are the main primary producers in polar regions, form the basis of polar food webs, and are responsible for a significant portion of global carbon fixation. Many cold-water algae are psychrophiles that thrive in the cold but cannot grow at moderate temperatures (≥20°C). Polar regions are at risk of rapid warming caused by climate change, and the sensitivity of psychrophilic algae to rising temperatures makes them, and the ecosystems they inhabit, particularly vulnerable. Recent research on the Antarctic psychrophile Chlamydomonas priscuii, an emerging algal model, has revealed unique adaptations to life in the permanent cold. Additionally, genome sequencing of C. priscuii and its relative Chlamydomonas sp. ICE-L has given rise to a plethora of computational tools that can help elucidate the genetic basis of psychrophily. This minireview summarizes new advances in characterizing the heat stress responses in psychrophilic algae and examines their extraordinary sensitivity to temperature increases. Further research in this field will help determine the impact of climate change on psychrophiles from threatened polar environments.

A review on design-build-test-learn cycle to potentiate progress in isoprenoid engineering of photosynthetic microalgae

Currently, the generation of isoprenoid factories in microalgae relies on two strategies: 1) enhanced production of endogenous isoprenoids; or 2) production of heterologous terpenes by metabolic engineering. Nevertheless, low titers and productivity are still a feature of isoprenoid biotechnology and need to be addressed. In this context, the mechanisms underlying isoprenoid biosynthesis in microalgae and its relationship with central carbon metabolism are reviewed. Developments in microalgal biotechnology are discussed, and a new approach of integrated "design-build-test-learn" cycle is advocated to the trends, challenges and prospects involved in isoprenoid engineering. The emerging and promising strategies and tools are discussed for microalgal engineering in the future. This review encourages a systematic engineering perspective aimed at potentiating progress in isoprenoid engineering of photosynthetic microalgae.

Different effecting mechanisms of two sized polystyrene microplastics on microalgal oxidative stress and photosynthetic responses

Increasing marine microplastics (MPs) pollution potentially threatens the stability of phytoplankton community structures in marine environments. MPs toxicities to microalgae are largely determined by particle size, while the size-dependent mechanisms are still not fully understood. In this study, two sizes (0.1 µm and 1 µm) of polystyrene (PS) MPs were used as experimental targets to systemically compare their different effecting mechanisms on the marine model diatom Thalassiosira pseudonana with respect to oxidative stress and photosynthesis. The results indicated the toxicity of 1 µm sized MPs was higher than 0.1 µm sized MPs regarding to population growth. In condition of similar microalgal population inhibition rates, we found more enhanced cellular oxidative stress and cell death happened in the 1 µm MPs treatments, which could be linked to higher zeta potential of 1 µm MPs and more severe cell surface damage; microalgal surface light shading and cellular pigments decline were more obvious in the 0.1 µm MPs treatment, which could be linked to high aggregation abilities of 0.1 µm MPs. Gene expressions supported the morphological and physiological findings on the transcriptional level. Environmental related MPs concentrations (5 μg L^-1) also aroused gene expression changes of T. pseudonana while more changing genes were found under 0.1 µm MPs than 1 µm MPs. These results provide novel insights into the size-dependent mechanisms of MPs toxicity on marine microalgae, as well as their potential influence on the marine environment.

Biochemistry and Biotechnology of Lipid Accumulation in the Microalga Nannochloropsis oceanica

Oils are among the most important agricultural commodities and have wide applications in food/nutrition, biofuels, and oleochemicals. The oleaginous microalga Nannochloropsis oceanica can produce large amounts of oils and the high-value ω-3 eicosapentaenoic acid, which represents a promising resource for oil production targeting biodiesel, nutraceutical, and aquaculture industries. In recent years, with the availability of omics databases and the development of genetic tools, N. oceanica has been extensively investigated as a model photosynthetic organism for studying lipid metabolism and as a green cellular factory to produce lipids for industrial applications. This review summarizes the current knowledge on the lipid composition and biosynthetic pathways of N. oceanica and reviews the recent advances in metabolic engineering of lipid production in this microalga.

Microalgae simultaneously promote antibiotic removal and antibiotic resistance genes/bacteria attenuation in algal-bacterial granular sludge system

This study investigated the effects of microalgae growth on antibiotic removal and the attenuation of antibiotic resistance genes (ARGs)/ARGs host bacteria in algal-bacterial granular sludge (ABGS) system. In the presence of tetracycline (TC) and sulfadiazine (SDZ) mixture (2-4 mg/L), microalgae could grow on bacterial granular sludge (BGS) to form ABGS, with a chlorophyll-a content of 7.68-8.13 mg/g-VSS being achieved. The removal efficiencies of TC and SDZ by ABGS were as high as 79.0 % and 94.0 %, which were 4.3-5.0 % higher than those by BGS. Metagenomic analysis indicated that the relative abundances of TC/SDZ- related ARGs and mobile genetic elements (MGEs) in BGS were 56.1 % and 22.1 % higher than those in ABGS. A total of 26 ARGs were detected from the granules, and they were identified to associate with 46 host bacteria. 13 out of 26 ARGs and 13 out of 46 hosts were shared ARGs and hosts, respectively. The total relative abundance of host bacteria in BGS was 30.8 % higher than that in ABGS. Scenedesmus and Chlorella were the dominant microalgae that may reduce the diversity of ARGs hosts. Overall, ABGS is a promising biotechnology for antibiotic-containing wastewater treatment.

Enhanced removal of antibiotics and decreased antibiotic resistance genes in the photo-sequencing batch reactor during the aquaculture wastewater treatment

The performance of photo-sequencing batch reactor (PSBR) in removing multiple antibiotics and nutrients from aquaculture wastewater as well as the antibiotic resistance genes (ARGs) proliferation were firstly investigated during the long-term experiments. The operational conditions (i.e. light intensity, light time, aeration and solid retention time) were optimised to realise the simultaneous removal of antibiotics and nutrients. It was found that, compared with traditional SBR, PSBR has similar nutrient removal rate and a 30% higher antibiotics removal rate due to the corporation of microalgae (Chlorella) and bacteria, and the absolute abundance of ARGs decreased by 78% in PSBR. Further investigation showed that PSBR had certain advantages in removing quinolones and the corresponding removal rate could reach up to 90%. In terms of the mechanisms, the possible metabolic pathway of antibiotic was analysed and the intermediate metabolites were different from that of the reported studies. The microbial communities were also affected by microalgae and the relative abundance of certain bacteria (such as members of the families Rhodocyclaceae and Burkholderiaceae), which were positively correlated with some ARGs, decreased in PSBR. This study provides an alternative and effective method to aquaculture wastewater treatment, which present high nutrients and antibiotics removal efficiencies and low ARGs transmission.