Search Results (156)

The use of microalgae as a food source is limited by consumers’ dislike of their organoleptic traits, primarily the intense green color and bitter taste associated with high chlorophyll content. The eukaryotic microalgae Chlorella vulgaris can grow under heterotrophic conditions, providing the opportunity to cultivate chlorophyll-less strains. In this work we applied random mutagenesis for breeding chlorophyll-deficient C. vulgaris strains. Wild-type strain was UVC-radiated, and 12 colonies with changed pigmentation were selected. Based on phenotypic stability two mutants, M6 and M11, were selected for characterization of growth, pigment and biomass accumulation. Cultivation under photo-, mixo- and heterotrophic conditions revealed distinct phenotypes for the two mutants. M6 remained chlorophyll-deficient in all cultivation conditions tested, while chlorophyll was observed in M11 when grown under light. Under heterotrophic and mixotrophic growth conditions, both mutants were chlorophyll-deficient while biomass productivity, protein content, and amino acid composition remained similar to wild type. Characterization of the cellular ultrastructure of the wild type and mutants using cryo Focused Ion-Beam Scanning Electron Microscopy revealed that functional chloroplasts and thylakoid membranes were absent in the mutants. Our work demonstrates how a simple approach using UV mutagenesis and visual screening can provide novel strains of C. vulgaris with traits for improved consumer acceptance, without compromising the use of the algae biomass as a protein-rich food source. Full article

Eukaryotic algae are key contributors to biodiversity and ecosystem functioning in aquatic environments. However, understanding their global diversity patterns and community assembly mechanisms remains limited by the lack of high-resolution, highly specific analytical methods. Here, we present the first eukaryotic algae-specific classification database, EukAlgae-T (Eukaryotic Algae Taxonomic database), constructed based on single-copy orthologous genes. The database integrates 50,581 non-redundant marker genes from 479 high-quality genomes and was applied to analyze 939 marine metagenomic samples from the Tara Oceans project. Our results reveal that the genomically represented fraction of the global algal community is dominated by a widely distributed core taxonomic group, comprising 125 of the 230 detected species. Redundancy analysis indicated that community structure is primarily regulated by latitude and iron concentration on a global scale. In contrast, Mantel tests revealed strong regional heterogeneity, with temperature, salinity, and iron concentration acting as universal local drivers, albeit with varying effect sizes and combinations across ocean basins. Co-occurrence network analysis further demonstrated predominantly cooperative interactions among taxa, forming a highly modular and stable network structure, and identified key hub taxa characterized by low abundance but high connectivity. Together, this study provides a dedicated framework for eukaryotic algae metagenomic analysis and demonstrates that algal community assembly is driven by multi-scale environmental filtering: broadly constrained by climate zones and iron limitation at the global scale and regionally reshaped by local oceanographic processes (e.g., thermohaline structure). Cooperative coexistence and niche differentiation among taxa jointly underpin the maintenance of global algal diversity. Full article

Polyglutamine expansion in Ataxin-2 (ATXN2) is responsible for rare, dominantly inherited Spinocerebellar Ataxia type 2 (SCA2). Together with its paralog Ataxin-2-like (ATXN2L), both proteins have received much interest, since the deletion of their yeast and fly orthologs alleviates TDP-43-triggered neurotoxicity in Amyotrophic Lateral Sclerosis models. Their typical structure across evolution combines LSm with LSm-Associated Domains and a PAM2 motif. To understand the physiological regulation and functions of Ataxin-2 homologs, the phylogenesis of sequences was analyzed. Human ATXN2 harbors multiple alternative start codons, e.g., from an intrinsically disordered sequence (IDR) present since armadillo, or from the polyQ sequence that arose since amphibians, or from the LSm domain since primitive eukaryotes. Multiple smaller isoforms also exist across the C-terminus. Therapeutic knockdown of polyQ expansions in human ATXN2 should selectively target exon 1B. PolyQ repeats developed repeatedly, usually framed and often interrupted by (poly)Pro, originally near PAM2. The LSmAD sequence appeared in algae as the characteristic Ataxin-2 feature with strong conservation. Frequently, Ataxin-2 has added domains, likely due to transcriptional readthrough of neighbor genes during cell stress. These chimerisms show enrichment of rRNA processing; nutrient store mobilization; membrane strengthening via lipid, protein, and glycosylated components; and cell protrusions. Thus, any mutation of Ataxin-2 has complex effects, also affecting membrane resilience. Full article

TPPP (tubulin polymerization promoting protein)-like proteins are found throughout the living world. The individual members of this protein family are distinguished according to how many times and how completely their characteristic structural element, the p25alpha domain, is found in them. Phylogenomic occurrences of the members of the family differ from each other. Animals, fungi, algae, and various groups of unicellular organisms have their characteristic proteins. The two phylogenomic multi-supergroups, Opimoda+ and Diphoda+, show very different patterns in the occurrence of TPPP types. By using BLAST search in protein and nucleotide databases, we found that the previously known phylogenomic distribution is not strictly true, e.g., fungal type TPPPs are not only found in fungi. We primarily analyzed the Opisthokonta clade but also examined broader relationships. It was confirmed that the occurrence of TPPPs/genes is linked to the presence of the eukaryotic flagellum. A TPPP that contains the entire p25alpha domain twice and occurs only in Opisthokonta was identified. We also identified a TPPP in choanoflagellates and in the uncertainly classified Opisthokonta Tunicaraptor unikontis, which was previously known only in the Diphoda+ clade. On the other hand, we found an Opisthokonta (Opimoda+)-specific TPPP in a Heterolobosea (Diphoda+). Based on these results, we need to rethink the evolutionary history of TPPPs. Full article

In freshwater ecosystems, cross-trophic interactions among biological communities underpin ecosystem stability and functionality. In arid and semi-arid rivers, however, hydrological fluctuations, invasive species, and other perturbations exacerbate the complexity of biological processes. To systematically assess the community structure of fish, eukaryotic plankton, and prokaryotic microorganism in the Irtysh River basin, this study employed environmental DNA (eDNA) metabarcoding for monitoring. High-throughput sequencing of taxa within the study area was conducted via eDNA metabarcoding, coupled with random forest and linear mixed models to dissect the effects of community structure. The eDNA approach effectively unraveled spatial patterns of biodiversity and identified taxon-specific diversity hotspots: invasive fish exerted a facilitative effect on algae and suppressed the richness of protozoa, fungi, and heterotrophic microorganisms, yet had minimal impact on the dominant structure of autotrophic microorganisms. These findings provide a scientific basis for basin-scale ecological management, emphasizing the necessity of balancing habitat preservation and invasive-species control to safeguard ecosystem functionality. Full article

Transcription factors (TFs) are important gene transcription regulators involved in myriad functions such as development, metabolism, and stress response. TFs are found in all eukaryotes, with many families of TFs unique to plants and algae. Algae are of interest due to a wide range of novel metabolites, of which TFs play an important role in regulating their biosynthesis. In particular, the red algae (phylum Rhodophyta) are a source of several important metabolites that are a current focus of further research. However, to date, investigations of TF families in rhodophytes have been limited due to the relative lack of genomic resources available and the small number of in silico analyses of their TFs. In this study, we used genomic and transcriptomic data to identify rhodophyte TFs. We found that the general proportion of TFs in rhodophytes was overall consistent with previous research. However, for the first time in the rhodophyte class Florideophyceae, we report the presence of a putative TF within the trihelix TF (TTF) family, which are light-sensitive TFs associated with growth and stress response. In particular, we demonstrate evidence suggesting the presence of putative TTFs in three Asparagopsis taxiformis genomes, as well as in several other florideophyte assemblies. This was supported by analyses including Neighbour-Joining phylogeny, protein structure prediction, and motif analysis. In summary, this research reported the repertoire of TFs in rhodophyte algae across a much greater range than previously reported and identified putative TTFs in several algae from the class Florideophyceae. This opens an avenue for further research into the evolution of various TFs in early plants, as well as key regulatory factors in rhodophyte metabolism, though future research, such as functional characterisation, will be required to confirm these findings. Full article

From a One Health perspective, the Ría de Vigo (NW Spain) represents a complex socio-ecological system where urban, industrial, and aquaculture activities converge, creating vulnerabilities due to the interconnection between human, animal, and environmental health. This study evaluates the utility of a multi-marker environmental DNA (eDNA) metabarcoding approach as an early warning tool to detect potentially harmful eukaryotic pathogens near wastewater discharge points in three distinct municipalities of the Ría de Vigo. Water and sediment samples were analyzed using the V4 and V9 regions of the 18S rRNA gene and the ITS-2 region for fungi. Bioinformatics analysis was performed with DADA2 and taxonomic assignments were based on SILVA and UNITE databases. Eukaryotic diversity varied by site and marker, with the highest richness found in inner estuary sediments. The V9 region provided broader taxonomic coverage, while V4 produced higher read abundances. Putative pathogens, including human, zoonotic, and aquaculture-related taxa, were more prevalent in inner estuarine zones. Pathogens such as Rhodotorula mucilaginosa, Acanthamoeba sp., Cryptosporidium sp., and harmful algae (HA) were detected. The findings emphasize the importance of a multi-marker strategy, sediment inclusion, and landscape-scale variables to improve early pathogen detection, contributing to effective eDNA-based surveillance systems for coastal health management. Full article

Oxidative stress caused by excessive reactive oxygen species (ROS) contributes to numerous chronic diseases. Marine green algae of the Caulerpa genus are rich in bioactive compounds with potential antioxidant activity. Objective: This study aimed to evaluate the intracellular antioxidant effects of caulerpin (CAU) and its derivative caulerpinic acid (CA) using Saccharomyces cerevisiae as a eukaryotic model. Methods: Yeast cells were pretreated with 1 μM of CAU or CA, or with 1 μM of resveratrol (RESV) as a positive control, then exposed to 2 mM of H₂O₂. Growth, ROS levels, oxidative damage markers, and antioxidant defenses were assessed. Results: Both CAU and CA significantly improved cell survival under oxidative stress, restoring growth rates (CAU: 0.129 h⁻¹, CA: 0.137 h⁻¹) and doubling times (CAU: 5.38 h, CA: 5.07 h) close to control values. Intracellular ROS accumulation, protein carbonylation, and lipid peroxidation were reduced to near-baseline levels. While catalase (Cat) and superoxide dismutase (Sod) activity remained unchanged, CAU and CA elevated intracellular glutathione (GSH) levels (1.6–1.8 fold) and preserved glutathione peroxidase (GPx) activity, compared to stressed cells without antioxidant pretreatment. Conclusions: CAU and CA act as effective intracellular antioxidants, primarily via ROS scavenging and GSH-dependent pathways. These findings support their potential as natural candidates for developing antioxidant-based therapies against ROS-related disorders. Full article

Dunaliella salina, a unicellular and eukaryotic alga, has been found to be one of the most salt-tolerant eukaryotes with a wide range of practical applications. To elucidate the underlying molecular mechanisms of D. salina in response to salinity stress, we performed transcriptome sequencing on samples under different stress conditions. A total of 82,333 unigenes were generated, 4720, 1111 and 2611 differentially expressed genes (DEGs) were identified under high salt stress, oxidative stress and hypertonic stress, respectively. Our analysis revealed that D. salina responds to salinity stress through a complex network of molecular mechanisms. Under high salt stress, starch degradation is regulated by AMY (α-amylase) and PYG (glycogen phosphorylase) with alternative expression patterns. This process is hypothesized to be initially constrained by low ATP levels due to impaired photosynthesis. The clustering analysis of DEGs indicated that starch and sucrose metabolism, as well as glycerol metabolism, are specifically reprogrammed under high salt stress. Glycerol metabolism, particularly involving GPDHs, plays a crucial role in maintaining osmotic balance under salinity stress. Key glycerol metabolism genes were up-regulated under salinity conditions, indicating the importance of this pathway in osmotic regulation. The G3P shuttle, involving mitochondrial GPDHs (c25199_g1 and c23777_g1), contributes to redox imbalance management under high salt, oxidative and hypertonic stresses. Notably, c23777_g1 is involved in the G3P shuttle under high salt, oxidative and hypertonic stresses, while c25199_g1 is specifically induced by hypertonic stress. The R2R3-MYB gene (c23845_g1) may respond to different effects of salinity stress by regulating the transcription of ROS-related genes. Our study provides a detailed understanding of the molecular responses of D. salina to salinity stress. We reveal the critical roles of starch and sucrose metabolism, glycerol metabolism and transcription factors in the D. salina adaptation to salinity. Full article

Membrane transporters are vital for solute movement and localisation across cellular compartments, particularly in extremophilic organisms such as Galdieriales. These red algae thrive in geothermal and metal-rich environments, where adaptive transporter systems contribute to their metabolic flexibility. While inventories of transporter genes in the species Galdieria sulphuraria have previously been compiled, their phylogenetic origins remain incompletely resolved. Here, we conduct a comparative phylogenetic analysis of three transporter families—Major Facilitator Superfamily (MFS). Amino acid–Polyamine–Organocation (APC) and the natural resistance–associated macrophage protein (Nramp)—selected from overexpressed transcripts in G. sulphuraria strain SAG 107.79. Using sequences from six Galdieriales species and orthologs from diverse taxa, we reconstructed maximum likelihood trees to assess conservation and potential horizontal gene transfer (HGT). The MFS subfamilies revealed contrasting patterns: sugar porters (SPs) exhibited polyphyly and fungal affinity, suggesting multiple HGT events, while phosphate:H⁺ symporters (PHSs) formed a coherent monophyletic group. APC sequences were exclusive in G. sulphuraria and extremophilic prokaryotes, indicating a likely prokaryotic origin. In contrast, Nramp transporters were broadly conserved across eukaryotes and prokaryotes, showing no signs of recent HGT. Together, these findings highlight the mosaic evolutionary history of membrane transporters in Galdieriales, shaped by a combination of vertical inheritance and taxon-specific gene acquisition events, and provide new insight into the genomic strategies underpinning environmental resilience in red algae. Full article

Photosynthetic eukaryotes have shaped the Earth’s biosphere by producing oxygen and organic compounds using light energy in specialized organelles called plastids. Plastids evolved from free-living cyanobacteria ingested by heterotrophic unicellular eukaryotes. Two such independent engulfment processes, called cyanobacterial endosymbioses, have been reported. The first gave rise to primary plastids and three Archaeplastida lineages: glaucophytes, red algae, and green algae with land plants, whereas the second resulted in chromatophores in the rhizarian amoeba Paulinella. Importantly, Archaeplastidans donated their plastids to many protist groups, further spreading photosynthesis across the tree of life. To reveal complex plastid evolution, we performed comprehensive phylogenetic and molecular clock analyses using new fossil calibrations and the largest number yet of plastid-encoded proteins from 108 taxa, representing diverse photosynthetic organisms. Our results indicate that primary plastids evolved prior to 2.1–1.8 Ga, i.e., before glaucophytes diverged from other Archaeplastidans, and Paulinella chromatophores were likely before 292–266 Ma. Red and green algae were engulfed by cryptophyte and chlorarachniophyte ancestors between 1.7–1.4 Ga and 1.1–1.0 Ga, respectively; the former subsequently triggered plastid transfers to other eukaryotes. We also examined the impact of molecular clocks and calibration sets on age estimates, showing that clocks are the main source of variation. Full article

Microalgae are microscopic unicellular organisms that inhabit marine, freshwater, and moist terrestrial ecosystems. The vast number and diversity of microalgal species provide a significant reservoir of biologically active compounds, highly promising for biomedical applications. Diatoms are unicellular eukaryotic algae belonging to the class Bacillariophyceae. They possess intricately structured silica-based cell walls, which contain long-chain polyamines that play important roles in the formation of silica. Long-chain polyamines are uncommon polyamines found only in organisms that produce biosilica. Diatomite, which is a marine sediment of the remains of the silica skeleton of diatoms, could be an abundant source of biogenic silica that can easily be converted to silica particles. This concise review focuses on the biofabrication of polyamine-based nanosilica from diatoms and highlights the possibility of utilizing diatom biosilica as a nanocarrier for drug and siRNA delivery, bioimaging, and bone tissue engineering. The challenges that may affect diatom production, including environmental stresses and climate change, are discussed together with the prospect of increasing diatom-based biosilica production with the desired nanostructures via genetic manipulation. Full article

The phytoplankton communities in lakes change seasonally within competitive areas, referred to as seasonal succession, which results in high compositional diversity if conditions remain stable. However, glacial lakes are generally far from human and terrestrial influences due to their location so very few species can be identified and large changes in phytoplankton composition cannot be anticipated. Nonetheless, molecular techniques, as well as classical methods, help us to determine the existence of different species. Additionally, these techniques allow us to evaluate the ecology of glacial lakes from different perspectives with developing technology. Horseshoe Island is located in the area known as Marguerite Bay on the Peninsula region in western Antarctica. This study was carried out to determine phytoplankton genome biodiversity by using the metagenomic analysis method used in 18S rRNA, 16S rRNA, and 23S rRNA gene analyses. 16S rRNA and 23S rRNA gene analyses revealed that bacteria belong to broadly distributed Cyanobacteria taxa, whereas 18S rRNA gene analysis revealed other eukaryotic phytoplankton groups. This method was used for the first time for Horseshoe Island lakes (Col 1, Col 2, Skua, and Zano), and species belonging to Cyanobacteria, Chlorophyta, Ochrophyta, and Bacillariophyta were identified. As a result, the phytoplankton genomic diversity of shallow and oligotrophic glacial lakes was determined, and benthic algal species were also identified in the water samples. These results indicate that benthic algae associated with the sediment can also contribute to aquatic phytoplankton communities in addition to oligotrophic lake phytoplankton biodiversity. Cyanobacterial biodiversity can also be recognized as a sentinel by which to monitor adaptation responses to climate change in this rapidly warming region. Full article

Understanding triacylglycerol (TAG) metabolism is crucial for developing algae as a source of biodiesel. TAGs are the main reservoir of energy in most eukaryotes. The final, rate-limiting step in the formation of TAGs is catalyzed by 1,2-diacylglycerol acyltransferases (DGATs). In the green alga Chlamydomonas reinhardtii, DGAT3 is phylogenetically related to plant DGAT3 but unrelated to other DGATs from eukaryotes, such as DGAT1 and DGAT2. In this study, we described the conformational preferences and the lipid-binding features of the DGAT3 from C. reinhardtii. To characterize its conformational stability and structural features, we used several biophysical probes, namely, fluorescence, circular dichroism (CD), and differential scanning calorimetry (DSC). Our results showed that the protein was mainly disordered, containing a small population of folded conformations in a narrow pH range (pH 8 to 10). The conformational stability of the folded structure of DGAT3 was very low, as shown by urea or guanidinium denaturations. Thermal denaturation, followed by fluorescence or CD, as well as calorimetric denaturation, followed by DSC, did not yield any transition in the pH range where DGAT3 acquired a “native-like” conformation. Furthermore, we used two approaches to demonstrate the interaction of DGAT3 with lipid membranes at the pH at which it had acquired a “native-like” conformation. The first involved the measurement of anisotropy and fluorescence quenching of the protein. The second approach focused on examining possible modifications of the biophysical properties of lipids due to their interaction with DGAT3, through anisotropy measurements and leakage assays. Both methods produced consistent results, suggesting that DGAT3 preferentially interacted with negatively charged membranes. These results will allow the design of a more efficient and stable DGAT3, as well as an in-depth understanding of how the metabolism of TAGs is accomplished in C. reinhardtii. Full article

Thermomineral springs are unique aquatic habitats characterized by high temperatures or mineral-rich water and often host specialized microbial communities. In Serbia, these springs represent an important but under-researched ecological resource whose diverse physicochemical properties are shaped by their geological context. In this study, the physical and chemical properties of Serbian thermomineral springs and their relationship with phototrophic communities in different substrates are investigated. Phototrophic biofilms were categorized into fully submerged and splash zone biofilms, with the former showing higher primary production. Cyanobacteria, Chlorophyta, and Bacillariophyta were recorded, with Bacillariophyta being the predominant division in terms of diversity, followed by Cyanobacteria. Among Cyanobacteria, coccoid forms like Aphanocapsa, Chroococcus, Gloeocapsa and Synechococcus dominated splash zones, while trichal forms such as Leptolyngbya, Oscillatoria and Pseudanabaena were abundant in submerged biofilms, forming thick mats. Unique cyanobacterial taxa, including Desertifilum, Elainella, Geitlerinema, Nodosilinea and Wilmottia, were identified through molecular analysis, underscoring the springs’ potential as habitats for specialized phototrophs. Diatom communities, dominated by Nitzschia and Navicula, exhibited site-specific species influenced by microenvironmental parameters. Statistical analysis revealed ammonia, total nitrogen, and organic carbon as key factors shaping community composition. This study enhances the understanding of these ecosystems, emphasizing their conservation importance and potential for biotechnological applications. Full article