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1.
Sci Rep ; 14(1): 18980, 2024 08 16.
Article in English | MEDLINE | ID: mdl-39152251

ABSTRACT

Desmodesmus spp. are one of the most dominant components of phytoplankton, which are present in most water bodies. However, identification of the species based only on morphological data is challenging. The aim of the present study was to provide a comprehensive understanding of the actual distribution of the Desmodesmus species in Saga City, Saga Prefecture, Japan. In the present study, 38 water bodies were surveyed between June 2017 and March 2023. A total of 86 culture strains were established from the samples collected from the 21 sites, and identified by molecular phylogenetic analysis, comparison of ITS2 rRNA secondary structures, and observation of surface microstructure. In total, four new species, including D. notatus Demura sp. nov., D. lamellatus Demura sp. nov., D. fragilis Demura sp. nov., and D. reticulatus Demura sp. nov. were proposed and 17 Desmodesmus species were identified as described species. The present study revealed > 20 Desmodesmus species, exhibiting high genetic diversity in a small area.


Subject(s)
Chlorophyceae , Phylogeny , Japan , Chlorophyceae/genetics , Chlorophyceae/classification , Phytoplankton/classification , Phytoplankton/genetics , Genetic Variation , Biodiversity , Chlorophyta/classification , Chlorophyta/genetics
2.
Antonie Van Leeuwenhoek ; 117(1): 113, 2024 Aug 19.
Article in English | MEDLINE | ID: mdl-39158755

ABSTRACT

Despite the long research history on the genus Coelastrella, its species diversity and biotechnological potential have not been fully explored. For the first time, cluster analysis of morphological characteristics was done in the representatives of the said genus. The results obtained have shown that morphological similarity does not necessarily indicate a molecular genetic relationship. It the light of it, the taxonomic status of species can reliably be determined using specific DNA region, such as 18S-ITS1-5.8S-ITS2. The V4 and V9 regions of gene 18S rRNA are relatively conservative fragments which are not suitable for species identification. The ITS2 can be used as a "short barcode". Among the advanced machine methods for delimitation species, the most effective algorithm for distinguishing Coelastrella species was the Generalized Mixed Yule Coalescent (GMYC) method. This paper represented for the first time our comprehensive review of the works devoted to the analysis of the biotechnological potential of representatives of the genus Coelastrella and shows that fatty acid composition of the three main chemogroups within the studied genus differs. In the future, this may form the basis for predicting the composition of the fatty acid profile of new strains, which is important while searching for organisms with specified biotechnological properties. In conclusion, an integrative approach was employed to describe Coelastrella affinis sp. nov., a new species of the genus Coelastrella with high biotechnological potential. Also, a new description of C. thermophila var. astaxanthina comb. nov. was proposed.


Subject(s)
Chlorophyceae , Phylogeny , RNA, Ribosomal, 18S , Chlorophyceae/classification , Chlorophyceae/genetics , RNA, Ribosomal, 18S/genetics , Fatty Acids/analysis , Biotechnology , DNA Barcoding, Taxonomic , DNA, Algal/genetics , DNA, Algal/chemistry , Cluster Analysis , Sequence Analysis, DNA , DNA, Ribosomal Spacer/genetics
3.
Bioresour Technol ; 410: 131291, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39153698

ABSTRACT

Overexpression of Dunaliella parva (D. parva) malic enzyme (ME) gene (DpME) significantly increased DpME expression and ME enzyme activity in transgenic D. parva. Nitrogen limitation had an inhibitory effect on protein content, and DpME overexpression could improve protein content. Nitrogen limitation increased carbohydrate content, and Dunaliella parva overexpressing malic enzyme gene under nitrogen limitation (DpME-N-) group showed the lowest starch content among all groups. Dunaliella parva overexpressing malic enzyme gene under nitrogen sufficient condition (DpME) and DpME-N- groups showed considerably high mRNA levels of DpME. ME activity was significantly enhanced by DpME overexpression, and nitrogen limitation caused a smaller increase. DpME overexpression and nitrogen limitation obviously enhanced lipid accumulation, and DpME overexpression had more obvious effect. Compared with control (wild type), lipid content (68.97%) obviously increased in DpME-N- group. This study indicated that the combination of DpME overexpression and nitrogen limitation was favorable to the production of microalgae biodiesel.


Subject(s)
Lipid Metabolism , Malate Dehydrogenase , Nitrogen , Nitrogen/metabolism , Malate Dehydrogenase/metabolism , Malate Dehydrogenase/genetics , Chlorophyceae/genetics , Chlorophyceae/metabolism
4.
PLoS One ; 19(8): e0307248, 2024.
Article in English | MEDLINE | ID: mdl-39172989

ABSTRACT

In the current study, systems biology approach was applied to get a deep insight regarding the regulatory mechanisms of Chromochloris zofingiensis under overall stress conditions. Meta-analysis was performed using p-values combination of differentially expressed genes. To identify the informative models related to stress conditions, two distinct weighted gene co-expression networks were constructed and preservation analyses were performed using medianRankand Zsummary algorithms. Moreover, functional enrichment analysis of non-preserved modules was performed to shed light on the biological performance of underlying genes in the non-preserved modules. In the next step, the gene regulatory networks between top hub genes of non-preserved modules and transcription factors were inferred using ensemble of trees algorithm. Results showed that the power of beta = 7 was the best soft-thresholding value to ensure a scale-free network, leading to the determination of 12 co-expression modules with an average size of 128 genes. Preservation analysis showed that the connectivity pattern of the six modules including the blue, black, yellow, pink, greenyellow, and turquoise changed during stress condition which defined as non-preserved modules. Examples of enriched pathways in non-preserved modules were Oxidative phosphorylation", "Vitamin B6 metabolism", and "Arachidonic acid metabolism". Constructed regulatory network between identified TFs and top hub genes of non-preserved module such as Cz06g10250, Cz03g12130 showed that some specific TFs such as C3H and SQUAMOSA promoter binding protein (SBP) specifically regulates the specific hubs. The current findings add substantially to our understanding of the stress responsive underlying mechanism of C. zofingiensis for future studies and metabolite production programs.


Subject(s)
Gene Expression Profiling , Gene Regulatory Networks , Microalgae , Stress, Physiological , Stress, Physiological/genetics , Microalgae/genetics , Microalgae/metabolism , Transcriptome , Chlorophyceae/genetics , Transcription Factors/genetics , Transcription Factors/metabolism , Gene Expression Regulation, Plant , Algorithms
5.
Nat Commun ; 15(1): 6046, 2024 Jul 18.
Article in English | MEDLINE | ID: mdl-39025848

ABSTRACT

Energy status and nutrients regulate photosynthetic protein expression. The unicellular green alga Chromochloris zofingiensis switches off photosynthesis in the presence of exogenous glucose (+Glc) in a process that depends on hexokinase (HXK1). Here, we show that this response requires that cells lack sufficient iron (-Fe). Cells grown in -Fe+Glc accumulate triacylglycerol (TAG) while losing photosynthesis and thylakoid membranes. However, cells with an iron supplement (+Fe+Glc) maintain photosynthesis and thylakoids while still accumulating TAG. Proteomic analysis shows that known photosynthetic proteins are most depleted in heterotrophy, alongside hundreds of uncharacterized, conserved proteins. Photosynthesis repression is associated with enzyme and transporter regulation that redirects iron resources to (a) respiratory instead of photosynthetic complexes and (b) a ferredoxin-dependent desaturase pathway supporting TAG accumulation rather than thylakoid lipid synthesis. Combining insights from diverse organisms from green algae to vascular plants, we show how iron and trophic constraints on metabolism aid gene discovery for photosynthesis and biofuel production.


Subject(s)
Chlorophyta , Glucose , Iron , Lipid Metabolism , Photosynthesis , Triglycerides , Iron/metabolism , Glucose/metabolism , Triglycerides/metabolism , Chlorophyta/metabolism , Chlorophyta/genetics , Thylakoids/metabolism , Proteomics , Hexokinase/metabolism , Hexokinase/genetics , Chlorophyceae/metabolism , Chlorophyceae/genetics
6.
Environ Microbiol ; 26(8): e16680, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39080862

ABSTRACT

The green algae of the genus Ancylonema, which belong to the zygnematophytes, are prevalent colonizers of glaciers worldwide. They display a striking reddish-brown pigmentation in their natural environment, due to vacuolar compounds related to gallic acid. This pigmentation causes glacier darkening when these algae bloom, leading to increased melting rates. The Ancylonema species known so far are true psychrophiles, which hinders experimental work and limits our understanding of these algae. For instance, the biosynthesis, triggering factors, and biological function of Ancylonema's secondary pigments remain unknown. In this study, we introduce a mesophilic Ancylonema species, A. palustre sp. nov., from temperate moorlands. This species forms the sister lineage to all known psychrophilic strains. Despite its morphological similarity to the latter, it exhibits unique autecological and photophysiological characteristics. It allows us to describe vegetative and sexual cellular processes in great detail. We also conducted experimental tests for abiotic factors that induce the secondary pigments of zygnematophytes. We found that low nutrient conditions combined with ultraviolet B radiation result in vacuolar pigmentation, suggesting a sunscreen function. Our thriving, bacteria-free cultures of Ancylonema palustre will enable comparative genomic studies of mesophilic and extremophilic zygnematophytes. These studies may provide insights into how Ancylonema species colonized the world's glaciers.


Subject(s)
Phylogeny , Pigments, Biological , Vacuoles , Pigments, Biological/metabolism , Vacuoles/metabolism , Chlorophyta/metabolism , Chlorophyta/genetics , Pigmentation , Chlorophyceae/metabolism , Chlorophyceae/genetics
7.
PLoS One ; 19(7): e0301680, 2024.
Article in English | MEDLINE | ID: mdl-39046949

ABSTRACT

The development of high molecular weight (HMW) genomic DNA (gDNA) extraction protocols for non-model species is essential to fully exploit long-read sequencing technologies in order to generate genome assemblies that can help answer complex questions about these organisms. Obtaining enough high-quality HMW gDNA can be challenging for these species, especially for tissues rich in polysaccharides such as biomass from species within the Botryococcus genus. The existing protocols based on column-based DNA extraction and biochemical lysis kits can be inefficient and may not be useful due to variations in biomass polysaccharide content. We developed an optimized protocol for the efficient extraction of HMW gDNA from Botryococcus biomass for use in long-read sequencing technologies. The protocol utilized an initial wash step with sorbitol to remove polysaccharides and yielded HMW gDNA concentrations up to 220 ng/µL with high purity. We then demonstrated the suitability of the HMW gDNA isolated from this protocol for long-read sequencing on the Oxford Nanopore PromethION platform for three Botryococcus species. Our protocol can be used as a standard for efficient HMW gDNA extraction in microalgae rich in polysaccharides and may be adapted for other challenging species.


Subject(s)
Biomass , Molecular Weight , DNA, Bacterial/isolation & purification , DNA, Bacterial/genetics , Chlorophyceae/genetics , Sequence Analysis, DNA/methods , Genome, Bacterial , Genomics/methods
8.
Enzyme Microb Technol ; 179: 110464, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38850682

ABSTRACT

Dunaliella salina is an innovative expression system due to its distinct advantages such as high salt tolerance, low susceptibility to contamination, and the absence of the cell wall. While nuclear transformation has been extensively studied, research on D. salina chloroplast transformation remains in the preliminary stages. In this study, we established an efficient chloroplast expression system for D. salina using Golden Gate assembly. We developed a D. salina toolkit comprising essential components such as chloroplast-specific promoters, terminators, homologous fragments, and various vectors. We confirmed its functionality by expressing the EGFP protein. Moreover, we detailed the methodology of the entire construction process. This expression system enables the specific targeting of foreign genes through simple homologous recombination, resulting in stable expression in chloroplasts. The toolkit achieved a relatively high transformation efficiency within a shorter experimental cycle. Consequently, the construction and utilization of this toolkit have the potential to enhance the efficiency of transgenic engineering in D. salina and advance the development of microalgal biofactories.


Subject(s)
Chloroplasts , Genetic Vectors , Green Fluorescent Proteins , Transformation, Genetic , Chloroplasts/genetics , Chloroplasts/metabolism , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Genetic Vectors/metabolism , Promoter Regions, Genetic , Plants, Genetically Modified/genetics , Plants, Genetically Modified/metabolism , Genetic Engineering/methods , Microalgae/genetics , Microalgae/metabolism , Chlorophyceae/genetics , Chlorophyceae/metabolism , Chlorophyta/genetics , Chlorophyta/metabolism , Homologous Recombination , Gene Expression
9.
Plant Physiol Biochem ; 211: 108697, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38705045

ABSTRACT

Dunaliella salina, a microalga that thrives under high-saline conditions, is notable for its high ß-carotene content and the absence of a polysaccharide cell wall. These unique characteristics render it a prime candidate as a cellular platform for astaxanthin production. In this study, our initial tests in an E. coli revealed that ß-ring-4-dehydrogenase (CBFD) and 4-hydroxy-ß-ring-4-dehydrogenase (HBFD) genes from Adonis aestivalis outperformed ß-carotene hydroxylase (BCH) and ß-carotene ketolase (BKT) from Haematococcus pluvialis counterparts by two-fold in terms of astaxanthin biosynthesis efficiency. Subsequently, we utilized electroporation to integrate either the BKT gene or the CBFD and HBFD genes into the genome of D. salina. In comparison to wild-type D. salina, strains transformed with BKT or CBFD and HBFD exhibited inhibited growth, underwent color changes to shades of red and yellow, and saw a nearly 50% decline in cell density. HPLC analysis confirmed astaxanthin synthesis in engineered D. salina strains, with CBFD + HBFD-D. salina yielding 134.88 ± 9.12 µg/g of dry cell weight (DCW), significantly higher than BKT-D. salina (83.58 ± 2.40 µg/g). This represents the largest amount of astaxanthin extracted from transgenic D. salina, as reported to date. These findings have significant implications, opening up new avenues for the development of specialized D. salina-based microcell factories for efficient astaxanthin production.


Subject(s)
Xanthophylls , Xanthophylls/metabolism , Chlorophyceae/metabolism , Chlorophyceae/genetics , Biosynthetic Pathways/genetics , Chlorophyta/metabolism , Chlorophyta/genetics , Escherichia coli/metabolism , Escherichia coli/genetics , Plant Proteins/metabolism , Plant Proteins/genetics , Mixed Function Oxygenases , Oxygenases
10.
PLoS One ; 19(5): e0299780, 2024.
Article in English | MEDLINE | ID: mdl-38758755

ABSTRACT

Microalgae's ability to mitigate flue gas is an attractive technology that can valorize gas components through biomass conversion. However, tolerance and growth must be ideal; therefore, acclimation strategies are suggested. Here, we compared the transcriptome and lipidome of Desmodesmus abundans strains acclimated to high CO2 (HCA) and low CO2 (LCA) under continuous supply of model flue gas (MFG) and incomplete culture medium (BG11-N-S). Initial growth and nitrogen consumption from MFG were superior in strain HCA, reaching maximum productivity a day before strain LCA. However, similar productivities were attained at the end of the run, probably because maximum photobioreactor capacity was reached. RNA-seq analysis during exponential growth resulted in 16,435 up-regulated and 4,219 down-regulated contigs in strain HCA compared to LCA. Most differentially expressed genes (DEGs) were related to nucleotides, amino acids, C fixation, central carbon metabolism, and proton pumps. In all pathways, a higher number of up-regulated contigs with a greater magnitude of change were observed in strain HCA. Also, cellular component GO terms of chloroplast and photosystems, N transporters, and secondary metabolic pathways of interest, such as starch and triacylglycerols (TG), exhibited this pattern. RT-qPCR confirmed N transporters expression. Lipidome analysis showed increased glycerophospholipids in strain HCA, while LCA exhibited glycerolipids. Cell structure and biomass composition also revealed strains differences. HCA possessed a thicker cell wall and presented a higher content of pigments, while LCA accumulated starch and lipids, validating transcriptome and lipidome data. Overall, results showed significant differences between strains, where characteristic features of adaptation and tolerance to high CO2 might be related to the capacity to maintain a higher flux of internal C, regulate intracellular acidification, active N transporters, and synthesis of essential macromolecules for photosynthetic growth.


Subject(s)
Acclimatization , Carbon Dioxide , Lipidomics , Transcriptome , Carbon Dioxide/metabolism , Acclimatization/genetics , Lipidomics/methods , Microalgae/genetics , Microalgae/metabolism , Microalgae/growth & development , Gene Expression Profiling , Photosynthesis/genetics , Lipid Metabolism/genetics , Chlorophyceae/genetics , Chlorophyceae/metabolism
11.
Plant Physiol Biochem ; 211: 108661, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38735153

ABSTRACT

Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.


Subject(s)
Chlorophyceae , Adaptation, Physiological , Chlorophyceae/cytology , Chlorophyceae/genetics , Chlorophyceae/metabolism , Chlorophyta/metabolism , Chlorophyta/genetics , Nitrogen/metabolism , Marine Biology
12.
Physiol Plant ; 176(2): e14296, 2024.
Article in English | MEDLINE | ID: mdl-38650503

ABSTRACT

In Dunaliella tertiolecta, a microalga renowned for its extraordinary tolerance to high salinity levels up to 4.5 M NaCl, the mechanisms underlying its stress response have largely remained a mystery. In a groundbreaking discovery, this study identifies a choline dehydrogenase enzyme, termed DtCHDH, capable of converting choline to betaine aldehyde. Remarkably, this is the first identification of such an enzyme not just in D. tertiolecta but across the entire Chlorophyta. A 3D model of DtCHDH was constructed, and molecular docking with choline was performed, revealing a potential binding site for the substrate. The enzyme was heterologously expressed in E. coli Rosetta (DE3) and subsequently purified, achieving enzyme activity of 672.2 U/mg. To elucidate the role of DtCHDH in the salt tolerance of D. tertiolecta, RNAi was employed to knock down DtCHDH gene expression. The results indicated that the Ri-12 strain exhibited compromised growth under both high and low salt conditions, along with consistent levels of DtCHDH gene expression and betaine content. Additionally, fatty acid analysis indicated that DtCHDH might also be a FAPs enzyme, catalyzing reactions with decarboxylase activity. This study not only illuminates the role of choline metabolism in D. tertiolecta's adaptation to high salinity but also identifies a novel target for enhancing the NaCl tolerance of microalgae in biotechnological applications.


Subject(s)
Betaine , Choline Dehydrogenase , Salt Tolerance , Betaine/metabolism , Salt Tolerance/genetics , Choline Dehydrogenase/metabolism , Choline Dehydrogenase/genetics , Choline/metabolism , Chlorophyceae/genetics , Chlorophyceae/physiology , Chlorophyceae/enzymology , Chlorophyceae/metabolism , Microalgae/genetics , Microalgae/enzymology , Microalgae/metabolism , Molecular Docking Simulation , Sodium Chloride/pharmacology
13.
J Agric Food Chem ; 72(17): 10005-10013, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38626461

ABSTRACT

Dunaliella bardawil is a marine unicellular green algal that produces large amounts of ß-carotene and is a model organism for studying the carotenoid synthesis pathway. However, there are still many mysteries about the enzymes of the D. bardawil lycopene synthesis pathway that have not been revealed. Here, we have identified a CruP-like lycopene isomerase, named DbLyISO, and successfully cloned its gene from D. bardawil. DbLyISO showed a high homology with CruPs. We constructed a 3D model of DbLyISO and performed molecular docking with lycopene, as well as molecular dynamics testing, to identify the functional characteristics of DbLyISO. Functional activity of DbLyISO was also performed by overexpressing gene in both E. coli and D. bardawil. Results revealed that DbLyISO acted at the C-5 and C-13 positions of lycopene, catalyzing its cis-trans isomerization to produce a more stable trans structure. These results provide new ideas for the development of a carotenoid series from engineered bacteria, algae, and plants.


Subject(s)
Chlorophyceae , Intramolecular Lyases , Lycopene , cis-trans-Isomerases , Algal Proteins/genetics , Algal Proteins/metabolism , Algal Proteins/chemistry , Amino Acid Sequence , Carotenoids/metabolism , Carotenoids/chemistry , Chlorophyceae/enzymology , Chlorophyceae/genetics , Chlorophyceae/chemistry , Chlorophyceae/metabolism , Chlorophyta/enzymology , Chlorophyta/genetics , Chlorophyta/chemistry , Chlorophyta/metabolism , cis-trans-Isomerases/genetics , cis-trans-Isomerases/metabolism , cis-trans-Isomerases/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Lycopene/metabolism , Lycopene/chemistry , Molecular Docking Simulation , Sequence Alignment
14.
J Phycol ; 60(2): 275-298, 2024 04.
Article in English | MEDLINE | ID: mdl-38439561

ABSTRACT

Thick-walled rosette-like snow algae were long thought to be a life stage of various other species of snow algae. Rosette-like cells have not been cultured, but by manually isolating cells from 38 field samples in southern British Columbia, we assigned a variety of rosette morphologies to DNA sequence. Phylogenetic analysis of Rubisco large-subunit (rbcL) gene, ribosomal internal transcribed spacer 2 (ITS2) rRNA region, and 18S rRNA gene revealed that the rosette-like cells form a new clade within the phylogroup Chloromonadinia. Based on these data, we designate a new genus, Rosetta, which comprises five novel species: R. castellata, R. floranivea, R. stellaria, R. rubriterra, and R. papavera. In a survey of 762 snow samples from British Columbia, we observed R. floranivea exclusively on snow overlying high-elevation glaciers, whereas R. castellata was observed at lower elevations, near the tree line. The other three species were rarely observed. Spherical red cells enveloped in a thin translucent sac were conspecific with Rosetta, possibly a developmental stage. These results highlight the unexplored diversity among snow algae and emphasize the utility of single-cell isolation to advance the centuries-old problem of disentangling life stages and cryptic species.


Subject(s)
Chlorophyceae , Chlorophyta , Rhodophyta , Phylogeny , Chlorophyta/genetics , Chlorophyceae/genetics , RNA, Ribosomal, 18S/genetics , Rhodophyta/genetics
15.
Funct Plant Biol ; 512024 02.
Article in English | MEDLINE | ID: mdl-38388445

ABSTRACT

Microalgae are photosynthetic organisms and a potential source of sustainable metabolite production. However, different stress conditions might affect the production of various metabolites. In this study, a meta-analysis of RNA-seq experiments in Dunaliella tertiolecta was evaluated to compare metabolite biosynthesis pathways in response to abiotic stress conditions such as high light, nitrogen deficiency and high salinity. Results showed downregulation of light reaction, photorespiration, tetrapyrrole and lipid-related pathways occurred under salt stress. Nitrogen deficiency mostly induced the microalgal responses of light reaction and photorespiration metabolism. Phosphoenol pyruvate carboxylase, phosphoglucose isomerase, bisphosphoglycerate mutase and glucose-6-phosphate-1-dehydrogenase (involved in central carbon metabolism) were commonly upregulated under salt, light and nitrogen stresses. Interestingly, the results indicated that the meta-genes (modules of genes strongly correlated) were located in a hub of stress-specific protein-protein interaction (PPI) network. Module enrichment of meta-genes PPI networks highlighted the cross-talk between photosynthesis, fatty acids, starch and sucrose metabolism under multiple stress conditions. Moreover, it was observed that the coordinated expression of the tetrapyrrole intermediated with meta-genes was involved in starch biosynthesis. Our results also showed that the pathways of vitamin B6 metabolism, methane metabolism, ribosome biogenesis and folate biosynthesis responded specifically to different stress factors. Since the results of this study revealed the main pathways underlying the abiotic stress, they might be applied in optimised metabolite production by the microalga Dunaliella in future studies. PRISMA check list was also included in the study.


Subject(s)
Chlorophyceae , Chlorophyceae/genetics , Chlorophyceae/metabolism , Stress, Physiological/genetics , Starch/metabolism , RNA-Seq , Nitrogen/metabolism , Tetrapyrroles
16.
FEMS Microbiol Ecol ; 99(12)2023 11 13.
Article in English | MEDLINE | ID: mdl-37880981

ABSTRACT

Melting snow and glacier surfaces host microalgal blooms in polar and mountainous regions. The aim of this study was to determine the dominant taxa at the species level in the European Arctic and the Alps. A standardized protocol for amplicon metabarcoding using the 18S rRNA gene and ITS2 markers was developed. This is important because previous biodiversity studies have been hampered by the dominance of closely related algal taxa in snow and ice. Due to the limited resolution of partial 18S rRNA Illumina sequences, the hypervariable ITS2 region was used to further discriminate between the genotypes. Our results show that red snow was caused by the cosmopolitan Sanguina nivaloides (Chlamydomonadales, Chlorophyta) and two as of yet undescribed Sanguina species. Arctic orange snow was dominated by S. aurantia, which was not found in the Alps. On glaciers, at least three Ancylonema species (Zygnematales, Streptophyta) dominated. Golden-brown blooms consisted of Hydrurus spp. (Hydrurales, Stramenophiles) and these were mainly an Arctic phenomenon. For chrysophytes, only the 18S rRNA gene but not ITS2 sequences were amplified, showcasing how delicate the selection of eukaryotic 'universal' primers for community studies is and that primer specificity will affect diversity results dramatically. We propose our approach as a 'best practice'.


Subject(s)
Chlorophyceae , Chlorophyta , Ice Cover , Snow , RNA, Ribosomal, 18S/genetics , Genes, rRNA , Chlorophyta/genetics , Chlorophyceae/genetics
17.
Am J Bot ; 110(11): e16238, 2023 11.
Article in English | MEDLINE | ID: mdl-37661934

ABSTRACT

PREMISE: Chaetopeltidales is a small, understudied order of the green algal class Chlorophyceae, that is slowly expanding with the occasional discoveries of novel algae. Here we demonstrate that hitherto unrecognized chaetopeltidaleans also exist among previously described but neglected and misclassified species. METHODS: Strain SAG 40.91 of Characium acuminatum, shown by previous preliminary evidence to have affinities with the orders Oedogoniales, Chaetophorales, and Chaetopeltidales (together constituting the OCC clade), was investigated with light and electron microscopy to characterize its morphology and ultrastructure. Sequence assemblies of the organellar and nuclear genomes were obtained and utilized in bioinformatic and phylogenetic analyses to address the phylogenetic position of the alga and its salient genomic features. RESULTS: The characterization of strain SAG 40.91 and a critical literature review led us to reinstate the forgotten genus Hydrocytium A.Braun 1855, with SAG 40.91 representing its type species, Hydrocytium acuminatum. Independent molecular markers converged on placing H. acuminatum as a deeply diverged lineage of the order Chaetopeltidales, formalized as the new family Hydrocytiaceae. Both chloroplast and mitochondrial genomes shared characteristics with other members of Chaetopeltidales and were bloated by repetitive sequences. Notably, the mitochondrial cox2a gene was transferred into the nuclear genome in the H. acuminatum lineage, independently of the same event in Volvocales. The nuclear genome data from H. acuminatum and from another chaetopeltidalean that was reported by others revealed endogenized viral sequences corresponding to novel members of the phylum Nucleocytoviricota. CONCLUSIONS: The resurrected genus Hydrocytium expands the known diversity of chaetopeltidalean algae and provides the first glimpse into their virosphere.


Subject(s)
Chlorophyceae , Chlorophyta , Genome, Mitochondrial , Base Sequence , Chlorophyceae/genetics , Chlorophyta/genetics , Genomics , Phylogeny
18.
J Phycol ; 59(4): 775-784, 2023 08.
Article in English | MEDLINE | ID: mdl-37261838

ABSTRACT

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.


Subject(s)
Chlorophyceae , Microalgae , Scenedesmus , Phylogeny , Scenedesmus/genetics , Microalgae/genetics , Chlorophyceae/genetics , DNA
19.
J Phycol ; 59(2): 342-355, 2023 04.
Article in English | MEDLINE | ID: mdl-36680562

ABSTRACT

The quadriflagellate genus Chlainomonas frequently dominates red snow globally. It is unusual in several respects, with two separated pairs of flagella, apparent cell division via extrusion of cytoplasmic threads, and being nested phylogenetically within the biflagellate genus Chloromonas. Here, we showed that the austral species Chloromonas (Cr.) rubroleosa, originally described from Antarctic red snow, is a close biflagellate relative of Chlainomonas, challenging the monophyly of Chlainomonas as currently conceived. Sequences of the 18S rRNA gene robustly linked Cr. rubroleosa with near-identical environmental sequences from Antarctic red snow and Chlainomonas from North America, Japan, and Europe. Furthermore, the 18S rRNA and rbcL gene sequences of Cr. rubroleosa were almost identical to New Zealand and North American collections of Chlainomonas. Cr. rubroleosa and New Zealand Chlainomonas are separated by only a single-base substitution across the ITS1-5.8S-ITS2 rRNA loci (and according to ITS2, the North American collection is the next closest relative). This again raises the possibility that Chlainomonas is a life-cycle stage of vegetatively biflagellate organisms, although this remains confounded by the scarcity of biflagellates in field populations, the apparent cell division by quadriflagellates, and the absence of Chlainomonas-type cells in cultures of Cr. rubroleosa. The latter species is broadly similar to Chlainomonas, being poor at swimming, with similar pigment, chloroplast arrangement and ultrastructure, and is relatively large. Increased size is a feature of the wider clade of "Group D" snow algae. A synthesis of field and laboratory investigations may be needed to unravel the life cycle and correct the systematics of this group.


Subject(s)
Chlorophyceae , Chlorophyceae/genetics , Phylogeny , Chloroplasts , Europe , RNA, Ribosomal, 18S/genetics
20.
J Microbiol Biotechnol ; 32(12): 1622-1631, 2022 Dec 28.
Article in English | MEDLINE | ID: mdl-36384973

ABSTRACT

Carotenoids, which are natural pigments found abundantly in wide-ranging species, have diverse functions and high industrial potential. The carotenoid biosynthesis pathway is very complex and has multiple branches, while the accumulation of certain metabolites often affects other metabolites in this pathway. The DsLCYB gene that encodes lycopene cyclase was selected in this study to evaluate ß-carotene production and the accumulation of ß-carotene in the alga Dunaliella salina. Compared with the wild type, the transgenic algal species overexpressed the DsLCYB gene, resulting in a significant enhancement of the total carotenoid content, with the total amount reaching 8.46 mg/g for an increase of up to 1.26-fold. Interestingly, the production of α-carotene in the transformant was not significantly reduced. This result indicated that the regulation of DsLCYB on the metabolic flux distribution of carotenoid biosynthesis is directional. Moreover, the effects of different light-quality conditions on ß-carotene production in D. salina strains were investigated. The results showed that the carotenoid components of ß-carotene and ß-cryptoxanthin were 1.8-fold and 1.23-fold higher than that in the wild type under red light stress, respectively. This suggests that the accumulation of ß-carotene under red light conditions is potentially more profitable.


Subject(s)
Chlorophyceae , beta Carotene , Carotenoids/metabolism , Chlorophyceae/genetics , Chlorophyceae/metabolism , Plants/metabolism , Light
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