Pub Date : 2026-04-01Epub Date: 2026-03-06DOI: 10.1016/j.algal.2026.104624
Yi-Yan Cai , Cheng Zhang , Si-Qi Chen , Zhi Li , Zhi-Gang Zhou , Yan-Hui Bi
The centromere is a chromosomal locus essential for accurate chromosome segregation, typically composed of repetitive DNA sequences. To date, the centromeric DNA of the commercially important brown alga Saccharina japonica remains uncharacterized. In this study, we screened a candidate centromeric satellite DNA, Sjsat998, through bioinformatic analysis of male gametophyte genome data using RepeatExplorer2 and local BLAST against a centromeric BAC clone. Sjsat998 was organized as tandem repeats with a 998-bp monomer. Fluorescence in situ hybridization (FISH) confirmed its specific enrichment at centromeric regions. Immuno-FISH (IF-FISH) demonstrated precise co-localization of Sjsat998 with the centromeric histone H3 variant SjCENH3. Furthermore, electrophoretic mobility shift assays (EMSAs) confirmed the specific binding of recombinant SjCENH3 protein to Sjsat998. Sjsat998 was the first identified centromeric element in S. japonica. It provides a foundation for studying centromere evolution in brown algae and will facilitate the construction of a telomere-to-telomere (T2T) genome for this species.
着丝粒是染色体精确分离所必需的染色体位点，通常由重复的DNA序列组成。迄今为止，商业上重要的褐藻Saccharina japonica的着丝粒DNA仍未被表征。在这项研究中，我们通过使用RepeatExplorer2和本地BLAST对雄性配子体基因组数据进行生物信息学分析，筛选出候选着丝粒卫星DNA Sjsat998。Sjsat998被组织为具有998-bp单体的串联重复序列。荧光原位杂交（FISH）证实了其在着丝粒区域的特异性富集。免疫- fish （IF-FISH）证实Sjsat998与着丝粒组蛋白H3变体SjCENH3精确共定位。此外，电泳迁移转移实验（EMSAs）证实了重组SjCENH3蛋白与Sjsat998的特异性结合。Sjsat998是粳稻中第一个鉴定到的着丝粒元素。这为研究褐藻着丝粒进化奠定了基础，并为该物种的端粒到端粒（T2T）基因组的构建提供了便利。
{"title":"Isolation and identification of a centromeric tandemly repeated DNA sequence in Saccharina japonica","authors":"Yi-Yan Cai , Cheng Zhang , Si-Qi Chen , Zhi Li , Zhi-Gang Zhou , Yan-Hui Bi","doi":"10.1016/j.algal.2026.104624","DOIUrl":"10.1016/j.algal.2026.104624","url":null,"abstract":"<div><div>The centromere is a chromosomal locus essential for accurate chromosome segregation, typically composed of repetitive DNA sequences. To date, the centromeric DNA of the commercially important brown alga <em>Saccharina japonica</em> remains uncharacterized. In this study, we screened a candidate centromeric satellite DNA, Sjsat998, through bioinformatic analysis of male gametophyte genome data using RepeatExplorer2 and local BLAST against a centromeric BAC clone. Sjsat998 was organized as tandem repeats with a 998-bp monomer. Fluorescence in situ hybridization (FISH) confirmed its specific enrichment at centromeric regions. Immuno-FISH (IF-FISH) demonstrated precise co-localization of Sjsat998 with the centromeric histone H3 variant SjCENH3. Furthermore, electrophoretic mobility shift assays (EMSAs) confirmed the specific binding of recombinant SjCENH3 protein to Sjsat998. Sjsat998 was the first identified centromeric element in <em>S. japonica</em>. It provides a foundation for studying centromere evolution in brown algae and will facilitate the construction of a telomere-to-telomere (T2T) genome for this species.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104624"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-01Epub Date: 2026-02-18DOI: 10.1016/j.algal.2026.104599
Negar Taheriashtiani , Zongyuan Ge , Mehrtash Harandi , Nicholas D. Crosbie , Glenn B. McGregor , Li Gao , Chao Chen , Linda Blackall , Michael Burch , Anna Lintern , Arash Zamyadi
Algal blooms are increasingly frequent and severe, threatening water quality, ecosystems, and public health. Accurate species-level identification is crucial for effective monitoring, yet conventional microscopy is slow, subjective and labour-intensive. Integration of deep learning with microscopy has recently emerged as a transformative solution. This systematic review synthesizes 62 studies that applied deep learning to microscopic images of microalgae and cyanobacteria, offering a comprehensive perspective that spans the entire workflow, from image acquisition and pre-processing to model architectures. A central contribution of this review is the structured synthesis of literature. Studies employing classification models are distinguished from those using detection models, and within each category, subgroups are identified and critically evaluated to clarify their strengths, limitations, and appropriate applications. The analysis shows that while classification models account for most studies overall, their dominance reflects earlier stages of the field. Recently, detection models have become more common and are emerging as preferred choice for addressing the complexity of real-world, multi-species images. Beyond synthesizing existing methods, this review identifies gaps in imaging techniques, dataset availability, and model development. It highlights ongoing challenges, including scarce annotated data and underexplored imaging and modelling approaches, while outlining promising future pathways such as semi-supervised learning, multimodal integration, and advanced detection and segmentation architectures. Finally, publicly available microalgae image datasets are introduced, whose integration with existing methodologies may enable more robust and universal identification models. By combining full workflow coverage, this study clarifies the state of the field and guides subsequent research in deep learning for algal monitoring.
{"title":"Artificial intelligence and microscopy: A systematic review of deep learning in microalgae and cyanobacteria species identification","authors":"Negar Taheriashtiani , Zongyuan Ge , Mehrtash Harandi , Nicholas D. Crosbie , Glenn B. McGregor , Li Gao , Chao Chen , Linda Blackall , Michael Burch , Anna Lintern , Arash Zamyadi","doi":"10.1016/j.algal.2026.104599","DOIUrl":"10.1016/j.algal.2026.104599","url":null,"abstract":"<div><div>Algal blooms are increasingly frequent and severe, threatening water quality, ecosystems, and public health. Accurate species-level identification is crucial for effective monitoring, yet conventional microscopy is slow, subjective and labour-intensive. Integration of deep learning with microscopy has recently emerged as a transformative solution. This systematic review synthesizes 62 studies that applied deep learning to microscopic images of microalgae and cyanobacteria, offering a comprehensive perspective that spans the entire workflow, from image acquisition and pre-processing to model architectures. A central contribution of this review is the structured synthesis of literature. Studies employing classification models are distinguished from those using detection models, and within each category, subgroups are identified and critically evaluated to clarify their strengths, limitations, and appropriate applications. The analysis shows that while classification models account for most studies overall, their dominance reflects earlier stages of the field. Recently, detection models have become more common and are emerging as preferred choice for addressing the complexity of real-world, multi-species images. Beyond synthesizing existing methods, this review identifies gaps in imaging techniques, dataset availability, and model development. It highlights ongoing challenges, including scarce annotated data and underexplored imaging and modelling approaches, while outlining promising future pathways such as semi-supervised learning, multimodal integration, and advanced detection and segmentation architectures. Finally, publicly available microalgae image datasets are introduced, whose integration with existing methodologies may enable more robust and universal identification models. By combining full workflow coverage, this study clarifies the state of the field and guides subsequent research in deep learning for algal monitoring.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104599"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-01Epub Date: 2026-02-18DOI: 10.1016/j.algal.2026.104595
Ayagoz Meirkhanova , Sabina Marks , Damir Ussibaliyev , Aizada Bexeitova , Stella A. Berger , Michael Melkonian , Ivan A. Vorobjev , Natasha S. Barteneva
The autofluorescence of algal pigments enables non-invasive, high-throughput characterization of microalgae at single-cell resolution. We applied full-spectrum cytometry, imaging flow cytometry, and cell sorting to analyze the spectral and morphological diversity among major microalgal groups and 102 Chlorophyta strains. The distinct spectral signatures from chlorophylls, carotenoids, and phycobiliproteins enabled clear separation of major pigment-defined algal groups, particularly those containing phycobiliproteins. Furthermore, principal component analysis of Volvocales (Chlorophyta) revealed three spectral clusters supported by corresponding differences in cell size and shape. Additionally, in Gonium cultures, we observed that spectral signatures in the yellow-green region were altered in the presence of bacteria, suggesting that interactions between the algal host and bacteria affect pigment-related fluorescence. Spectral heterogeneity observed within monocultures was linked to pigment accumulation, cell size, and morphological variability. These findings establish full-spectrum cytometry as a powerful method for profiling pigment composition, physiology, and structural diversity in microalgae, with broad applications in microbial ecology, environmental monitoring, and biotechnology.
{"title":"Analysis of autofluorescence using full-spectrum cytometry to discriminate and monitor microalgae and bacteria","authors":"Ayagoz Meirkhanova , Sabina Marks , Damir Ussibaliyev , Aizada Bexeitova , Stella A. Berger , Michael Melkonian , Ivan A. Vorobjev , Natasha S. Barteneva","doi":"10.1016/j.algal.2026.104595","DOIUrl":"10.1016/j.algal.2026.104595","url":null,"abstract":"<div><div>The autofluorescence of algal pigments enables non-invasive, high-throughput characterization of microalgae at single-cell resolution. We applied full-spectrum cytometry, imaging flow cytometry, and cell sorting to analyze the spectral and morphological diversity among major microalgal groups and 102 Chlorophyta strains. The distinct spectral signatures from chlorophylls, carotenoids, and phycobiliproteins enabled clear separation of major pigment-defined algal groups, particularly those containing phycobiliproteins. Furthermore, principal component analysis of Volvocales (Chlorophyta) revealed three spectral clusters supported by corresponding differences in cell size and shape. Additionally, in <em>Gonium</em> cultures, we observed that spectral signatures in the yellow-green region were altered in the presence of bacteria, suggesting that interactions between the algal host and bacteria affect pigment-related fluorescence. Spectral heterogeneity observed within monocultures was linked to pigment accumulation, cell size, and morphological variability. These findings establish full-spectrum cytometry as a powerful method for profiling pigment composition, physiology, and structural diversity in microalgae, with broad applications in microbial ecology, environmental monitoring, and biotechnology.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104595"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Breast cancer is one of the most common malignancies among women, and early diagnosis significantly improves survival rates. The severe side effects associated with conventional cytotoxic treatments have emphasized the need for targeted therapies in combination with natural compounds. Fucoidan, a sulfated polysaccharide extracted from the brown algae Fucus vesiculosus, exhibits anticancer activity and inhibits proliferation in MCF-7 breast cancer cells; however, its effects on the regulation of caveolin-1, a membrane protein involved in breast cancer progression, remain largely unexplored. In the current study, the anticancer effects of fucoidan in MCF-7 cells were investigated by evaluating cytotoxicity, membrane integrity, colony formation, migration, and caveolin-1 expression using established in vitro assays. Both fucoidan and the chemotherapeutic agent tamoxifen demonstrated dose-dependent cytotoxic effects, with fucoidan showing higher potency in reducing colony formation. Both compounds also inhibited cell migration and significantly downregulated caveolin-1 expression, suggesting a potential role in modulating tumor progression. These findings highlight the therapeutic potential of fucoidan as a natural anticancer agent, although further studies are needed to clarify its mechanisms and in vivo efficacy.
{"title":"Effect of fucoidan, a sulfated polysaccharide, on caveolin-1 levels in breast cancer cell line MCF-7","authors":"Dilara Çakmak, Nesrin Özsoy Erdaş, Buse Safrancı, Fadime Kıran","doi":"10.1016/j.algal.2026.104593","DOIUrl":"10.1016/j.algal.2026.104593","url":null,"abstract":"<div><div>Breast cancer is one of the most common malignancies among women, and early diagnosis significantly improves survival rates. The severe side effects associated with conventional cytotoxic treatments have emphasized the need for targeted therapies in combination with natural compounds. Fucoidan, a sulfated polysaccharide extracted from the brown algae <em>Fucus vesiculosus</em>, exhibits anticancer activity and inhibits proliferation in MCF-7 breast cancer cells; however, its effects on the regulation of caveolin-1, a membrane protein involved in breast cancer progression, remain largely unexplored. In the current study, the anticancer effects of fucoidan in MCF-7 cells were investigated by evaluating cytotoxicity, membrane integrity, colony formation, migration, and caveolin-1 expression using established in vitro assays. Both fucoidan and the chemotherapeutic agent tamoxifen demonstrated dose-dependent cytotoxic effects, with fucoidan showing higher potency in reducing colony formation. Both compounds also inhibited cell migration and significantly downregulated caveolin-1 expression, suggesting a potential role in modulating tumor progression. These findings highlight the therapeutic potential of fucoidan as a natural anticancer agent, although further studies are needed to clarify its mechanisms and in vivo efficacy.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104593"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-01Epub Date: 2026-02-24DOI: 10.1016/j.algal.2026.104608
Julia Catiane Arenhart Braun , Milena Anita Beuter , Alan Rempel , José Luís Trevizan Chiomento , Nadia Canali Lângaro , Luciane Maria Colla
Microalgae biostimulants have gained attention as a promising solution for sustainable approaches in agriculture. This study assessed Spirulina platensis biostimulants in seed treatment (ST) for soybean, wheat, and oat. In the first stage, laboratory tests evaluated early plant growth and compared two biomass disruption methods: ultrasonic probe (1%, 5%, 10% m/v); and freeze/thaw (5% m/v). In the second stage, field experiments with soybean applied optimal ST concentrations, testing combinations of chemical, biological, and microalgal treatments, with and without conventional fertilization. The cyanobacteria extract produced by ultrasonic probe disruption, rich in amino acids and nutrients, enhanced the emergence speed index of wheat plants by up to 6.8% in laboratory tests compared to the control. In the early stages of plant development, the cyanobacteria extract positively affected the root growth of soybeans, wheat, and oat, increasing the dry root biomass of soybeans by up to 26.9%. In the second stage, treatments with cyanobacteria resulted in greater plant height (up to 12%) and dry mass (up to 32%) in the shoot compared to treatments with only chemical seed treatment. Under field conditions, microalgal treatments increased shoot length and dry mass compared to chemical seed treatments. They also enhanced nodule formation by up to 50%, whereas conventional fertilizer reduced nodule development. The results showed that these extracts may enhance the physiological characteristics of plants, and their biostimulant properties suggest benefits for various cultivars, with no negative effects when combined with chemical and biological treatments for soybean ST.
{"title":"Seed treatment of soybean, wheat, and oat with cyanobacteria extracts: Germination and field performance analysis","authors":"Julia Catiane Arenhart Braun , Milena Anita Beuter , Alan Rempel , José Luís Trevizan Chiomento , Nadia Canali Lângaro , Luciane Maria Colla","doi":"10.1016/j.algal.2026.104608","DOIUrl":"10.1016/j.algal.2026.104608","url":null,"abstract":"<div><div>Microalgae biostimulants have gained attention as a promising solution for sustainable approaches in agriculture. This study assessed <em>Spirulina platensis</em> biostimulants in seed treatment (ST) for soybean, wheat, and oat. In the first stage, laboratory tests evaluated early plant growth and compared two biomass disruption methods: ultrasonic probe (1%, 5%, 10% m/v); and freeze/thaw (5% m/v). In the second stage, field experiments with soybean applied optimal ST concentrations, testing combinations of chemical, biological, and microalgal treatments, with and without conventional fertilization. The cyanobacteria extract produced by ultrasonic probe disruption, rich in amino acids and nutrients, enhanced the emergence speed index of wheat plants by up to 6.8% in laboratory tests compared to the control. In the early stages of plant development, the cyanobacteria extract positively affected the root growth of soybeans, wheat, and oat, increasing the dry root biomass of soybeans by up to 26.9%. In the second stage, treatments with cyanobacteria resulted in greater plant height (up to 12%) and dry mass (up to 32%) in the shoot compared to treatments with only chemical seed treatment. Under field conditions, microalgal treatments increased shoot length and dry mass compared to chemical seed treatments. They also enhanced nodule formation by up to 50%, whereas conventional fertilizer reduced nodule development. The results showed that these extracts may enhance the physiological characteristics of plants, and their biostimulant properties suggest benefits for various cultivars, with no negative effects when combined with chemical and biological treatments for soybean ST.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104608"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-01Epub Date: 2026-02-25DOI: 10.1016/j.algal.2026.104610
Bruna Dias , Marlene Lopes , Isabel Belo
The relatively low protein content of Fucus vesiculosus and Palmaria palmata compared to other seaweeds, combined with their high carbohydrate content, makes these seaweeds particularly suitable as biorefinery feedstocks. This study explored the two algae F. vesiculosus and P. palmata to obtain hydrolysates and use them as substrates for Yarrowia lipolytica NCYC 2904 cultivation in stirred-tank bioreactors. Hydrolysates from F. vesiculosus (FH), non-washed P. palmata (PH), and washed P. palmata (WPH) were obtained after hydrothermal pretreatment (121 °C, 30 min) followed by enzymatic hydrolysis (Cellic CTec3). Y. lipolytica efficiently assimilated different carbon sources from PH and WPH (glucose, xylose, and formic acid), and from FH (fucose, mannitol, glucuronic acid, and acetic acid). To date, the consumption of fucose and glucuronic acid by Y. lipolytica has not been described. The yeast consumed high amounts of xylose (60 g·L−1) and produced erythritol from PH and WPH, a feature not previously reported. The highest erythritol concentration (40 g·L−1) and protein content in yeast biomass (29%, w/w, dry basis) were obtained in PH cultures, while the highest cellular lipids accumulation (15%, w/w, dry basis) was attained using WPH. Lipids produced under all conditions were enriched in mono- (71%–78%) and polyunsaturated (20%–22%) fatty acids, while the yeast biomass from PH, WPH, and FH exhibited a well-balanced amino acid profile, including essential amino acids. These findings have significant implications for the development of sustainable blue biorefineries based on Y. lipolytica as a microbial platform for valorizing seaweed biomass into bioproducts, such as protein-rich yeast biomass (approved for human consumption), lipids, and erythritol, supporting sustainable food and feed applications.
{"title":"Use of Palmaria palmata and Fucus vesiculosus hydrolysates for Yarrowia lipolytica biomass and erythritol production","authors":"Bruna Dias , Marlene Lopes , Isabel Belo","doi":"10.1016/j.algal.2026.104610","DOIUrl":"10.1016/j.algal.2026.104610","url":null,"abstract":"<div><div>The relatively low protein content of <em>Fucus vesiculosus</em> and <em>Palmaria palmata</em> compared to other seaweeds, combined with their high carbohydrate content, makes these seaweeds particularly suitable as biorefinery feedstocks. This study explored the two algae <em>F. vesiculosus</em> and <em>P. palmata</em> to obtain hydrolysates and use them as substrates for <em>Yarrowia lipolytica</em> NCYC 2904 cultivation in stirred-tank bioreactors. Hydrolysates from <em>F. vesiculosus</em> (FH), non-washed <em>P. palmata</em> (PH), and washed <em>P. palmata</em> (WPH) were obtained after hydrothermal pretreatment (121 °C, 30 min) followed by enzymatic hydrolysis (Cellic CTec3). <em>Y. lipolytica</em> efficiently assimilated different carbon sources from PH and WPH (glucose, xylose, and formic acid), and from FH (fucose, mannitol, glucuronic acid, and acetic acid). To date, the consumption of fucose and glucuronic acid by <em>Y. lipolytica</em> has not been described. The yeast consumed high amounts of xylose (60 g·L<sup>−1</sup>) and produced erythritol from PH and WPH, a feature not previously reported. The highest erythritol concentration (40 g·L<sup>−1</sup>) and protein content in yeast biomass (29%, w/w, dry basis) were obtained in PH cultures, while the highest cellular lipids accumulation (15%, w/w, dry basis) was attained using WPH. Lipids produced under all conditions were enriched in mono- (71%–78%) and polyunsaturated (20%–22%) fatty acids, while the yeast biomass from PH, WPH, and FH exhibited a well-balanced amino acid profile, including essential amino acids. These findings have significant implications for the development of sustainable blue biorefineries based on <em>Y. lipolytica</em> as a microbial platform for valorizing seaweed biomass into bioproducts, such as protein-rich yeast biomass (approved for human consumption), lipids, and erythritol, supporting sustainable food and feed applications.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104610"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-01Epub Date: 2026-02-24DOI: 10.1016/j.algal.2026.104605
Tianze Zheng , Xu Zhang , Tianren Liu , Xinzhu Liu , Chris Bowler , Xin Lin
Diatoms are key players in aquatic ecosystems, having evolved through secondary endosymbiosis. Using long-read sequencing, we investigated how transposable elements (TEs) and gene family dynamics have shaped diatom diversification from inter-lineage to intra-species scales. Across diatom lineages, we identified ecological adaptation-linked expansions, including polyamine synthesis genes for silicification and glutathione S-transferases for oxidative stress resistance. Centric diatoms showed lineage-specific expansion of flotation-associated microtubule genes, while pennate diatoms expanded motility-related actin and myosin genes. At the intra-species level, distinct Phaeodactylum tricornutum strains revealed genomic adaptations correlated with their unique features, including strain-specific expansion and contraction in the cruciform strain's morphological genes and the Baltic Sea isolate's amine metabolism genes. Our estimates of major lineage divergence times in diatoms (∼202 Myr and ∼ 173 Myr) were highly consistent with the two deep whole-genome duplication (WGD) events (∼200 Myr and ∼ 170 Myr). At these evolutionary nodes, gene families showed extensive lineage-specific expansions and contractions, likely linking ancient polyploidy to subsequent gene content evolution. Substantial TE expansions occurred more recently (0.5–5 Ma), with most diatoms showing recent bursts of Long Terminal Repeat Retrotransposons (LTR-RTs) and araphid pennate diatoms displaying more ancient TE insertion peaks. This likely reflects the progressive loss of ancient TE copies, leaving only recent TE insertions detectable. Our findings provide genomic evidence for the adaptive evolution of diatoms, highlighting the crucial roles of TEs and gene family dynamics in shaping their morphological diversity and environmental adaptations, and suggesting a potential connection between WGDs, gene family dynamics, and TE insertions in genome evolution.
{"title":"The roles of transposable elements and gene family dynamics in shaping diversity and evolution in diatoms","authors":"Tianze Zheng , Xu Zhang , Tianren Liu , Xinzhu Liu , Chris Bowler , Xin Lin","doi":"10.1016/j.algal.2026.104605","DOIUrl":"10.1016/j.algal.2026.104605","url":null,"abstract":"<div><div>Diatoms are key players in aquatic ecosystems, having evolved through secondary endosymbiosis. Using long-read sequencing, we investigated how transposable elements (TEs) and gene family dynamics have shaped diatom diversification from inter-lineage to intra-species scales. Across diatom lineages, we identified ecological adaptation-linked expansions, including polyamine synthesis genes for silicification and glutathione S-transferases for oxidative stress resistance. Centric diatoms showed lineage-specific expansion of flotation-associated microtubule genes, while pennate diatoms expanded motility-related actin and myosin genes. At the intra-species level, distinct <em>Phaeodactylum tricornutum</em> strains revealed genomic adaptations correlated with their unique features, including strain-specific expansion and contraction in the cruciform strain's morphological genes and the Baltic Sea isolate's amine metabolism genes. Our estimates of major lineage divergence times in diatoms (∼202 Myr and ∼ 173 Myr) were highly consistent with the two deep whole-genome duplication (WGD) events (∼200 Myr and ∼ 170 Myr). At these evolutionary nodes, gene families showed extensive lineage-specific expansions and contractions, likely linking ancient polyploidy to subsequent gene content evolution. Substantial TE expansions occurred more recently (0.5–5 Ma), with most diatoms showing recent bursts of Long Terminal Repeat Retrotransposons (LTR-RTs) and araphid pennate diatoms displaying more ancient TE insertion peaks. This likely reflects the progressive loss of ancient TE copies, leaving only recent TE insertions detectable. Our findings provide genomic evidence for the adaptive evolution of diatoms, highlighting the crucial roles of TEs and gene family dynamics in shaping their morphological diversity and environmental adaptations, and suggesting a potential connection between WGDs, gene family dynamics, and TE insertions in genome evolution.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104605"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-01Epub Date: 2026-02-24DOI: 10.1016/j.algal.2026.104611
Viviane de Carvalho Arabidian , Alexander S.K. Müller , Luiz Antonio de Almeida Pinto , Débora Pez Jaeschke , Tito Roberto Sant'Anna Cadaval Jr. , Wolfgang Frey , Christian Gusbeth
The growing interest in sustainable biomass sources has encouraged research on microalgae, particularly focusing on improving the efficiency of cell separation and extraction processes. Currently, the harvesting step is primarily performed by centrifugation, which requires high energy consumption, especially for large-scale cultivation volumes. Therefore, this study aimed to explore coagulation/flocculation as an alternative harvesting method for Chlorella vulgaris, using FeCl2, FeCl3, and chitosan. Additionally, this study aimed to evaluate the effect of the different flocculants on subsequent protein extraction, comparing extraction yields obtained by pulsed electric field (PEF) and high-pressure homogenization (HPH) treatment for the first time. The results indicated that FeCl3 had the highest flocculation efficiency, reaching over 99% with a lower dosage than the other flocculants (200 mg L−1). Although FeCl₃ achieved the highest flocculation efficiency (over 99% at a low dosage of 200 mg·L−1), the subsequent protein extraction yields were lower compared to centrifuged biomass. Protein recovery from FeCl₃-flocculated biomass reached only 9.22% of cell dry weight (CDW) with HPH and 0.5% of CDW with PEF, whereas centrifugation resulted in higher yields of 49.4% and 19.5% of CDW, respectively. These results indicate that while floc formation is effective for biomass harvesting, it may hinder protein extraction and reduce biomolecule recovery. Additionally, the protein profile analyzed by SDS-PAGE confirmed the negative impact of using flocculants, showing a disappearance or reduction of bands.
{"title":"Impact of harvesting via flocculation on protein yield from Chlorella vulgaris following pulsed electric field and high-pressure homogenization treatments","authors":"Viviane de Carvalho Arabidian , Alexander S.K. Müller , Luiz Antonio de Almeida Pinto , Débora Pez Jaeschke , Tito Roberto Sant'Anna Cadaval Jr. , Wolfgang Frey , Christian Gusbeth","doi":"10.1016/j.algal.2026.104611","DOIUrl":"10.1016/j.algal.2026.104611","url":null,"abstract":"<div><div>The growing interest in sustainable biomass sources has encouraged research on microalgae, particularly focusing on improving the efficiency of cell separation and extraction processes. Currently, the harvesting step is primarily performed by centrifugation, which requires high energy consumption, especially for large-scale cultivation volumes. Therefore, this study aimed to explore coagulation/flocculation as an alternative harvesting method for <em>Chlorella vulgaris</em>, using FeCl<sub>2</sub>, FeCl<sub>3</sub>, and chitosan. Additionally, this study aimed to evaluate the effect of the different flocculants on subsequent protein extraction, comparing extraction yields obtained by pulsed electric field (PEF) and high-pressure homogenization (HPH) treatment for the first time. The results indicated that FeCl<sub>3</sub> had the highest flocculation efficiency, reaching over 99% with a lower dosage than the other flocculants (200 mg L<sup>−1</sup>). Although FeCl₃ achieved the highest flocculation efficiency (over 99% at a low dosage of 200 mg·L<sup>−1</sup>), the subsequent protein extraction yields were lower compared to centrifuged biomass. Protein recovery from FeCl₃-flocculated biomass reached only 9.22% of cell dry weight (CDW) with HPH and 0.5% of CDW with PEF, whereas centrifugation resulted in higher yields of 49.4% and 19.5% of CDW, respectively. These results indicate that while floc formation is effective for biomass harvesting, it may hinder protein extraction and reduce biomolecule recovery. Additionally, the protein profile analyzed by SDS-PAGE confirmed the negative impact of using flocculants, showing a disappearance or reduction of bands.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104611"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A reliable growth-prediction model is essential for optimizing outdoor cultivation of Isochrysis galbana, particularly under rapidly changing light and temperature conditions induced by photovoltaic (PV) shading. In this study, an extended Monod-type kinetic model integrating the combined effects of light intensity, temperature, and nutrient (nitrate) availability, specifically designed for a PV-integrated photobioreactor (PBR), is developed and validated. A 19 experimental runs Central Composite Design (CCD) was employed to examine how PV–PBR spacing and LED supplementation influence biomass accumulation and specific growth rate. The experimental data highlighted clear interactions among light, temperature, and nutrient uptake. LED supplementation enhanced growth at sub-optimal PV–PBR distances, but its impact diminished as natural irradiance increased. The extended Monod model showed strong predictive capability, outperforming the classical model with lower RMSE and higher R2 values. Parameter fitting showed that μmax, Ks, and light-related coefficients responded sensitively to diurnal irradiance dynamics, reflecting the physiological behavior of Isochrysis galbana exposed to mixed natural–artificial illumination. Model validation across all CCD conditions further confirmed its robustness, with residuals indicating no systematic deviation. Overall, the multi-factor Monod framework developed here provides an accurate and scalable approach for predicting outdoor Isochrysis galbana growth in solar-integrated systems. These findings offer practical direction for refining PV–PBR layouts, boosting biomass productivity, and guiding future efforts to build dynamic, real-world microalgal cultivation models.
{"title":"Light–temperature–nutrient dependent Monod modeling of optimized Isochrysis galbana growth in a PV-integrated photobioreactor","authors":"M.S.N. Atikah , Mohammad Effendy Ya'acob , R.A. Ilyas , Razif Harun","doi":"10.1016/j.algal.2026.104621","DOIUrl":"10.1016/j.algal.2026.104621","url":null,"abstract":"<div><div>A reliable growth-prediction model is essential for optimizing outdoor cultivation of <em>Isochrysis galbana</em>, particularly under rapidly changing light and temperature conditions induced by photovoltaic (PV) shading. In this study, an extended Monod-type kinetic model integrating the combined effects of light intensity, temperature, and nutrient (nitrate) availability, specifically designed for a PV-integrated photobioreactor (PBR), is developed and validated. A 19 experimental runs Central Composite Design (CCD) was employed to examine how PV–PBR spacing and LED supplementation influence biomass accumulation and specific growth rate. The experimental data highlighted clear interactions among light, temperature, and nutrient uptake. LED supplementation enhanced growth at sub-optimal PV–PBR distances, but its impact diminished as natural irradiance increased. The extended Monod model showed strong predictive capability, outperforming the classical model with lower RMSE and higher R<sup>2</sup> values. Parameter fitting showed that μ<sub>max</sub>, <em>Ks</em>, and light-related coefficients responded sensitively to diurnal irradiance dynamics, reflecting the physiological behavior of <em>Isochrysis galbana</em> exposed to mixed natural–artificial illumination. Model validation across all CCD conditions further confirmed its robustness, with residuals indicating no systematic deviation. Overall, the multi-factor Monod framework developed here provides an accurate and scalable approach for predicting outdoor <em>Isochrysis galbana</em> growth in solar-integrated systems. These findings offer practical direction for refining PV–PBR layouts, boosting biomass productivity, and guiding future efforts to build dynamic, real-world microalgal cultivation models.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104621"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-01Epub Date: 2026-02-24DOI: 10.1016/j.algal.2026.104607
Rebecca M. Brown , Bradley D. Wahlen , Cody Steven , Harry W. Rollins , Peter J. Valdez
Microalgae cultivation on wastewater can provide remediation and generate valuable feedstocks for biofuel production. Wastewater algae typically have a high percentage of inorganic ash, which can reduce yield and quality of biocrude produced during hydrothermal liquefaction (HTL). In this work, we evaluated the ability of hydrocyclone pre-processing to remove inorganic ash from wastewater algae. The pH of the algae slurry was adjusted to 9.5 to encourage the formation of precipitates and create a density differential between ash particles and algal cells. Hydrocyclone processing successfully concentrated ash particles in the underflow fraction and reduced the total ash percentage in the overflow fraction. Overall, hydrocyclone processing reduced the total ash by 21%, while only 8% of organics were lost. Elemental analysis showed that Mg and P were concentrated in the underflow and the presence of quartz, baricite, struvite, dittmarite, and calcite were confirmed with mineral analysis. Future research should focus on prioritizing crystal growth during precipitation, as well as improving Mg and P precipitation via the formation of baricite and/or vivianite and struvite and/or dittmarite. We concluded that hydrocyclone treatment of wastewater algae is a feasible method to remove inorganic ash, but further process optimization is required.
{"title":"Hydrocyclone pre-processing of wastewater algae: A strategy for inorganic ash separation","authors":"Rebecca M. Brown , Bradley D. Wahlen , Cody Steven , Harry W. Rollins , Peter J. Valdez","doi":"10.1016/j.algal.2026.104607","DOIUrl":"10.1016/j.algal.2026.104607","url":null,"abstract":"<div><div>Microalgae cultivation on wastewater can provide remediation and generate valuable feedstocks for biofuel production. Wastewater algae typically have a high percentage of inorganic ash, which can reduce yield and quality of biocrude produced during hydrothermal liquefaction (HTL). In this work, we evaluated the ability of hydrocyclone pre-processing to remove inorganic ash from wastewater algae. The pH of the algae slurry was adjusted to 9.5 to encourage the formation of precipitates and create a density differential between ash particles and algal cells. Hydrocyclone processing successfully concentrated ash particles in the underflow fraction and reduced the total ash percentage in the overflow fraction. Overall, hydrocyclone processing reduced the total ash by 21%, while only 8% of organics were lost. Elemental analysis showed that Mg and P were concentrated in the underflow and the presence of quartz, baricite, struvite, dittmarite, and calcite were confirmed with mineral analysis. Future research should focus on prioritizing crystal growth during precipitation, as well as improving Mg and P precipitation via the formation of baricite and/or vivianite and struvite and/or dittmarite. We concluded that hydrocyclone treatment of wastewater algae is a feasible method to remove inorganic ash, but further process optimization is required.</div></div>","PeriodicalId":7855,"journal":{"name":"Algal Research-Biomass Biofuels and Bioproducts","volume":"95 ","pages":"Article 104607"},"PeriodicalIF":4.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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