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Microorganisms
Special Issues
Research on Biology of Dinoflagellates
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Research on Biology of Dinoflagellates

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 10430

Special Issue Editors

Prof. Dr. Marco Villanueva

E-Mail Website
Guest Editor
Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, UNAM, Prolongación Avenida Niños Héroes S/N, Puerto Morelos, Quintana Roo 77580, Mexico
Interests: dinoflagellate; signal-transduction; proteins; cytoskeleton
Dr. Tania Islas-Flores

E-Mail Website
Guest Editor
Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos 77580, Mexico
Interests: environmental microbiology; dinoflagellate
Dr. Estefanía Morales-Ruiz

E-Mail Website
Guest Editor
Institute of Ocean Sciences and Limnology, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
Interests: environmental microbiology; dinoflagellate

Special Issue Information

Dear Colleagues,

Dinoflagellates are key players in both freshwater and marine ecosystems, as they are one of the main microorganisms in the planktonic environment. They contribute an important fraction of the ocean’s primary production and have become a spotlight in light of the Anthropocene and ocean global warming as some species are key players in coral symbiosis and thus critical for coral reef survival. Yet, other species can cause the formation of harmful algal blooms. Furthermore, dinoflagellates have many unusual cellular features, including a large-size nuclear genome and chromosomes that remain condensed throughout the cell cycle without histones, chloroplasts that are derived from a secondary endosymbiosis, and an ability to synthesize a wide range of toxins. 

For this Special Issue of Microorganisms, we invite you to send contributions concerning any aspect of dinoflagellate biology examined using biochemistry, cell and molecular biology, genomics, transcriptomics, proteomics or metabolomics.

Prof. Dr. Marco Villanueva
Dr. Tania Islas-Flores
Dr. Estefanía Morales-Ruiz
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • dinoflagellate
  • molecular biology
  • genomics
  • transcriptomics
  • proteomics
  • metabolomic

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Published Papers (6 papers)

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Research

Jump to: Review

11 pages, 4719 KiB  
Article
Comparison of Lipid Content in Nine Dinoflagellate Species Using Flow Cytometry
by Jaeyeon Park, Eun Young Yoon, Seung Joo Moon, Jun-Ho Hyung and Hangy Lee
Microorganisms 2025, 13(1), 44; https://doi.org/10.3390/microorganisms13010044 - 30 Dec 2024
Viewed by 827
Abstract
The lipid content of nine dinoflagellates was analyzed using flow cytometry to compare lipid levels. Additionally, the correlation between lipid content, cell size, and carbon content in dinoflagellates was evaluated using BODIPY 505/515 staining. The flow cytometry side scatter (SSC) effectively represented relative [...] Read more.
The lipid content of nine dinoflagellates was analyzed using flow cytometry to compare lipid levels. Additionally, the correlation between lipid content, cell size, and carbon content in dinoflagellates was evaluated using BODIPY 505/515 staining. The flow cytometry side scatter (SSC) effectively represented relative cell size, showing a linear relationship with the equivalent spherical diameter (ESD). Larger cells exhibited higher relative lipid content; however, lipid accumulation was influenced by nutritional modes and habitats, with mixorophic and benthic species displaying higher lipid content than heterotrophic species. A comparison of fluorescent dyes revealed that Nile Red overestimated lipid content, suggesting overlap with chlorophyll autofluorescence. Flow cytometry analysis with BODIPY 505/515 demonstrated a linear correlation with the sulfo-phospho-vanillin (SPV) method, enabling determination of actual lipid content using FL1 fluorescence and the slope value. As the carbon content increased, the lipid content initially increased rapidly but plateaued at higher carbon levels, indicating saturation. These findings suggest that relative fluorescence via flow cytometry provides an effective means to estimate the lipid content and carbon content as a function of cell size. Full article
(This article belongs to the Special Issue Research on Biology of Dinoflagellates)
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15 pages, 4536 KiB  
Article
Transcriptome Analysis of the Harmful Dinoflagellate Heterocapsa bohaiensis Under Varied Nutrient Stress Conditions
by Peng Peng, Fangxin Han, Xue Gong, Xiangyuan Guo, Ying Su, Yiwen Zhang and Jingjing Zhan
Microorganisms 2024, 12(12), 2665; https://doi.org/10.3390/microorganisms12122665 - 22 Dec 2024
Cited by 1 | Viewed by 1534
Abstract
The increasing prevalence of harmful algal blooms (HABs) driven by eutrophication, particularly in China’s nearshore waters, is a growing concern. Dinoflagellate Heterocapsa bohaiensis blooms have caused significant ecological and economic damage, as well as mass mortality, in cultivated species. Nutrients are one of [...] Read more.
The increasing prevalence of harmful algal blooms (HABs) driven by eutrophication, particularly in China’s nearshore waters, is a growing concern. Dinoflagellate Heterocapsa bohaiensis blooms have caused significant ecological and economic damage, as well as mass mortality, in cultivated species. Nutrients are one of the primary inducers of H. bohaiensis blooms. However, the transcriptomic studies of H. bohaiensis remain sparse, and its metabolic pathways are unknown. This study analyzed the transcriptome of H. bohaiensis under varying nutrient conditions (nitrogen at 128, 512, and 880 μM; phosphate at 8, 6, and 32 μM), focusing on differential gene expression. The results indicated that deviations in nutrient conditions (higher or lower N:P ratios) led to a higher number of differentially expressed genes compared to the control (N:P ratios = 27.5), thereby underscoring their pivotal role in growth. Gene Ontology (GO) enrichment analyses showed that nutrient limitation upregulated the biosynthesis and catabolism processes while downregulating the cell cycle and division functions. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that, under nitrogen limitation, the proteasome pathways were upregulated, while photosynthesis and carbon fixation were downregulated; under phosphorus limitation, the proteasome pathways were upregulated and nitrogen metabolism was downregulated. These findings suggest that H. bohaiensis adapts to nutrient stress by adjusting its metabolic processes. Full article
(This article belongs to the Special Issue Research on Biology of Dinoflagellates)
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13 pages, 2213 KiB  
Article
Allelopathic Effect of a Chilean Strain of Karenia selliformis (Gymnodiniales, Dinoflagellata) on Phytoplankton Species
by Victoria Alfaro-Ahumada, Sandra Jara-Toro, Catharina Alves-de-Souza, Alejandra Rivera-Latorre, Jorge I. Mardones, Juan José Gallardo-Rodriguez and Allisson Astuya-Villalón
Microorganisms 2024, 12(9), 1834; https://doi.org/10.3390/microorganisms12091834 - 5 Sep 2024
Cited by 2 | Viewed by 1167
Abstract
Blooms of the dinoflagellate Karenia selliformis in Chile, often associated with massive fish kills, have been noted alongside other species from the Kareniaceae family, such as Karenia spp. and Karlodinium spp. However, the potential allelopathy impact of Chilean K. selliformis on other phytoplankton [...] Read more.
Blooms of the dinoflagellate Karenia selliformis in Chile, often associated with massive fish kills, have been noted alongside other species from the Kareniaceae family, such as Karenia spp. and Karlodinium spp. However, the potential allelopathy impact of Chilean K. selliformis on other phytoplankton species remains unexplored. Here, we assessed the allelopathic effects of cell-free exudates from a Chilean K. selliformis strain on six phytoplankton strains representing diverse microalgal groups. The findings of these experiments offer valuable insights into the varied responses of both non-toxic and toxic microalgae to allelochemicals produced by a toxic microalga, showcasing the intricate and multifaceted nature of allelopathic interactions in microalgal communities. The study revealed species-dependent effects, with variable response in cell growth, photosynthetic efficiency (i.e., Fv/Fm), and intracellular reactive oxygen species (ROS) production. While certain strains exhibited significant growth inhibition in response to the allelochemicals, others demonstrated no apparent effect on cell proliferation, indicating varying sensitivity to specific allelochemicals or potentially distinct detoxification mechanisms. Similarly, the diverse effects on Fv/Fm highlight the complexity of allelopathic interactions, with some species showing reduced efficiency without alterations in intracellular ROS production, while others displayed increased ROS production alongside impaired photosynthesis. Full article
(This article belongs to the Special Issue Research on Biology of Dinoflagellates)
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19 pages, 6279 KiB  
Article
Dinoflagellate Proton-Pump Rhodopsin Genes in Long Island Sound: Diversity and Spatiotemporal Distribution
by Huan Zhang, Kelly J. Nulick, Zair Burris, Melissa Pierce, Minglei Ma and Senjie Lin
Microorganisms 2024, 12(3), 628; https://doi.org/10.3390/microorganisms12030628 - 21 Mar 2024
Cited by 1 | Viewed by 1764
Abstract
Microbial proton-pump rhodopsin (PPR)-based phototrophy, a light-harvesting mechanism different from chlorophyll-based photosystems, may contribute significantly to solar energy entry into the marine ecosystem. PPR transforms solar energy into cellular energy that is used for various metabolic processes in the cells or flagellar movement. [...] Read more.
Microbial proton-pump rhodopsin (PPR)-based phototrophy, a light-harvesting mechanism different from chlorophyll-based photosystems, may contribute significantly to solar energy entry into the marine ecosystem. PPR transforms solar energy into cellular energy that is used for various metabolic processes in the cells or flagellar movement. Although rhodopsins or their encoding genes have been documented in a wide phylogenetic range of cultured dinoflagellates, information is limited about how widespread and how spatiotemporally dynamical dinoflagellate PPR (DiPPR) are in natural marine ecosystems. In this study, we investigated DiPPR in Long Island Sound (LIS), a temperate estuary of the Atlantic Ocean between Connecticut and Long Island, New York, USA. We isolated six novel full-length dinoflagellate proton-pump rhodopsin cDNAs, expanding the DiPPR database that is crucial to PPR research. Based on these new sequences and existing sequences of DiPPR, we designed primers and conducted quantitative PCR and sequencing to determine the abundance and diversity of DiPPR genes spatially and temporally throughout a year in the water samples collected from LIS. DiPPR genes were found year-round and throughout LIS but with higher abundances in the eutrophic Western Sound and in April and July. The gene diversity data suggest that there are at least five distinct rhodopsin-harboring groups of dinoflagellates throughout the year. The abundance of DiPPR genes, measured as copy number per mL of seawater, appeared not to be influenced by water temperature or nitrogen nutrient concentration but exhibited weak negative correlations with orthophosphate concentration and salinity and a positive correlation with the abundance of DiPPR-harboring dinoflagellates. This first quantitative profiling of PPR in natural plankton reveals the prevalence and dynamics of this plastid-independent photoenergy harvesting mechanism in a temperate estuary and provides efficient DiPPR primers potentially useful for future research. Furthermore, this study shed light on the potential role of DiPPR in phosphor nutrition and dinoflagellate population, which warrants further studies. Full article
(This article belongs to the Special Issue Research on Biology of Dinoflagellates)
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Review

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26 pages, 19485 KiB  
Review
Some Insights into the Inventiveness of Dinoflagellates: Coming Back to the Cell Biology of These Protists
by Marie-Odile Soyer-Gobillard
Microorganisms 2025, 13(5), 969; https://doi.org/10.3390/microorganisms13050969 - 24 Apr 2025
Viewed by 294
Abstract
In this review dedicated to the great protistologist Edouard Chatton (1883–1947), I wanted to highlight the originality and remarkable diversity of some dinoflagellate protists through the lens of cell biology. Their fossilized traces date back to more than 538 million years (Phanerozoic eon). [...] Read more.
In this review dedicated to the great protistologist Edouard Chatton (1883–1947), I wanted to highlight the originality and remarkable diversity of some dinoflagellate protists through the lens of cell biology. Their fossilized traces date back to more than 538 million years (Phanerozoic eon). However, they may be much older because acritarchs from the (Meso) Proterozoic era (1500 million years ago) could be their most primitive ancestors. Here, I described several representative examples of the various lifestyles of free-living (the autotrophic thecate Prorocentrum micans Ehrenberg and the heterotrophic athecate Noctiluca scintillans McCartney and other “pseudo-noctilucidae”, as well as the thecate Crypthecodinium cohnii Biecheler) and of parasitic dinoflagellates (the mixotroph Syndinium Chatton). Then, I compared the different dinoflagellate mitotic systems and reported observations on the eyespot (ocelloid), an organelle that is present in the binucleated Glenodinium foliaceum Stein and in some Warnowiidae dinoflagellates and can be considered an evolutionary marker. The diversity and innovations observed in mitosis, meiosis, reproduction, sexuality, cell cycle, locomotion, and nutrition allow us to affirm that dinoflagellates are among the most innovative unicells in the Kingdom Protista. Full article
(This article belongs to the Special Issue Research on Biology of Dinoflagellates)
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15 pages, 3441 KiB  
Review
BiP Proteins from Symbiodiniaceae: A “Shocking” Story
by Estefanía Morales-Ruiz, Tania Islas-Flores and Marco A. Villanueva
Microorganisms 2024, 12(11), 2126; https://doi.org/10.3390/microorganisms12112126 - 23 Oct 2024
Viewed by 1125
Abstract
More than four decades ago, the discovery of a companion protein of immunoglobulins in myeloma cells and soon after, of their ability to associate with heavy chains, made the term immunoglobulin binding protein (BiP) emerge, prompting a tremendous amount of effort to understand [...] Read more.
More than four decades ago, the discovery of a companion protein of immunoglobulins in myeloma cells and soon after, of their ability to associate with heavy chains, made the term immunoglobulin binding protein (BiP) emerge, prompting a tremendous amount of effort to understand their versatile cellular functions. BiPs belong to the heat shock protein (Hsp) 70 family and are crucial for protein folding and cellular stress responses. While extensively studied in model organisms such as Chlamydomonas, their roles in dinoflagellates, especially in photosynthetic Symbiodiniaceae, remain largely underexplored. Given the importance of Symbiodiniaceae-cnidarian symbiosis, critical for the sustaining of coral reef ecosystems, understanding the contribution of Hsps to stress resilience is essential; however, most studies have focused on Hsps in general but none on BiPs. Moreover, despite the critical role of light in the physiology of these organisms, research on light effects on BiPs from Symbiodiniaceae has also been limited. This review synthesizes the current knowledge from the literature and sequence data, which reveals a high degree of BiP conservation at the gene, protein, and structural levels in Symbiodiniaceae and other dinoflagellates. Additionally, we show the existence of a potential link between circadian clocks and BiP regulation, which would add another level of regulatory complexity. The evolutionary relationship among dinoflagellates overall suggests conserved functions and regulatory mechanisms, albeit expecting confirmation by experimental validation. Finally, our analysis also highlights the significant knowledge gap and underscores the need for further studies focusing on gene and protein regulation, promoter architecture, and structural conservation of Symbiodiniaceae and dinoglagellate BiPs in general. These will deepen our understanding of the role of BiPs in the Symbiodiniaceae-cnidarian interactions and dinoflagellate physiology. Full article
(This article belongs to the Special Issue Research on Biology of Dinoflagellates)
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