Special Issue "Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012)"

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A special issue of Microorganisms (ISSN 2076-2607).

Deadline for manuscript submissions: closed (30 August 2013)

Special Issue Editor

Guest Editor
Prof. Dr. Senjie Lin (Website)

Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
Fax: +1 860 405 9153
Interests: marine algae; eukaryotic microbes; molecular ecology; functional genomics; microbial interactions

Special Issue Information

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Keywords

  • taxonomy and phylogeny
  • biodiversity
  • nuclear biology
  • mitochondrial biology
  • plastid biology
  • nutrient physiology
  • heterotrophy
  • growth rate
  • bioluminescence
  • toxins
  • HABS
  • genomics

Published Papers (8 papers)

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Research

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Open AccessArticle Towards an Ecological Understanding of Dinoflagellate Cyst Functions
Microorganisms 2014, 2(1), 11-32; doi:10.3390/microorganisms2010011
Received: 24 September 2013 / Revised: 17 November 2013 / Accepted: 23 November 2013 / Published: 3 January 2014
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Abstract
The life cycle of many dinoflagellates includes at least one nonflagellated benthic stage (cyst). In the literature, the different types of dinoflagellate cysts are mainly defined based on morphological (number and type of layers in the cell wall) and functional (long- or [...] Read more.
The life cycle of many dinoflagellates includes at least one nonflagellated benthic stage (cyst). In the literature, the different types of dinoflagellate cysts are mainly defined based on morphological (number and type of layers in the cell wall) and functional (long- or short-term endurance) differences. These characteristics were initially thought to clearly distinguish pellicle (thin-walled) cysts from resting (double-walled) dinoflagellate cysts. The former were considered short-term (temporal) and the latter long-term (resting) cysts. However, during the last two decades further knowledge has highlighted the great intricacy of dinoflagellate life histories, the ecological significance of cyst stages, and the need to clarify the functional and morphological complexities of the different cyst types. Here we review and, when necessary, redefine the concepts of resting and pellicle cysts, examining both their structural and their functional characteristics in the context of the life cycle strategies of several dinoflagellate species. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Review

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Open AccessReview A Comparative Overview of the Flagellar Apparatus of Dinoflagellate, Perkinsids and Colpodellids
Microorganisms 2014, 2(1), 73-91; doi:10.3390/microorganisms2010073
Received: 24 November 2013 / Revised: 29 January 2014 / Accepted: 8 February 2014 / Published: 10 March 2014
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Abstract
Dinoflagellates are a member of the Alveolata, and elucidation of the early evolution of alveolates is important for our understanding of dinoflagellates, and vice versa. The ultrastructure of the flagellar apparatus has been described from several dinoflagellates in the last few decades, [...] Read more.
Dinoflagellates are a member of the Alveolata, and elucidation of the early evolution of alveolates is important for our understanding of dinoflagellates, and vice versa. The ultrastructure of the flagellar apparatus has been described from several dinoflagellates in the last few decades, and the basic components appear to be well conserved. The typical dinoflagellate apparatus is composed of two basal bodies surrounded by striated collars attached to a connective fiber. The longitudinal basal body is connected to a longitudinal microtubular root (LMR; equivalent of R1) and single microtubular root (R2), whereas the transverse basal body is connected to a transverse microtubular root (TMR; R3) and transverse striated root (TSR) with a microtubule (R4). Some of these components, especially the connective fibers and collars, are dinoflagellate specific characteristics that make their flagellar apparatus relatively complex. We also compare these structures with the flagellar apparatus from a number of close relatives of dinoflagellates and their sister, the apicomplexans, including colpodellids, perkinsids, and Psammosa. Though the ultrastructural knowledge of these lineages is still relatively modest, it provides us with an interesting viewpoint of the character evolution of the flagellar apparatus among those lineages. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview Transcription and Maturation of mRNA in Dinoflagellates
Microorganisms 2013, 1(1), 71-99; doi:10.3390/microorganisms1010071
Received: 22 July 2013 / Revised: 10 September 2013 / Accepted: 14 October 2013 / Published: 1 November 2013
Cited by 5 | PDF Full-text (1028 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Dinoflagellates are of great importance to the marine ecosystem, yet scant details of how gene expression is regulated at the transcriptional level are available. Transcription is of interest in the context of the chromatin structure in the dinoflagellates as it shows many [...] Read more.
Dinoflagellates are of great importance to the marine ecosystem, yet scant details of how gene expression is regulated at the transcriptional level are available. Transcription is of interest in the context of the chromatin structure in the dinoflagellates as it shows many differences from more typical eukaryotic cells. Here we canvas recent transcriptome profiles to identify the molecular building blocks available for the construction of the transcriptional machinery and contrast these with those used by other systems. Dinoflagellates display a clear paucity of specific transcription factors, although surprisingly, the rest of the basic transcriptional machinery is not markedly different from what is found in the close relatives to the dinoflagellates. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview An Updated List of Generic Names in the Thoracosphaeraceae
Microorganisms 2013, 1(1), 122-136; doi:10.3390/microorganisms1010122
Received: 28 August 2013 / Revised: 12 September 2013 / Accepted: 23 October 2013 / Published: 1 November 2013
Cited by 5 | PDF Full-text (788 KB) | HTML Full-text | XML Full-text
Abstract
Calcareous dinophytes produce exoskeletal calcified structures during their life history (a unique character among the alveolates) and are subsumed under the Thoracosphaeraceae as part of the Peridiniales. We provide a brief synopsis about the taxonomic history of the group, from the first [...] Read more.
Calcareous dinophytes produce exoskeletal calcified structures during their life history (a unique character among the alveolates) and are subsumed under the Thoracosphaeraceae as part of the Peridiniales. We provide a brief synopsis about the taxonomic history of the group, from the first descriptions of fossils in the 19th century through to the results of molecular phylogenetics studies undertaken during the past two decades. Delimitation and circumscription of the Thoracosphaeraceae are challenging, as they comprise both phototrophic (presumably including endosymbiotic) as well as heterotrophic (and even parasitic) dinophytes from marine and freshwater environments, respectively. However, calcareous structures are not known from all members of the Thoracosphaeraceae, and the corresponding species and groups are considered to have lost the capacity to calcify. Five years ago, a taxonomic list of 99 generic names assigned to the Thoracosphaeraceae was published, and we update this compendium with 19 additional names based on recent studies. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview The Genus Neoceratium (Planktonic Dinoflagellates) as a Potential Indicator of Ocean Warming
Microorganisms 2013, 1(1), 58-70; doi:10.3390/microorganisms1010058
Received: 14 August 2013 / Revised: 25 September 2013 / Accepted: 10 October 2013 / Published: 25 October 2013
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Abstract
Among the planktonic dinoflagellates, the species-rich genus Neoceratium has particularly remarkable features that include its easily recognizable outline and large size. This ubiquitous genus shows consistent presence in all plankton samples and has been a model for numerous studies since the end [...] Read more.
Among the planktonic dinoflagellates, the species-rich genus Neoceratium has particularly remarkable features that include its easily recognizable outline and large size. This ubiquitous genus shows consistent presence in all plankton samples and has been a model for numerous studies since the end of the 19th century. It has already been described as a good candidate to monitor water masses and describe ocean circulation. We argue that the sensitivity displayed by Neoceratium to water temperature also makes it relevant as an indicator of ocean warming. The advantages and interests of using Neoceratium species to monitor climate change on a large scale are reassessed in view of recent advances in understanding their biology and ecology. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview Biology of the Marine Heterotrophic Dinoflagellate Oxyrrhis marina: Current Status and Future Directions
Microorganisms 2013, 1(1), 33-57; doi:10.3390/microorganisms1010033
Received: 2 July 2013 / Revised: 2 September 2013 / Accepted: 8 October 2013 / Published: 21 October 2013
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Abstract
Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhis marina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of [...] Read more.
Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhis marina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of ecological, biogeographic, and evolutionary studies. Despite the increasing research effort on this species, there lacks a synthesis of the existing data and a coherent picture of this organism. Here we reviewed the literature to provide an overview of what is known regarding the biology of O. marina, and identify areas where further studies are needed. As an early branch of the dinoflagellate lineage, O. marina shares similarity with typical dinoflagellates in permanent condensed chromosomes, less abundant nucleosome proteins compared to other eukaryotes, multiple gene copies, the occurrence of trans-splicing in nucleus-encoded mRNAs, highly fragmented mitochondrial genome, and disuse of ATG as a start codon for mitochondrial genes. On the other hand, O. marina also exhibits some distinct cytological features (e.g., different flagellar structure, absence of girdle and sulcus or pustules, use of intranuclear spindle in mitosis, presence of nuclear plaque, and absence of birefringent periodic banded chromosomal structure) and genetic features (e.g., a single histone-like DNA-associated protein, cob-cox3 gene fusion, 5′ oligo-U cap in the mitochondrial transcripts of protein-coding genes, the absence of mRNA editing, the presence of stop codon in the fused cob-cox3 mRNA produced by post-transcriptional oligoadenylation, and vestigial plastid genes). The best-studied biology of this dinoflagellate is probably the prey and predators types, which include a wide range of organisms. On the other hand, the abundance of this species in the natural waters and its controlling factors, genome organization and gene expression regulation that underlie the unusual cytological and ecological characteristics are among the areas that urgently need study. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview Circadian Rhythms in Dinoflagellates: What Is the Purpose of Synthesis and Destruction of Proteins?
Microorganisms 2013, 1(1), 26-32; doi:10.3390/microorganisms1010026
Received: 21 June 2013 / Revised: 26 August 2013 / Accepted: 9 September 2013 / Published: 18 September 2013
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Abstract
There is a prominent circadian rhythm of bioluminescence in many species of light-emitting dinoflagellates. In Lingulodinium polyedrum a daily synthesis and destruction of proteins is used to regulate activity. Experiments indicate that the amino acids from the degradation are conserved and incorporated [...] Read more.
There is a prominent circadian rhythm of bioluminescence in many species of light-emitting dinoflagellates. In Lingulodinium polyedrum a daily synthesis and destruction of proteins is used to regulate activity. Experiments indicate that the amino acids from the degradation are conserved and incorporated into the resynthesized protein in the subsequent cycle. A different species, Pyrocystis lunula, also exhibits a rhythm of bioluminescence, but the luciferase is not destroyed and resynthesized each cycle. This paper posits that synthesis and destruction constitutes a cellular mechanism to conserve nitrogen in an environment where the resource is limiting. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview Understanding Bioluminescence in Dinoflagellates—How Far Have We Come?
Microorganisms 2013, 1(1), 3-25; doi:10.3390/microorganisms1010003
Received: 3 May 2013 / Revised: 20 August 2013 / Accepted: 24 August 2013 / Published: 5 September 2013
Cited by 6 | PDF Full-text (658 KB) | HTML Full-text | XML Full-text
Abstract
Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to [...] Read more.
Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to the organisms’ lifestyle. In this paper, we review the literature on the cellular mechanisms, molecular evolution, diversity, and ecology of bioluminescence in dinoflagellates, highlighting significant discoveries of the last quarter of a century. We identify significant gaps in our knowledge and conflicting information and propose some important research questions that need to be addressed to advance this research field. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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