Morphology and Phylogeny of the Pseudocolonial Dinoflagellates Polykrikos lebourae and Polykrikos herdmanae n. sp

Diversity of 'simple' multicellular eukaryotes: 45 independent cases and six types of multicellularity

Multicellularity evolved multiple times in the history of life, with most reviewers agreeing that it appeared at least 20 times in eukaryotes. However, a specific list of multicellular eukaryotes with clear criteria for inclusion has not yet been published. Herein, an updated critical review of eukaryotic multicellularity is presented, based on current understanding of eukaryotic phylogeny and new discoveries in microbiology, phycology and mycology. As a result, 45 independent multicellular lineages are identified that fall into six distinct types. Functional criteria, as distinct from a purely topological definition of a cell, are introduced to bring uniformity and clarity to the existing definitions of terms such as colony, multicellularity, thallus or plasmodium. The category of clonal multicellularity is expanded to include: (i) septated multinucleated thalli found in Pseudofungi and early-branching Fungi such as Chytridiomycota and Blastocladiomycota; and (ii) multicellular reproductive structures formed by plasmotomy in intracellular parasites such as Phytomyxea. Furthermore, (iii) endogeneous budding, as found in Paramyxida, is described as a form of multicellularity. The best-known case of clonal multicellularity, i.e. (iv) non-separation of cells after cell division, as known from Metazoa and Ochrophyta, is also discussed. The category of aggregative multicellularity is expanded to include not only (v) pseudoplasmodial forms, such a sorocarp-forming Acrasida, but also (vi) meroplasmodial organisms, such as members of Variosea or Filoreta. A common set of topological, geometric, genetic and life-cycle criteria are presented that form a coherent, philosophically sound framework for discussing multicellularity. A possibility of a seventh type of multicellularity is discussed, that of multi-species superorganisms formed by protists with obligatory bacterial symbionts, such as some members of Oxymonada or Parabasalia. Its inclusion is dependent on the philosophical stance taken towards the concepts of individuality and organism in biology. Taxa that merit special attention are identified, such as colonial Centrohelea, and a new speculative form of multicellularity, possibly present in some reticulopodial amoebae, is briefly described. Because of insufficient phylogenetic and morphological data, not all lineages could be unequivocally identified, and the true total number of all multicellular eukaryotic lineages is therefore higher, likely close to a hundred.

q-PCR-based assay for the toxic dinoflagellate Karenia selliformis monitoring along the Tunisian coasts

Karenia selliformis is a marine dinoflagellate responsible for fish-kill events. Its presence has been reported along the Tunisian coasts (south-eastern Mediterranean Sea) since the 1990s. In the present study, a quantitative-PCR assay, based on the internal transcribed spacer (ITS) molecular marker, was developed to detect and quantify K. selliformis in environmental bivalve mollusk samples and in seawater samples. The assay was optimized, and its specificity was confirmed using cross-reactivity experiments against microalgal species commonly found on the Tunisian coasts and/or closely related to K. selliformis. Calibration curves were performed by tenfold dilutions of plasmid DNA harboring target sequence and genomic DNA, attaining a limit of detection of around 5 copies of target DNA per reaction, far below one K. selliformis cell per reaction. The field application of the developed assay showed a powerful detection capability. Thus, the designed assay could contribute to the deployment of in-field diagnostic tools for K. selliformis blooms monitoring.

Morpho-molecular description of a new HAB species, Pseudocochlodinium profundisulcus gen. et sp. nov., and its LSU rRNA gene based genetic diversity and geographical distribution

Harmful algal blooms (HABs) caused by an unknown dinoflagellate species have frequently occurred in the Pearl River Estuary, China Since 2006. These blooms were associated with severe water discoloration and economic losses, ranging from several km² to 300 km² with the maximum recorded cell density being 2.77 × 10⁷ cells⋅L^-1. This unknown dinoflagellate species was initially identified as Cochlodinium geminatum and subsequently reclassified as Polykrikos geminatus. However, after reviewing the original descriptions for Cochlodinium geminatum sensu Schütt (1895) and the genus Polykrikos, we considered this species is incongruent with their original descriptions. Further morphological examinations and particularly phylogenetic analyses based on the SSU and partial LSU rRNA genes of isolates and resting cysts from China and Japan prompted us to consider it a new species of a new genus. This new species was proposed to be Pseudocochlodinium profundisulcus gen. et sp. nov., based on its open comma-shaped apical structure complex (ASC), cingulum encircling the cell less than one and a half turns, a deep sulcus with a torsion of a half turn, either single cell or cell chain consisting of two cells with the same number of nuclei and zooids, the resting cyst bearing lobed ornaments, and the evolutionary distances from Polykrikos (and others) on the phylogenetic trees constructed using the concatenated SSU and partial LSU rRNA gene sequences. Metabarcoding investigation of surface sediment samples collected in China revealed that the species to be widely present along the entire Chinese coast with the highest abundance in the South China Sea. Further re-analysis of the Tara Oceans metabarcoding dataset targeting the SSU rRNA gene V9 domain suggested a global distribution of this new genus. Phylogenetic analyses on 46 OTUs (average length: ∼552 bases) of its LSU rRNA gene sequences (mainly D1-D2 domains) obtained from surface sediment samples revealed intraspecific genetic diversity of this species. Interestingly, based on the different distributions and the abundance of these OTUs along the coast of China, this species appeared to have expanded its distribution from the South China Sea to the northern Yellow Sea, or preferred a warm water habitat. We consider that the present work improves the taxonomy and provides important insights into the biogeography of Pseudocochlodinium profundisulcus.⋅.

Insights into the Morphology of Haplozoan Parasites (Dinoflagellata) using Confocal Laser Scanning Microscopy

We describe new insights into the morphology and life history of the bizarre parasite Haplozoon axiothellae (Dinoflagellata) using light microscopy (LM), scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM). Trophonts were isolated from the intestines of host maldanid polychaetes, Axiothella rubrocincta, collected from San Juan Island, Washington, USA. LM and SEM confirmed features previously observed, such as amphiesmal projections, mature and immature junctions between the nucleated compartments of the vermiform syncytium and visible polygonal alveoli. CLSM of adult trophonts fluorescently stained for DNA, tubulin, centrin, and plasma membrane demonstrated several new ultrastructural traits: (1) an extensive basket of parallel microtubules within the trophomere used for host attachment, (2) two physically separated MTOCs (i.e. putative pairs of basal bodies) beneath pores on the ventral side of each compartment, (3) robust mitotic and/or meiotic spindles associated with one to four nuclei in each compartment, (4) spindles with polar bodies that are disconnected from the MTOCs, (5) a centrin-stained fibril within the trophomeres that potentially functions to retract the motile stylet, and (6) cytokinesis in the posterior-most compartments. This study renames haplozoan compartments using the suffix "-mere" rather than "-cyte" (i.e. trophomere, gonomere, sporomere) to reflect their status within a single syncytium.

Ultrastructure and Systematics of Two New Species of Dinoflagellate, Paragymnodinium Asymmetricum sp. nov. and Paragymnodinium Inerme sp. nov. (Gymnodiniales, Dinophyceae)1

The genus Paragymnodinium currently includes two species, P. shiwhaense and P. stigmaticum, that are characterized by mixotrophic nutrition and the possession of nematocysts. In this study, two new dinoflagellates belonging to this genus were described based on observations using LM, SEM, and TEM together with a molecular analysis. Cells of P. asymmetricum sp. nov., isolated from Nha Trang Beach, Vietnam, were 7.9-12.6 μm long and 4.7-9.0 μm wide. The species showed no evidence of feeding behavior and was able to sustain itself phototrophically. Paragymnodinium asymmetricum shared many features with P. shiwhaense, including presence of nematocysts, absence of an eyespot, and a planktonic lifestyle, but was clearly distinguished by the asymmetric shape of the hyposome, possession of a single chloroplast, and its nutritional mode. Cells of P. inerme sp. nov., isolated from Jogashima, Kanagawa Pref, Japan, were 15.3-23.7 μm long and 10.9-19.6 μm wide. This species also showed no evidence of feeding behavior. Paragymnodinium inerme was similar to cells of P. shiwhaense in shape and planktonic lifestyle, but its nutritional mode was different. The presence of incomplete nematocysts was also a unique feature. A phylogenetic analysis inferred from concatenated SSU and LSU rDNA sequences recovered the two dinoflagellates in a robust clade with Paragymnodinium spp., within the clade of Gymnodinium sensu stricto. This evidence, together with their morphological similarities, made it reasonable to conclude that these two dinoflagellates are new species of Paragymnodinium.

Morphology and Molecular Phylogeny of a New Marine, Sand-dwelling Dinoflagellate Genus, Pachena (Dinophyceae), with Descriptions of Three New Species

Marine benthic dinoflagellates are interesting not only because some epiphytic genera can cause harmful algal blooms but also for understanding dinoflagellate evolution and diversification. Our understanding of their biodiversity is far from complete, and many thecate genera have unusual tabulation patterns that are difficult to relate to the diverse known phytoplankton taxa. A new sand-dwelling genus, Pachena gen. nov., is described based on morphological and DNA sequence data. Three species were discovered in distant locations and are circumscribed, namely, P. leibnizii sp. nov. from Canada, P. abriliae sp. nov. from Spain, and P. meriddae sp. nov. from Italy. All species are tiny (about 9-23 μm long) and heterotrophic. Species are characterized by their tabulation (APC 4' 3a 6'' 5c 5s 5''' 2''''), an apical hook covering the apical pore, an ascending cingulum, and a sulcus with central list. The first anterior intercalary plate is uniquely "sandwiched" between two plates. The species share these features and differ in the relative sizes and arrangements of their plates, especially on the epitheca. The ornamentation of thecal plates is species-specific. The new molecular phylogenies based on SSU and LSU rDNA sequences contribute to understanding the evolution of the planktonic relatives of Pachena, the Thoracosphaeraceae.

Morphology, ultrastructure, and molecular phylogeny of Wangodinium sinense gen. et sp. nov. (Gymnodiniales, Dinophyceae) and revisiting of Gymnodinium dorsalisulcum and Gymnodinium impudicum

The genus Gymnodinium includes many morphologically similar species, but molecular phylogenies show that it is polyphyletic. Eight strains of Gymnodinium impudicum, Gymnodinium dorsalisulcum and a novel Gymnodinium-like species from Chinese and Malaysian waters and the Mediterranean Sea were established. All of these strains were examined with light microscopy, scanning electron microscopy and transmission electron microscopy. SSU, LSU and internal transcribed spacers rDNA sequences were obtained. A new genus, Wangodinium, was erected to incorporate strains with a loop-shaped apical structure complex (ASC) comprising two rows of amphiesmal vesicles, here referred to as a new type of ASC. The chloroplasts of Wangodinium sinense are enveloped by two membranes. Pigment analysis shows that peridinin is the main accessory pigment in W. sinense. Wangodinium differs from other genera mainly in its unique ASC, and additionally differs from Gymnodinium in the absence of nuclear chambers, and from Lepidodinium in the absence of Chl b and nuclear chambers. New morphological information was provided for G. dorsalisulcum and G. impudicum, e.g., a short sulcal intrusion in G. dorsalisulcum; nuclear chambers in G. impudicum and G. dorsalisulcum; and a chloroplast enveloped by two membranes in G. impudicum. Molecular phylogeny was inferred using maximum likelihood and Bayesian inference with independent SSU and LSU rDNA sequences. Our results support the classification of Wangodinium within the Gymnodiniales sensu stricto clade and it is close to Lepidodinium. Our results also support the close relationship among G. dorsalisulcum, G. impudicum, and Barrufeta. Further research is needed to assign these Gymnodinium species to Barrufeta or to erect new genera.

Feeding by common heterotrophic protists on the mixotrophic alga Gymnodinium smaydae (Dinophyceae), one of the fastest growing dinoflagellates

Gymnodinium smaydae is one of the fastest growing dinoflagellates. However, its population dynamics are affected by both growth and mortality due to predation. Thus, feeding by common heterotrophic dinoflagellates Gyrodinium dominans, Gyrodinium moestrupii, Oblea rotunda, Oxyrrhis marina, and Polykrikos kofoidii, and the naked ciliate Pelagostrobilidium sp. on G. smaydae was investigated in the laboratory. Furthermore, growth and ingestion rates of O. marina, G. dominans, and Pelagostrobilidium sp. on G. smaydae in response to prey concentration were also determined. Oxyrrhis marina, G. dominans, G. moestrupii, and Pelagostrobilidium sp. were able to feed on G. smaydae, but P. kofoidii and O. rotunda did not feed on this dinoflagellate. The maximum growth rate of O. marina on G. smaydae was 0.411 per day. However, G. smaydae did not support the positive growth of Pelagostrobilidium sp. The maximum ingestion rates of O. marina and Pelagostrobilidium sp. on G. smaydae were 0.27 and 6.91 ng C · predator^-1  · d^-1 , respectively. At the given mean prey concentrations, the highest growth and ingestion rates of G. dominans on G. smaydae were 0.114 per day and 0.04 ng C · predator^-1  · d^-1 , respectively. The maximum growth and ingestion rates of O. marina on G. smaydae are lower than those on most of the other algal prey species. Therefore, O. marina may be an effective predator of G. smaydae, but G. smaydae may not be the preferred prey for supporting high growth of the predator in comparison to other species as inferred from a literature survey.

dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosystems where they occupy various ecological niches. They play a major role as primary producers, but many species are mixotrophic or heterotrophic. Environmental metabarcoding based on high-throughput sequencing is increasingly applied to assess diversity and abundance of planktonic organisms, and reference databases are definitely needed to taxonomically assign the huge number of sequences. We provide an updated 18S rRNA reference database of dinoflagellates: dinoref. Sequences were downloaded from genbank and filtered based on stringent quality criteria. All sequences were taxonomically curated, classified taking into account classical morphotaxonomic studies and molecular phylogenies, and linked to a series of metadata. dinoref includes 1,671 sequences representing 149 genera and 422 species. The taxonomic assignation of 468 sequences was revised. The largest number of sequences belongs to Gonyaulacales and Suessiales that include toxic and symbiotic species. dinoref provides an opportunity to test the level of taxonomic resolution of different 18S barcode markers based on a large number of sequences and species. As an example, when only the V4 region is considered, 374 of the 422 species included in dinoref can still be unambiguously identified. Clustering the V4 sequences at 98% similarity, a threshold that is commonly applied in metabarcoding studies, resulted in a considerable underestimation of species diversity.

On the extrusomes of Oxyrrhis marina (Dinophyceae)

Oxyrrhis marina was subjected to conventional transmission electron microscopy, with emphasis being laid on its extrusomes. Mainly regular trichocysts were obvious in ultrathin sections. They were highly abundant, approximately 2 μm in length and 200 nm in width, and composed of the characteristic features, i.e., an anterior tip and the posterior crystalline body. The tip measures approximately 440 nm in length and is built by an outer less electron-dense concentric layer followed by an inner electron-dense core with a translucent center in the middle. The less electron-dense layer most likely ends up in a bundle of filaments which are concentrically placed around the electron-dense core in the transition zone between the tip and body. Trichocyst bodies which are sectioned along the longitudinal axis are approximately 1.5 μm in length and show a regular striation of electron-dense and electron-translucent lines with a spacing of 9 nm. Cross-sectioned bodies are square-shaped and show a crystalline lattice composed of particles which are 8-9 nm in size. Discharge of regular trichocysts results in long rigid rods. They are square-shaped, 54 nm broad, and with a regular striation of approximately 54 nm along their longitudinal axes. Besides regular trichocysts, an additional type of extrusome was registered. It is not as abundant as regular trichocysts, membrane-enclosed, 2 μm in length and 180 nm in width, and resembles two bullets adjacent to each other with the tips facing in opposite directions. The two parts are slightly of different lengths (anterior part, 740 nm; posterior part, 590 nm) and widths (anterior part, 126 nm; posterior part, 117 nm) and separated from each other by a gap of 30 nm. The anterior part is more electron-dense than the posterior one. A faint electron-dense sheet-like structure was registered between the envelope membrane and these two inner structures. In extrusomes which had been arrested in the process of discharge, the anterior part gives rise to an oozing, amorphous, fibrous blob, while the posterior part consists of twisted filaments which most likely function as the charge of a gun for the release of the anterior part.

Differential interactions between the nematocyst-bearing mixotrophic dinoflagellate Paragymnodinium shiwhaense and common heterotrophic protists and copepods: Killer or prey

To investigate interactions between the nematocyst-bearing mixotrophic dinoflagellate Paragymnodinium shiwhaense and different heterotrophic protist and copepod species, feeding by common heterotrophic dinoflagellates (Oxyrrhis marina and Gyrodinium dominans), naked ciliates (Strobilidium sp. approximately 35μm in cell length and Strombidinopsis sp. approximately 100μm in cell length), and calanoid copepods Acartia spp. (A. hongi and A. omorii) on P. shiwhaense was explored. In addition, the feeding activities of P. shiwhaense on these heterotrophic protists were investigated. Furthermore, the growth and ingestion rates of O. marina, G. dominans, Strobilidium sp., Strombidinopsis sp., and Acartia spp. as a function of P. shiwhaense concentration were measured. O. marina, G. dominans, and Strombidinopsis sp. were able to feed on P. shiwhaense, but Strobilidium sp. was not. However, the growth rates of O. marina, G. dominans, Strobilidium sp., and Strombidinopsis sp. feeding on P. shiwhaense were very low or negative at almost all concentrations of P. shiwhaense. P. shiwhaense frequently fed on O. marina and Strobilidium sp., but did not feed on Strombidinopsis sp. and G. dominans. G. dominans cells swelled and became dead when incubated with filtrate from the experimental bottles (G. dominans+P. shiwhaense) that had been incubated for one day. The ingestion rates of O. marina, G. dominans, and Strobilidium sp. on P. shiwhaense were almost zero at all P. shiwhaense concentrations, while those of Strombidinopsis sp. increased with prey concentration. The maximum ingestion rate of Strombidinopsis sp. on P. shiwhaense was 5.3ngC predator^-1d^-1 (41 cells predator^-1d^-1), which was much lower than ingestion rates reported in the literature for other mixotrophic dinoflagellate prey species. With increasing prey concentrations, the ingestion rates of Acartia spp. on P. shiwhaense increased up to 930ngCml^-1 (7180cellsml^-1) at the highest prey concentration. The highest ingestion rate of Acartia spp. on P. shiwhaense was 4240ngC predator^-1d^-1 (32,610 cells predator^-1d^-1), which is comparable to ingestion rates from previous studies on other dinoflagellate prey species calculated at similar prey concentrations. Thus, P. shiwhaense might play diverse ecological roles in marine planktonic communities by having an advantage over competing phytoplankton in anti-predation against potential protistan grazers.

Myxozoan polar tubules display structural and functional variation

BACKGROUND

Myxozoa is a speciose group of endoparasitic cnidarians that can cause severe ecological and economic effects. Although highly reduced compared to free-living cnidarians, myxozoans have retained the phylum-defining stinging organelles, known as cnidae or polar capsules, which are essential to initiating host infection. To explore the adaptations of myxozoan polar capsules, we compared the structure, firing process and content release mechanism of polar tubules in myxospores of three Myxobolus species including M. cerebralis, the causative agent of whirling disease.

RESULTS

We found novel functions and morphologies in myxozoan polar tubules. High-speed video analysis of the firing process of capsules from the three Myxobolus species showed that all polar tubules rapidly extended and then contracted, an elasticity phenomenon that is unknown in free-living cnidarians. Interestingly, the duration of the tubule release differed among the three species by more than two orders of magnitude, ranging from 0.35 to 10 s. By dye-labeling the polar capsules prior to firing, we discovered that two of the species could release their entire capsule content, a delivery process not previously known from myxozoans. Having the role of content delivery and not simply anchoring suggests that cytotoxic or proteolytic compounds may be present in the capsule. Moreover, while free-living cnidarians inject most of the toxic content through the distal tip of the tubule, our video and ultrastructure analyses of the myxozoan tubules revealed patterns of double spirals of nodules and pores along parts of the tubules, and showed that the distal tip of the tubules was sealed. This helical pattern and distribution of openings may minimize the tubule mechanical weakness and improve resistance to the stress impose by firing. The finding that myxozoan tubule characteristics are very different from those of free-living cnidarians is suggestive of their adaptation to parasitic life.

CONCLUSIONS

These findings show that myxozoan polar tubules have more functions than previously assumed, and provide insight into their evolution from free-living ancestors.

Cyst-motile stage relationship, morphology, ultrastructure, and molecular phylogeny of the gymnodinioid dinoflagellate Barrufeta resplendens comb. nov., formerly known as Gyrodinium resplendens, isolated from the Gulf of Mexico

In the present study, we redescribed Gyrodinium resplendens through incubation of process bearing cysts extracted from sediment collected in the northern Gulf of Mexico. The morphology and ultrastructure of the motile stage and cyst stage were examined using light microscopy, scanning electron microscopy, and transmission electron microscopy and this revealed that the species should be transferred to the genus Barrufeta. This genus differs from other gymnodinioid genera in possessing a Smurf-cap apical structure complex (ASC) and currently encompasses only one species, Barrufeta bravensis. B. resplendens shows a Smurf-cap ASC that consists of three rows of elongated vesicles with small knobs in the middle one. B. resplendens is very similar to B. bravensis in cell morphology, but can be separated using the ultrastructure such as the shape and location of nucleus and pyrenoids, which highlights the importance of ultrastructure at inter-specific level in the genus Barrufeta. The unique cysts of B. resplendens are brown and process bearing, and have a tremic archeopyle with a zigzag margin on the dorsal side of the epicyst, and not polar as in cysts of Polykrikos. The cysts do not survive the palynological treatment used here and probably have a wide distribution. Maximum-likelihood and Bayesian inference were carried out based on partial large subunit ribosomal DNA (LSU rDNA) sequences. Molecular phylogeny supports that the genus Barrufeta is monophyletic, and that the genus Gymnodinium is polyphyletic. Our results suggest that details of the ASC together with ultrastructure are potential features to subdivide the genus Gymnodinium.

Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates

BACKGROUND

Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but this hypothesis has been difficult to test as P. lebouriae dwells in marine sand rife with potential genetic contaminants.

RESULTS

We applied spliced-leader targeted PCR (SLPCR) to obtain dinoflagellate-specific transcriptomes on single-cell isolates of P. lebouriae from marine sediments. Polykrikos lebouriae expressed nuclear-encoded photosynthetic genes that were characteristic of the peridinin-plastids of dinoflagellates, rather than those from a diatom of haptophyte. We confirmed these findings at the genomic level using multiple displacement amplification (MDA) to obtain a partial plastome of P. lebouriae.

CONCLUSION

From these data, we infer that P. lebouriae has retained the peridinin plastids ancestral for dinoflagellates as a whole, while its closest relatives have lost photosynthesis multiple times independently. We discuss these losses with reference to mixotrophy in polykrikoid dinoflagellates. Our findings demonstrate new levels of variation associated with the peridinin plastids of dinoflagellates and the usefulness of SLPCR approaches on single cell isolates. Unlike other transcriptomic methods, SLPCR has taxonomic specificity, and can in principle be adapted to different splice-leader bearing groups.

Isolation and characterisation of the trichocysts of the dinophyte Prorocentrum micans

Trichocyst-enriched fractions were isolated from the marine dinophyte Prorocentrum micans. Transmission electron microscopy revealed that most of the trichocysts were discharged and had elongated to long filaments. Some trichocysts were still condensed. Fragments of discharged trichocysts measured up to 20 μm in length and 260 nm in width, those still condensed measured up to 1 μm in width and 16 μm in length. A distinct banding pattern with a transversal periodicity of approximately 16-18 nm and a periodic longitudinal striation of 3-4 nm could be measured along the trichocyst filaments. At higher magnifications, a fragile, alveolated, net-like organisation became obvious which resembled the one shown for the trichocysts of ciliates. When trichocyst-enriched fractions were treated with sodium dodecyl sulfate and centrifuged subsequently, no trichocysts were registered any longer in the sodium dodecyl sulfate-insoluble fraction by electron microscopy. Sodium dodecyl sulfate polyacrylamide gel electrophoresis of trichocyst-enriched fractions and of the SDS-soluble fractions revealed a protein banding pattern which was dominated by polypeptides of 50-30, 12.5, and approximately 8.5 kDa. The polypeptide banding pattern deviated significantly from those registered for ejectisomes of cryptophytes and of the prasinophyte Pyramimonas grossii, for the Reb polypeptides which constitute the R-bodies of Caedibacter taeniospiralis, and also from the banding pattern of trichocysts of Paramecium. An antiserum directed against trichocysts of Paramecium did not cross-react with the polypeptides present in the trichocyst-enriched fraction of Prorocentrum micans.

Morphology, phylogeny, dynamics, and ichthyotoxicity of Pheopolykrikos hartmannii (Dinophyceae) isolates and blooms from New York, USA

We report on morphological observations, phylogenetic analyses, bloom dynamics, and ichthyotoxicity of the common but poorly characterized dinoflagellate Pheopolykrikos hartmannii (Zimmermann) Matsuoka et Fukuyo. From 2008 to 2010 in the Forge River Estuary, NY, USA, P. hartmannii bloomed during summer and early fall, achieving densities exceeding 8,000 cells · mL(-1) and often dominating microphytoplankton communities. Large subunit (LSU) and small subunit (SSU) rDNA sequences demonstrated that NY isolates of P. hartmannii sequences were 99%-100% identical to P. hartmannii isolates from eastern US and Korea. In both the LSU and SSU rDNA phylogenies, the clades containing P. hartmannii sequences were distinct sister clades to those composed of Polykrikos schwartzii and P. kofoidii. In the LSU rDNA phylogeny, however, the clade composed of P. hartmannii and a sequence of the photosynthetic Polykrikos lebourae was well separated from the clade composed of 10 entries of Polykrikos schwartzii and P. kofoidii. In addition, a gap of ~180 bases was observed when the LSU rDNA sequences of P. hartmannii were aligned with P. schwartzii and P. kofoidii but was not observed in the alignment between P. hartmannii and P. lebourae. Using scanning electron microscopy, several morphological features previously not reported for P. hartmannii were observed: a ventral groove located in the sulcus, a deep arc-like apical concavity within the area of apical groove, scale-like vesicles, and a shallow, completely enclosed, loop-like apical groove. Resting cysts with arrow-like surface spines were produced heterothallically by crossing clonal isolates and germinated single gymnoid cells. Finally, filtered and unfiltered bloom water from the Forge River and clonal cultures of P. hartmannii exhibited acute ichthyotoxicity to juvenile sheepshead minnows (Cyprinodon variegates) and aeration did not mitigate this effect, suggesting P. hartmannii is an ichthyotoxic, harmful alga.

Apical groove type and molecular phylogeny suggests reclassification of Cochlodinium geminatum as Polykrikos geminatum

Traditionally Cocholodinium and Gymnodinium sensu lato clade are distinguished based on the cingulum turn number, which has been increasingly recognized to be inadequate for Gymnodiniales genus classification. This has been improved by the combination of the apical groove characteristics and molecular phylogeny, which has led to the erection of several new genera (Takayama, Akashiwo, Karenia, and Karlodinium). Taking the apical groove characteristics and molecular phylogeny combined approach, we reexamined the historically taxonomically uncertain species Cochlodinium geminatum that formed massive blooms in Pearl River Estuary, China, in recent years. Samples were collected from a bloom in 2011 for morphological, characteristic pigment, and molecular analyses. We found that the cingulum in this species wraps around the cell body about 1.2 turns on average but can appear under the light microscopy to be >1.5 turns after the cells have been preserved. The shape of its apical groove, however, was stably an open-ended anticlockwise loop of kidney bean shape, similar to that of Polykrikos. Furthermore, the molecular phylogenetic analysis using 18S rRNA-ITS-28S rRNA gene cistron we obtained in this study also consistently placed this species closest to Polykrikos within the Gymnodinium sensu stricto clade and set it far separated from the clade of Cochlodinium. These results suggest that this species should be transferred to Polykrikos as Polykrikos geminatum. Our results reiterate the need to use the combination of apical groove morphology and molecular phylogeny for the classification of species within the genus of Cochlodinium and other Gymnodiniales lineages.

Life Cycle of the pseudocolonial dinoflagellate Polykrikos kofoidii (Gymnodiniales, Dinoflagellata)

The athecate, pseudocolonial polykrikoid dinoflag-ellates show a greater morphological complexity than many other dinoflagellate cells and contain not only elaborate extrusomes but sulci, cinguli, flagellar pairs, and nuclei in multiple copies. Among polykrikoids, Polykrikos kofoidii is a common species that plays an important role as a grazer of toxic planktonic algae but whose life cycle is poorly known. In this study, the main life cycle stages of P. kofoidii were examined and documented for the first time. The formation of gametes, 2-zooid-1-nucleus stages very different from vegetative cells, was observed and the process of gamete fusion, isogamy, was recorded. Karyogamy followed shortly after completed plasmogamy. A complex reorganization of furrows (cinguli and sulci) and flagella followed zygote formation, resulting in a 4-zooid zygote with one nucleus. The fate of zygotes under different nutritional conditions was also investigated; well-fed zygotes were able to reenter the vegetative cycle via meiotic divisions as indicated by nuclear cyclosis. However, nuclear cyclosis was preceded by a presumably mitotic division of the primary zygote nucleus which by definition would imply that P. kofoidii has a diplohaplontic life cycle. Nuclear cyclosis in germlings hatched from spiny resting cysts indicate that these cysts are of zygote origin (hypnozygotes). Hypnozygote formation, cyst hatching, the morphology of the germling (a 1-zooid cell), and its development into a normal pseudocolony are documented here for the first time. There is evidence that P. kofoidii has a system of complex heterothallism.

MORPHOLOGY AND MOLECULAR PHYLOGENY OF ANKISTRODINIUM GEN. NOV. (DINOPHYCEAE), A NEW GENUS OF MARINE SAND-DWELLING DINOFLAGELLATES FORMERLY CLASSIFIED WITHIN AMPHIDINIUM(1)

The classical athecate dinoflagellate genera (Amphidinium, Gymnodinium, Gyrodinium) have long been recognized to be polyphyletic. Amphidinium sensu lato is the most diverse of all marine benthic dinoflagellate genera; however, following the redefinition of this genus ∼100 species remain now of uncertain or unknown generic affiliation. In an effort to improve our taxonomic and phylogenetic understanding of one of these species, namely Amphidinium semilunatum, we re-investigated organisms from several distant sites around the world using light and scanning electron microscopy and molecular phylogenetic methods. Our results enabled us to describe this species within a new heterotrophic genus, Ankistrodinium. Cells of A. semilunatum were strongly laterally flattened, rounded-quadrangular to oval in lateral view, and possessed a small asymmetrical epicone. The sulcus was wide and characteristically deeply incised on the hypocone running around the antapex and reaching the dorsal side. The straight acrobase with hook-shaped end started at the sulcal extension and continued onto the epicone. The molecular phylogenetic results clearly showed that A. semilunatum is a distinct taxon and is only distantly related to species within the genus Amphidinium sensu stricto. The nearest sister group to Ankistrodinium could not be reliably determined.

Isolation, purification and some ultrastructural details of discharged ejectisomes of cryptophytes

The first successful isolation of discharged ejectisomes from pigmented cryptophytes is reported. Discharged ejectisomes from a Chroomonas and two Cryptomonas species were characterized by transmission electron microscopy using negative staining and freeze-etching. Tubular-shaped fragments of variable lengths and diameters were obtained which showed a paracrystalline lattice. Particle periodicities of 4.1 nm along the longitudinal axis and 3.1 nm in the transverse direction were measured in negative-stained fragments. The dimensions measured from freeze-etched ejectisome fragments were about 0.5-1 nm larger. Sodium dodecyl sulfate polyacrylamide gel electrophoresis revealed a protein banding pattern, dominated by polypeptides of 40-44, 23-25 and 16-18 kDa. The results are discussed in the context of what is currently known about extrusomes of protists.

BARRUFETA BRAVENSIS GEN. NOV. SP. NOV. (DINOPHYCEAE): A NEW BLOOM-FORMING SPECIES FROM THE NORTHWEST MEDITERRANEAN SEA(1)

The present study describes a new dinoflagellate genus, Barrufeta N. Sampedro et S. Fraga gen. nov., with one new species, B. bravensis Sampedro et S. Fraga sp. nov., isolated from the Costa Brava (NW Mediterranean Sea). The dinoflagellate was characterized at the genus and species levels by LM and EM; LSU and internal transcribed spacer (ITS) rDNA sequences; and HPLC analyses of the pigments, fatty acids, and possible presence of toxins of several cultured strains. The new Barrufeta species is oval shaped (22-35 μm long and 16-25 μm wide) and dorsoventrally flattened. It possesses numerous small chloroplasts that radiate from two large equatorially located pyrenoids and is a typical peridinin-containing dinoflagellate. The nucleus is in the anterior part of the epicone. The apical groove has a characteristic "Smurf-cap" shape that runs counterclockwise on the epicone and terminates on its right posterior part. B. bravensis is similar to the previously described species Gyrodinium resplendens Hulburt in its external morphology, but the original report of the latter lacked a description of the complete shape of the apical groove. It is therefore likely that some of the G. resplendens species reported in the literature are Barrufeta since they possess a Barrufeta-type apical groove. Fatty acids of Barrufeta were more similar to those of Karenia brevis than those obtained from other unarmored analyzed species including three species of Gymnodinium and Akashiwo sanguinea.

Dinoflagellate phylogeny as inferred from heat shock protein 90 and ribosomal gene sequences

Background

Interrelationships among dinoflagellates in molecular phylogenies are largely unresolved, especially in the deepest branches. Ribosomal DNA (rDNA) sequences provide phylogenetic signals only at the tips of the dinoflagellate tree. Two reasons for the poor resolution of deep dinoflagellate relationships using rDNA sequences are (1) most sites are relatively conserved and (2) there are different evolutionary rates among sites in different lineages. Therefore, alternative molecular markers are required to address the deeper phylogenetic relationships among dinoflagellates. Preliminary evidence indicates that the heat shock protein 90 gene (Hsp90) will provide an informative marker, mainly because this gene is relatively long and appears to have relatively uniform rates of evolution in different lineages.

Methodology/Principal Findings

We more than doubled the previous dataset of Hsp90 sequences from dinoflagellates by generating additional sequences from 17 different species, representing seven different orders. In order to concatenate the Hsp90 data with rDNA sequences, we supplemented the Hsp90 sequences with three new SSU rDNA sequences and five new LSU rDNA sequences. The new Hsp90 sequences were generated, in part, from four additional heterotrophic dinoflagellates and the type species for six different genera. Molecular phylogenetic analyses resulted in a paraphyletic assemblage near the base of the dinoflagellate tree consisting of only athecate species. However, Noctiluca was never part of this assemblage and branched in a position that was nested within other lineages of dinokaryotes. The phylogenetic trees inferred from Hsp90 sequences were consistent with trees inferred from rDNA sequences in that the backbone of the dinoflagellate clade was largely unresolved.

Conclusions/Significance

The sequence conservation in both Hsp90 and rDNA sequences and the poor resolution of the deepest nodes suggests that dinoflagellates reflect an explosive radiation in morphological diversity in their recent evolutionary past. Nonetheless, the more comprehensive analysis of Hsp90 sequences enabled us to infer phylogenetic interrelationships of dinoflagellates more rigorously. For instance, the phylogenetic position of Noctiluca, which possesses several unusual features, was incongruent with previous phylogenetic studies. Therefore, the generation of additional dinoflagellate Hsp90 sequences is expected to refine the stem group of athecate species observed here and contribute to future multi-gene analyses of dinoflagellate interrelationships.

Description of a new planktonic mixotrophic dinoflagellate Paragymnodinium shiwhaense n. gen., n. sp. from the coastal waters off Western Korea: morphology, pigments, and ribosomal DNA gene sequence

The mixotrophic dinoflagellate Paragymnodinium shiwhaense n. gen., n. sp. is described from living cells and from cells prepared by light, scanning electron, and transmission electron microscopy. In addition, sequences of the small subunit (SSU) and large subunit (LSU) rDNA and photosynthetic pigments are reported. The episome is conical, while the hyposome is hemispherical. Cells are covered with polygonal amphiesmal vesicles arranged in 16 rows and containing a very thin plate-like component. There is neither an apical groove nor apical line of narrow plates. Instead, there is a sulcal extension-like furrow. The cingulum is as wide as 0.2-0.3 x cell length and displaced by 0.2-0.3 x cell length. Cell length and width of live cells fed Amphidinium carterae were 8.4-19.3 and 6.1-16.0 microm, respectively. Paragymnodinium shiwhaense does not have a nuclear envelope chamber nor a nuclear fibrous connective (NFC). Cells contain chloroplasts, nematocysts, trichocysts, and peduncle, though eyespots, pyrenoids, and pusules are absent. The main accessory pigment is peridinin. The sequence of the SSU rDNA of this dinoflagellate (GenBank AM408889) is 4% different from that of Gymnodinium aureolum, Lepidodinium viride, and Gymnodinium catenatum, the three closest species, while the LSU rDNA was 17-18% different from that of G. catenatum, Lepidodinium chlorophorum, and Gymnodinium nolleri. The phylogenetic trees show that this dinoflagellate belongs within the Gymnodinium sensu stricto clade. However, in contrast to Gymnodinium spp., cells lack nuclear envelope chambers, NFC, and an apical groove. Unlike Polykrikos spp., which have a taeniocyst-nematocyst complex, P. shiwhaense has nematocysts without taeniocysts. In addition, P. shiwhaense does not have ocelloids in contrast to Warnowia spp. and Nematodinium spp. Therefore, based on morphological and molecular analyses, we suggest that this taxon is a new species, also within a new genus.

Re-classification of Pheopolykrikos hartmannii as Polykrikos (Dinophyceae) based partly on the ultrastructure of complex extrusomes

Athecate, pseudocolony-forming dinoflagellates have been classified within two genera of polykrikoids, Polykrikos and Pheopolykrikos, and different views about the boundaries and composition of these genera have been expressed in the literature. The photosynthetic polykrikoid Pheopolykrikos hartmannii, for instance, was originally described within Polykrikos and is now known to branch closely with several Polykrikos species in molecular phylogenetic analyses of ribosomal gene sequences. In this study, we report the first ultrastructural data for this species and demonstrate that Ph. hartmannii has all of the features that characterize the genus Polykrikos, including the synapomorphic "taeniocyst-nematocyst complex". We also demonstrate that the ultrastructure of the chloroplasts in Ph. hartmannii conforms to the usual peridinin-containing chloroplasts of most photosynthetic dinoflagellates, which improves inferences about the origin(s) and evolution of photosynthesis within the genus. After taking into account all of the ultrastructural data on polykrikoids presented here and in the literature, this species is re-classified to its original status as Polykrikos hartmannii.

Molecular phylogeny of ocelloid-bearing dinoflagellates (Warnowiaceae) as inferred from SSU and LSU rDNA sequences

Background

Dinoflagellates represent a major lineage of unicellular eukaryotes with unparalleled diversity and complexity in morphological features. The monophyly of dinoflagellates has been convincingly demonstrated, but the interrelationships among dinoflagellate lineages still remain largely unresolved. Warnowiid dinoflagellates are among the most remarkable eukaryotes known because of their possession of highly elaborate ultrastructural systems: pistons, nematocysts, and ocelloids. Complex organelles like these are evolutionary innovations found only in a few athecate dinoflagellates. Moreover, the taxonomy of warnowiids is extremely confusing and inferences about the evolutionary history of this lineage are mired by the absence of molecular phylogenetic data from any member of the group. In this study, we provide the first molecular phylogenetic data for warnowiids and couple them with a review of warnowiid morphological features in order to formulate a hypothetical framework for understanding character evolution within the group. These data also enabled us to evaluate the evolutionary relationship(s) between warnowiids and the other group of dinoflagellates with complex organelles: polykrikoids.

Results

Molecular phylogenetic analyses of SSU and LSU rDNA sequences demonstrated that warnowiids form a well-supported clade that falls within the more inclusive Gymnodinium sensu stricto clade. These data also confirmed that polykrikoids are members of the Gymnodinium sensu stricto clade as well; however, a specific sister relationship between the warnowiid clade and the polykrikoid clade was unresolved in all of our analyses. Nonetheless, the new DNA sequences from different isolates of warnowiids provided organismal anchors for several previously unidentified sequences derived from environmental DNA surveys of marine biodiversity.

Conclusion

Comparative morphological data and molecular phylogenetic data demonstrate that the polykrikoid and the warnowiid clade are closely related to each other, but the precise branching order within the Gymnodinium sensu stricto clade remains unresolved. We regard the ocelloid as the best synapomorphy for warnowiids and infer that the most recent common ancestor of polykrikoids and warnowiids possessed both nematocysts and photosynthetic plastids that were subsequently lost during the early evolution of warnowiids. Our summary of species and genus concepts in warnowiids demonstrate that the systematics of this poorly understood group is highly problematic and a comprehensive revision is needed.

MORPHOLOGY AND MOLECULAR PHYLOGENY OF A NEW MARINE SAND-DWELLING PROROCENTRUM SPECIES, P. TSAWWASSENENSE (DINOPHYCEAE, PROROCENTRALES), FROM BRITISH COLUMBIA, CANADA(1)

A new marine benthic, sand-dwelling Prorocentrum species from the temperate region of the Pacific coast of British Columbia, Canada, is described using LM and EM and molecular phylogenetic analyses. The cells have a broad oval shape, 40.0-55.0 μm long and 30.0-47.5 μm wide, and a wide U-shaped periflagellar area on the right thecal plate. The left thecal plate consists of a straighter apical outline in the form of a raised ridge. Five to six delicate apical spines in the center of the periflagellar area are present. The nucleus is located in the posterior region of the cell, and a conspicuous pusule is located in the anterior region of the cell. The cells have golden-brown chloroplasts with a compound, intrachloroplast pyrenoid that lacks a starch sheath. The thecal plates are smooth with round pores of two different sizes. The larger pores are arranged in a specific pattern of radial rows that are evenly spaced around the plate periphery and of irregular rows (or double rows) that form an incomplete "V" at the apical end of the plates. Large pores are absent in the center of the left and right thecal plates. The intercalary band is striated transversely and also has faint horizontal striations. Trichocysts and two types of mucocysts are present. The molecular phylogenetic position of Prorocentrum tsawwassenense sp. nov. was inferred using SSU rDNA sequences. This new species branched with high support in a Prorocentrum clade containing both benthic and planktonic species.

Comparative morphology and molecular phylogeny of Apicoporus n. Gen.: a new genus of marine benthic dinoflagellates formerly classified within Amphidinium

The composition of the dinoflagellate genus Amphidinium is currently polyphyletic and includes several species in need of re-evaluation using modern morphological and phylogenetic methods. We investigated a broad range of uncultured morphotypes extracted from marine sediments in the Eastern Pacific Ocean that were similar in morphology to Amphidinium glabrum Hoppenrath and Okolodkov. To determine the number of distinct species associated with this phenotypic diversity, we collected LM, SEM, TEM and small subunit ribosomal DNA sequence information from different morphotypes, including the previously described A. glabrum. Both comparative morphological and molecular phylogenetic data supported the establishment of a new genus, Apicoporus n. gen., including at least two species, A. glaber n. comb., and A. parvidiaboli n. sp. Apicoporus is characterized by having amphiesmal pores and an apical pore covered by a hook-like protrusion; neither of these characters has been observed in other athecate dinoflagellates. The posterior end of Apicoporus parvidiaboli possessed varying degrees of "horn formation", ranging from slight to prominent. By contrast, the posterior end of Apicoporus glaber was distinctively rounded and lacked evidence of horn formation. Although these species were previously interpreted to be obligate heterotrophs, TEM and epifluorescence microscopy demonstrated that some cells of both species had unusually small but otherwise typical dinoflagellate plastids. The number and density of plastids in any particular cell varied significantly in the genus, but the plastids were almost always concentrated at the posterior end of the cells or around the nucleus. The presence of cryptic photosynthetic plastids in these benthic species suggests that photosynthesis might be much more widespread in dinoflagellates than is currently assumed.