Partial Large Subunit rDNA Sequences Research Articles

Feeding behavior, spatial distribution and phylogenetic affinities of the heterotrophic dinoflagellate Oxyphysis oxytoxoides

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 62:279-287 (2011) - DOI: https://doi.org/10.3354/ame01474 Feeding behavior, spatial distribution and phylogenetic affinities of the heterotrophic dinoflagellate Oxyphysis oxytoxoides Myung Gil Park1, Hwayoung Lee1, Kwang Young Kim1, Sunju Kim2,* 1Department of Oceanography, Chonnam National University, Gwangju 500-757, Republic of Korea 2Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USA *Corresponding author. Email: sunjukim75@gmail.com ABSTRACT: We documented the abundance of the heterotrophic dinoflagellate Oxyphysis oxytoxoides Kofoid along the Korean coast, cultured it (food source: the marine ciliate Myrionecta rubra Jankowski [= Mesodinium rubrum Lohmann]), sequenced its nuclear-encoded large-subunit (LSU) rDNA, and resolved its phylogenetic relationship within the Dinophysiales. Abundance was low, usually <9.7 × 103 cells l–1, in samples from 2005 and 2006. It co-occurred with the mixotrophic dinoflagellate Dinophysis acuminata, possibly indicating a common pool of prey. Growth on M. rubra reached a density of 38 × 105 cells l–1. Observations on live cells from our established cultures revealed that O. oxytoxoides uses a peduncle to suck up the cell contents of M. rubra, the number of food vacuoles increasing as feeding proceeds. No regional variability was found in partial LSU rDNA sequences (domains D1–D2) of our strains, despite different sampling sites and dates. Phylogenetic analysis, based on LSU rDNA, showed that while Amphisolenia forms an early divergent basal group in the Dinophysiales, the other dinophysoids form 2 separate groups: (1) Oxyphysis and Phalacroma, and (2) Histioneis, Ornithocercus, Citharistes and Dinophysis. The presence of a peduncle in several genera, and the widespread distribution of pedunculate dinophysoids, indicate that these species may be fundamentally heterotrophic with a common feeding mechanism. Our results shed light on the feeding ecology and phylogenetic position of O. oxytoxoides. KEY WORDS: Dinophysiales · Myrionecta rubra · Oxyphysis oxytoxoides · Peduncle feeding · Phylogeny Full text in pdf format Supplementary material PreviousNextCite this article as: Park MG, Lee H, Kim KY, Kim S (2011) Feeding behavior, spatial distribution and phylogenetic affinities of the heterotrophic dinoflagellate Oxyphysis oxytoxoides. Aquat Microb Ecol 62:279-287. https://doi.org/10.3354/ame01474 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 62, No. 3. Online publication date: February 08, 2011 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2011 Inter-Research.

Heterogeneity of LSU rDNA sequences and morphology of Gymnodinium catenatum dinoflagellate strains in Bahia Concepcion, Gulf of California, Mexico

We report the large subunit (LSU) rDNA sequences and morphology of several Gymnodinium catenatum dinoflagellate strains isolated from Bahia Concepcion, Mexico. PCR amplifications of the D1-D2 fragment of the nuclear LSU rDNA gene resulted in a single product of � 889 bp. A phylogenetic tree was constructed from the partial LSU rDNA (350 bp) sequences from six strains of G. catenatum isolated from the bay and 12 isolates from around the world. Strains from the bay grouped within the G. catenatum clade; however, a constant characteristic of G. catenatum strains from the bay is that, at position � 453, a single nucleotide polymorphism was observed, presenting cytosine instead of guanine. This single base polymorphism could indicate a mutation or genetic isolation from other G. catenum populations. It is suggested that the Western Pacific could be the ancestral population of this species. Significant differences were found between cell length (CL), cell width (CW) and CW/CL ratios in laboratory cultures in the late exponential growth phase. Average CL varied between 41 and 53.69 mm, with a range between 26.94 and 69.99 mm; average CW varied between 33.75 and 40.68 mm, with a range between 25.04 and 54.73 mm; the average CW/CL varied between 0.76 and 0.97 mm, with a range between 0.49 and 1.27 mm. Cingulum thickness was between 3 and 4.11 mm, with a range between 1.97 and 6.74 mm. Cell size varied with the length of the chain and position in the chain.

Molecular phylogeny of the Siphonocladales (Chlorophyta: Cladophorophyceae)

The Siphonocladales are tropical to warm-temperate, marine green macro-algae characterized by a wide variety of thallus morphologies, ranging from branched filaments to pseudo-parenchymatous plants. Phylogenetic analyses of partial large subunit (LSU) rDNA sequences sampled from 166 isolates revealed nine well-supported siphonocladalean clades. Analyses of a concatenated dataset of small subunit (SSU) and partial LSU rDNA sequences greatly clarified the phylogeny of the Siphonocladales. However, the position of the root of the Siphonocladales could not be determined unambiguously, as outgroup rooting and molecular clock rooting resulted in a different root placement. Different phylogenetic methods (likelihood, parsimony and distance) yielded similar tree topologies with comparable internal node resolution. Likewise, analyses under more realistic models of sequence evolution, taking into account differences in evolution between stem and loop regions of rRNA, did not differ markedly from analyses using standard four-state models. The molecular phylogeny revealed that all siphonocladalean architectures may be derived from a single Cladophora-like ancestor. Parallel and convergent evolution of various morphological characters (including those traditionally employed to circumscribe the families and genera) have occurred in the Siphonocladales. Consequently, incongruence with traditional classifications, including non-monophyly in all families and most genera, was shown.

Ultrastructure and large subunit rDNA sequences of Lepidodinium viride reveal a close relationship to Lepidodinium chlorophorum comb. nov. (=Gymnodinium chlorophorum)

SUMMARYThe ultrastructure of the green dinoflagellate Lepididodinium viride M. M. Watanabe, S. Suda, I. Inouye Sawaguchi et Chihara was studied in detail. The nuclear envelope possessed numerous chambers each furnished with a nuclear pore, a similar arrangement to that found in other gymnodinioids. The flagellar apparatus was essentially identical to Gymnodinium chlorophorum Elbrächter et Schnepf, a species also containing chloroplasts of chlorophyte origin. Of particular interest was the connection of the flagellar apparatus to the nuclear envelope by means of both a fiber and a microtubular extension of the R3 flagellar root. This feature has not been found in other dinoflagellates and suggests a close relationship between these two species. This was confirmed by phylogenetic analysis based on partial sequences of the large subunit (LSU) rDNA gene of L. viride, G. chlorophorum and 16 other unarmoured dinoflagellates, including both the ‘type’ culture and a new Tasmanian isolate of G. chlorophorum. These two isolates had identical sequences and differed from L. viride by only 3.75% of their partial LSU sequences, considerably less than the difference between other Gymnodinium species. Therefore, based on ultrastructure, pigments and partial LSU rDNA sequences, the genus Lepidodinium was emended to encompass L. chlorophorum comb. nov.

Cooccurring plants forming distinct arbuscular mycorrhizal morphologies harbor similar AM fungal species

Arbuscular mycorrhizal (AM) fungal spores were isolated from field transplants and rhizosphere soil of Hedera rhombea (Miq) Bean and Rubus parvifolius L., which form Paris-type and Arum-type AM, respectively. DNA from the spore isolates was used to generate molecular markers based on partial large subunit (LSU) ribosomal RNA (rDNA) sequences to determine AM fungi colonizing field-collected roots of the two plant species. Species that were isolated as spores and identified morphologically and molecularly were Gigaspora rosea and Scutellospora erythropa from H. rhombea, Acaulospora longula and Glomus etunicatum from R. parvifolius, and Glomus claroideum from both plants. The composition of the AM fungal communities with respect to plant trap cultures was highly divergent between plant species. Analysis of partial LSU rDNA sequences amplified from field-collected roots of the two plant species with PCR primers designed for the AM fungi indicated that both plants were colonized by G. claroideum, G. etunicatum, A. longula, and S. erythropa. G. rosea was not detected in the field-collected roots of either plant species. Four other AM fungal genotypes, which were not isolated as spores in trap cultures from the two plant species, were also found in the roots of both plant species; two were closely related to Glomus intraradices and Glomus clarum. One genotype, which was most closely related to Glomus microaggregatum, was confined to R. parvifolius, whereas an uncultured Glomeromycotan fungus occurred only in roots of H. rhombea. S. erythropa was the most dominant fungus found in the roots of H. rhombea. The detection of the same AM fungal species in field-collected roots of H. rhombea and R. parvifolius, which form Paris- and Arum-type AM, respectively, shows that AM morphology in these plants is strongly influenced by the host plant genotypes as appears to be the case in many plant species in natural ecosystems, although there are preferential associations between the hosts and colonizing AM fungi in this study.

Nucleotide diversity within and between four species of Laminaria (Phaeophyceae) analysed using partial LSU and ITS rDNA sequences and AFLP

In order to estimate the nucleotide diversity of the four kelp species Laminaria digitata, L. hyperborea, L. saccharina and L. faeroensis, three approaches were used. First we sequenced 1320 base pairs (bp) of nuclear-encoded large subunit (LSU) rDNA, which included some of the most variable domains. These sequences discriminated between L. digitata, L. hyperborea and L. saccharina, but L. faeroensis was identical to L. saccharina. A phylogeny inferred based on 672 bp of the nuclear-encoded non-coding internal transcribed spacer regions (ITS1 and ITS2) rDNA, which are more variable than LSU rDNA, likewise failed to resolve a monophyletic L. saccharina with respect to L. faeroensis. Thirdly, we tested the usefulness of the amplified fragment length polymorphism (AFLP) technique to provide a resolved phylogeny for 43 Laminaria specimens. Laminaria digitata and L. hyperborea were resolved as strongly supported monophyletic groups. A third robust clade consisted of L. saccharina plus L. faeroensis. Within this clade, L. faeroensis samples were grouped with bootstrap support of 80%, but the L. saccharina clade was less well supported. The AFLP data in combination with rDNA sequences indicated subspecies status for L. faeroensis. AFLP analyses of different morphotypes of L. digitata and L. saccharina from Danish coastal waters did not reveal any differences. However, L. digitata from the Faroe Islands was genetically distinct from other samples.

Cryptadelphia (Trichosphaeriales), a new genus for holomorphs with Brachysporium anamorphs and clarification of the taxonomic status of Wallrothiella

The genus Cryptadelphia (Trichosphaeriales) is described for the presumed teleomorphs of six species of the dematiaceous hyphomycete genus Brachysporium. Cryptadelphia is characterized by the production of dark, leathery perithecia with two-layered walls, cylindrical, long-stipitate asci with eight hyaline, initially aseptate but ultimately 1-septate as-cospores. Zignoëlla groenendalensis is transferred to Cryptadelphia with Wallrothiella melanostigmoides as a synonym. Five new species, i.e., Cryptadelphia abietis, C. brevior, C. obovata, C. pendulispora and C. polyseptata, with their respective Brachysporium anamorphs, are described and illustrated. Phylogenetic analysis of partial large subunit rDNA sequences of two species supports the monophyly of Cryptadelphia and suggests a relationship with the Trichosphaeriales. The monophyly of the Trichosphaeriaceae and the relationships between the Trichosphaeriaceae, Annula-tascaceae and the Sordariales can be questioned, but a conclusive assessment requires phylogenetic analysis of more related taxa. The genus Wallrothiella is redescribed based on new collections of W. congregata and is characterized by the production of tiny, globose ascospores in cylindrical asci. The new collection is proposed as a neotype for the genus.

Cryptadelphia (Trichosphaeriales), a New Genus for Holomorphs with Brachysporium Anamorphs and Clarification of the Taxonomic Status of Wallrothiella

The genus Cryptadelphia (Trichosphaeriales) is described for the presumed teleomorphs of six species of the dematiaceous hyphomycete genus Brachysporium. Cryptadelphia is characterized by the production of dark, leathery perithecia with two-layered walls, cylindrical, long-stipitate asci with eight hyaline, initially aseptate but ultimately 1-septate as-cospores. Zignoëlla groenendalensis is transferred to Cryptadelphia with Wallrothiella melanostigmoides as a synonym. Five new species, i.e., Cryptadelphia abietis, C. brevior, C. obovata, C. pendulispora and C. polyseptata, with their respective Brachysporium anamorphs, are described and illustrated. Phylogenetic analysis of partial large subunit rDNA sequences of two species supports the monophyly of Cryptadelphia and suggests a relationship with the Trichosphaeriales. The monophyly of the Trichosphaeriaceae and the relationships between the Trichosphaeriaceae, Annula-tascaceae and the Sordariales can be questioned, but a conclusive assessment requires phylogenetic analysis of more related taxa. The genus Wallrothiella is redescribed based on new collections of W. congregata and is characterized by the production of tiny, globose ascospores in cylindrical asci. The new collection is proposed as a neotype for the genus.

Morphology, toxin composition and LSU rDNA phylogeny of Alexandrium minutum (Dinophyceae) from Denmark, with some morphological observations on other European strains

The morphology of Alexandrium minutum Halim from Denmark was studied and compared to the morphology of material from Portugal, Spain, France and Ireland. Strains from Denmark and the French coast of the English Channel differed from the typical minutum morphotype by the absence of a ventral pore. Cells without a pore also dominated field material from Ireland but a small fraction (6%) did have a pore. Many cells had a heavily areolated theca. In the exponential growth phase, the PSP-toxin profile of the Danish strain of A. minutum was dominated by C1 and C2 (up to 70%), whereas GTX2 and 3 made up more than 17%, and STX almost 13%. Cells entering the stationary phase contained 30% STX with a concomitant decrease of the other toxins. Partial large subunit rDNA sequences (664 bp) confirmed that the Danish A. minutum strain clusters together with other European strains of this species, and a strain from Australia. However, sequencing of this part of the gene did not resolve intraspecific relationships and could not differentiate populations with or without pore and/ or different toxin signatures. A strain from New Zealand had a remarkably high sequence divergence (up to 6%) compared to the other strains of A. minutum and its identity should be further investigated. A distribution map of A. minutum has been compiled and it is suggested that A. minutum and A. angustitabulatum Taylor are conspecific.

Nuclear rDNA sequences from Ballia prieurii support recognition of Balliopsis gen. nov. in the Batrachospermales (Florideophyceae, Rhodophyta)

Nuclear small-subunit and partial large-subunit rDNA sequences were determined for the freshwater rhodophyte species Ballia prieurii, from northern Brazil, to assess its relationship to the marine species that have recently been transferred to a new order, Balliales, in the Florideophyceae. Ballia prieurii unequivocally associated with species of the freshwater order Batrachospermales, rather than with the marine Balliales, in all molecular analyses. In addition to habitat, asexual reproduction by monosporangia in the freshwater species of Ballia is consistent with inclusion in the Batrachospermales and has not been reported for any marine Ballia species, which reproduce exclusively by asexual tetrasporangia. As B. prieurii is distinct in morphological and molecular features from all other members of Batrachospermales, a new genus Balliopsis G.W. Saunders & Necchi gen. nov. is proposed to accommodate this species, which becomes Balliopsis prieurii (Kützing) G.W. Saunders & Necchi comb. nov. Previously published morphological and anatomical observations indicate that a second freshwater species of Ballia, B. pinnulata, is clearly related to Balliopsis prieurii and it too is transferred to the new genus. The familial affinities of Balliopsis are discussed, but Balliopsis is left as a genus Incertae sedis within the Batrachospermales.

Phylogeny of some of the major genera of dinoflagellates based on ultrastructure and partial LSU rDNA sequence data, including the erection of three new genera of unarmoured dinoflagellates

Evidence from partial large-subunit (LSU) rDNA sequencing has been combined with ultrastructure, including details of the flagellar apparatus, in a number of phototrophic dinoflagellates, with the aim of trying to solve some of the most pressing taxonomic problems and to contribute to an improved understanding of the phylogeny within the group. Special attention has been paid to the unarmoured (naked) genera, many of which were described during the 1800s or early 1900s and whose taxonomy is artificial and misleading. This is particularly unsatisfactory because many of the species cause extensive plankton blooms, fish kills and other harmful events. Our studies have indicated that the path of the so-called apical groove (acrobase) is of particular importance for the taxonomy of the unarmoured genera of dinoflagellates. Features presently used to characterize many of the genera, such as the relative size of the epicone and hypocone, are misleading. Our data have resulted in the splitting of the large genus Gymnodinium into four genera. The fish-killing species are confined to two genera, Karenia G. Hansen & Moestrup gen. nov. and Karlodinium J. Larsen gen. nov. The paralytic shellfish poisoning-producing species Gymnodinium catenatum is retained within Gymnodinium, together with a number of harmless species. The fourth genus, Akashiwo G. Hansen & Moestrup gen. nov., presently comprises only the large nontoxic species previously known as Gymnodinium sanguineum. The genus Gyrodinium is redefined. The genus Amphidinium is artificial, but more data are needed before redescription of the genus can be made with any confidence. Within the armoured dinoflagellates, LSU and previously published small-subunit rDNA data show the Gonyaulacales to be a natural group. Peridiniella catenata, sometimes included in the Gonyaulacales based on gross morphology, falls outside this order both genetically and ultrastructurally. Based on the DNA data, the genus Peridinium appears to be artificial. Ultrastructure as well as gene sequences confirm that the genus Heterocapsa is unusual, since it includes both apparently unarmoured species (but with very thin plates) and armoured species.

Molecular phylogeny of European Fucales (Phaeophyceae) based on partial large-subunit rDNA sequence comparisons

Partial nucleotide sequences from the 5′ terminus of the nuclear large-subunit (LSU) ribosomal DNA gene (domains C1, C2, D1, and D2) have been determined for ten fucalean species representing eight genera to assess their interfamilial and intergeneric relationships: Ascophyllum nodosum (Linnaeus) Le Jolis, Fucus vesiculosus Linnaeus, Pelvetia canaliculata (Linnaeus) Decaisne et Thuret, Himanthalia elongata (Linnaeus) S.F. Gray, Bifurcaria bifitrcata Ross, Cystoseira humilis Kützing, C. nodicaulis (Withering) M. Roberts, C. tamariscifolia (Hudson) Papenfuss, Halidrys siliquosa (Linnaeus) Lyngbye, and Sargassum muticum (Yendo) Fensholt. Sequences of five other species were used as an outgroup: three from Laminariales [Chorda filum (Linnaeus) Stackhouse, Macrocystis pyrifera (Linnaeus) C. Agardh, and Saccorhiza polyschides (Lightfoot) Batters], one from Sphacelariales [Cladostephus spongiosus (Hudson) C. Agardh,] and one from Cutleriales [Cutleria multifida (Smith) Greville as both its gametophytic and sporophytic (‘Aglaozonia parvula’) phases]. Sequences were analyzed using neighbor-joining (distance) and PAUP (parsimony) methods. Low homoplasy level and suitable divergence in the sequence data, especially within the most divergent domains D1 and D2, provided suitable information for assessing phylogenetic relationships among the fucalean families, genera, and species of Cystoseira. European Fucales appeared as a monophyletic group well supported by high bootstrap proportions. Two robust clades, one corresponding to the families Fucaceae and Himanthaliaceae, and the other to a Cystoseiraceae–Sargassaceae group, were obtained. Fucacean genera were strongly supported as a monophyletic group. Himanthalia elongata of the monotypic Himanthaliaceae, the family status of which is confirmed, appeared as the sister group of Fucaceae. In the Cystoseiraceae–Sargassaceae group, the Sargassum relative position was not well defined vs the robust Halidrys–Bifurcaria–Cystoseira clade. The genus Cystoseira appeared polyphyletic. Within the outgroup, the suspicion that the Laminariales is not monophyletic seems to be confirmed; more surprising was the position of Cutleria, which appeared as the sister taxon of Saccorhiza and needs further investigation.

Taxonomic Identification of Foraminifera Using Ribosomal DNA Sequences

Taxonomic Identification of Foraminifera Using Ribosomal DNA Sequences