Intrageneric Variability Between the Chloroplast Genomes of Trachelomonas grandis and Trachelomonas volvocina and Phylogenomic Analysis of Phototrophic Euglenoids

The latest studies of chloroplast genomes of phototrophic euglenoids yielded different results according to intrageneric variability such as cluster arrangement or diversity of introns. Although the genera Euglena and Monomorphina in those studies show high syntenic arrangements at the intrageneric level, the two investigated Eutreptiella species comprise low synteny. Furthermore Trachelomonas volvocina show low synteny to the chloroplast genomes of the sister genera Monomorphina aenigmatica, M. parapyrum, Cryptoglena skujae, Euglenaria anabaena, Strombomonas acuminata, all of which were highly syntenic. Consequently, this study aims at the analysis of the cpGenome of Trachelomonas grandis and a comparative examination of T. volvocina to investigate whether the cpGenomes are of such resemblance as could be expected for a genus within the Euglenaceae. Although these analyses resulted in almost identical gene content to other Euglenaceae, the chloroplast genome showed significant novelties: In the rRNA operon, we detected group II introns, not yet found in any other cpGenome of Euglenaceae and a substantially heterogeneous cluster arrangement in the genus Trachelomonas. The phylogenomic analysis with 84 genes of 19 phototrophic euglenoids and 18 cpGenome sequences from Chlorophyta and Streptophyta resulted in a well‐supported cpGenome phylogeny, which is in accordance to former phylogenetic analyses.     

PHYLOGENETIC ANALYSIS OF THE GENUS EUGLENA (EUGLENOPHYCEAE) WITH PARTICULAR REFERENCE TO THE TYPE SPECIES EUGLENA VIRIDIS1

Euglena viridis (subgenus Euglena) serves as the type species for the genus Euglena. In this study, molecular phylogenetic analyses using a small subunit (SSU) and a combined SSU–partial large subunit rDNA data set for members of the genus Euglena showed that strains identified as E. viridis on the basis of morphology are distributed between two separate nonsister clades. Although all the E. viridis strains examined were morphologically indistinguishable and possessed spherical mucocysts and stellate chloroplasts with one paramylon center, there was a high degree of sequence divergence between the E. viridis strains in different clades, making this a cryptic species. Like E. viridis, all taxa from the subgenus Euglena are characterized by having one or more stellate chloroplasts with paramylon grains clustered around the center of the chloroplast. These additional taxa were divided into four clades in all the molecular analyses. Strains of Euglena stellata formed two nonsister clades whose members had a single aggregate chloroplast with paramylon center and spindle‐shaped mucocysts. A geniculata clade included species with one or two stellate chloroplasts with paramylon centers and spherical mucocysts, and the cantabrica clade had members with one stellate chloroplast with paramylon center and spherical mucocysts often arranged in spiral rows. Interspersed among these were three additional clades bearing taxa from the subgenus Calliglena that contains members with discoid plastids and pyrenoids that may or may not be capped with paramylon. These taxa formed a laciniata clade, mutabilis clade, and gracilis clade. This study demonstrates that E. viridis and E. stellata are cryptic species that can only be distinguished at the molecular level. Because E. viridis is the designated type species for the genus Euglena, we designated an epitype for E. viridis.     

PHYLOGENY AND SYSTEMATICS OF THE GENUS MONOMORPHINA (EUGLENACEAE) BASED ON MORPHOLOGICAL AND MOLECULAR DATA1

Morphological studies of 16 strains belonging to the genus Monomorphina revealed a single, parietal, orbicular chloroplast in their cells. The chloroplast has a tendency to be perforated and disintegrates in aging populations and thus may appear to be many chloroplasts under the light microscope. A single chloroplast in the cells of Cryptoglena skujae is also parietally located and highly perforated. It never forms a globular and closed structure, but is open from the side of the furrow, resembling the letter C. We have verified the Monomorphina pyrum group (M. pyrum–like) on the basis of phylogenetic analysis of SSU rDNA and morphological data. The strain CCAC 0093 (misidentified as M. reeuwykiana) diverges first on the SSU rDNA phylogenetic tree. The rest of the M. pyrum–like strains form a tight cluster, subdivided into several smaller ones. Because morphological differences between the M. pyrum–like strains (including the strain CCAC 0093) do not conform to the tree topology, we suggest that they all (except the strain CCAC 0093) belong to M. pyrum. We designate a new species, M. pseudopyrum, for the strain CCAC 0093, solely on the basis of molecular characters. We also suggest that M. reeuwykiana and similar species should stay in Phacus and Lepocinclis unless detailed molecular and morphological studies show otherwise. Emended diagnoses of the genera Monomorphina and Cryptoglena and the species M. aenigmatica are also proposed, as well as the delimitation of an epitype for M. pyrum, the type species for the genus Monomorphina.     

Cryptic Speciation in the Genus Cryptoglena (Euglenaceae) Revealed by Nuclear and Plastid SSU and LSU rRNA Gene

The photosynthetic euglenoid genus Cryptoglena is differentiated from other euglenoid genera by having a longitudinal sulcus, one chloroplast, two large trough‐shaped paramylon plates positioned between the chloroplast and pellicle, and lack of metaboly. The genus contains only two species. To understand genetic diversity and taxonomy of Cryptoglena species, we analyzed molecular and morphological data from 25 strains. A combined data set of nuclear SSU and LSU and plastid SSU and LSU rRNA genes was analyzed using Bayesian, maximum likelihood, maximum parsimony, and distance (neighbor joining) methods. Although morphological data of all strains showed no significant species‐specific pattern, molecular data segregated the taxa into five clades, two of which represented previously known species: C. skujae and C. pigra, and three of which were designated as the new species, C. soropigra, C. similis, and C. longisulca. Each species had unique molecular signatures that could be found in the plastid SSU rRNA Helix P23_1 and LSU rRNA H2 domain. The genetic similarity of intraspecies based on nr SSU rDNA ranged from 97.8% to 100% and interspecies ranged from 95.3% to 98.9%. Therefore, we propose three new species based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.     

MORPHOLOGY AND MOLECULAR PHYLOGENY OF ANKISTRODINIUM GEN. NOV. (DINOPHYCEAE), A NEW GENUS OF MARINE SAND‐DWELLING DINOFLAGELLATES FORMERLY CLASSIFIED WITHIN AMPHIDINIUM1

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.     

LIGHT MICROSCOPY AND ELECTRON MICROSCOPY OF NEPHROSELMIS SPINOSA SP. NOV. (PRASINOPHYCEAE,CHLOROPHYTA)1

Nephroselmis spinosa Suda sp. nov. is described based on LM and EM observations. Two strains of N. spinosa (S222 and SD959‐3) were isolated from sand samples collected from the northwest coast of western Australia. The cells were remarkably right–left flattened and appeared ellipse or bean‐shaped when viewed from their right or left side. A single, parietal, crescent chloroplast was pale green to yellowish green and contained one conspicuous eyespot in its anterior ventral edge near the base of the short flagellum. A pyrenoid with three starch plates was located at the dorsal of the chloroplast. The cells divided by transverse binary cell division, as is common in other species of this genus. This alga possessed four types of body scales, and three scale types were similar to N. olivacea Stein and N. astigmatica Inouye & Pienaar. However, the fourth and outermost scale type was distinctive because although it was a spiny stellate scale with nine spines, one of them extended about 1 μm and was slightly curved with a hook at the end. This scale morphology, an important taxonomic characteristic, has never been described for the genus Nephroselmis. The cell's morphology, pyrenoid structure, hair scales, and cell size were distinctive from previously described Nephroselmis species, and its unique scale characteristic led me to name this newly proposed species “spinosa,” meaning spiny.     

Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon‐rich Analyses of Five Genes

Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear‐encoded genes (nSSU, nLSU, hsp90), one chloroplast‐encoded gene (cpSSU) and one nuclear‐encoded chloroplast gene (psbO) to estimate phylogenetic relationships among 59 photosynthetic euglenid species. Our results were consistent with previous works; most genera were monophyletic, except for the polyphyletic genus Euglena, and the paraphyletic genus Phacus. We also analyzed character evolution in photosynthetic euglenids using our phylogenetic tree and eight morphological traits commonly used for generic and species diagnoses, including: characters corresponding to well‐defined clades, apomorphies like presence of lorica and mucilaginous stalks, and homoplastic characters like rigid cells and presence of large paramylon grains. This research indicated that pyrenoids were lost twice during the evolution of phototrophic euglenids, and that mucocysts, which only occur in the genus Euglena, evolved independently at least twice. In contrast, the evolution of cell shape and chloroplast morphology was difficult to elucidate, and could not be unambiguously reconstructed in our analyses.     

Phylogenetic Reappraisal of the Genus Monomorphina (Euglenophyceae) Based on Molecular and Morphological Data

A morphological and molecular examination of the genus Monomorphina was conducted on 46 strains isolated mainly from Korea. The strains were divided into two types based on morphological data: Monomorphina aenigmatica and M. pyrum ‐ like species. Phylogenetic analysis based on a combined data set of nuclear SSU and LSU and plastid SSU and LSU rDNA showed that the strains could be divided into eight clades: Clade A of M. aenigmatica, Clade B of the isolates (M. pyropsis) from Michigan, USA, Clade C of M. pseudopyrum, Clade D of the isolates (M. pyroria) from Bremen, Germany, Clade E of M. soropyrum, Clade F of M. pyriformis, Clade G of M. parapyrum, and Clade H of M. pyrum. Six of these clades came from strains that would be considered M. pyrum sensu Kosmala et Zakry?, one of which could be recognized as a traditional species (M. pyrum) and five were designated as new species; each species had unique molecular signatures at nr SSU rDNA helix 17 and 17′ and spacer E23_14′‐E23_15. The species of Monomorphina had a wide range of genetic diversity with interspecies sequence similarity of 85.6%–97.1% and intraspecies similarity of 96.4%–99.9%. Our results suggested that genetic diversity found in the M. pyrum complex justifies the recognition of a minimum of eight species within this genus, based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.     

TAXONOMIC REVISIONS OF MORPHOLOGICALLY SIMILAR SPECIES FROM TWO EUGLENOID GENERA: EUGLENA (E. GRANULATA AND E. VELATA) AND EUGLENARIA (EU. ANABAENA,EU. CAUDATA,AND EU. CLAVATA)1

The establishment of epitypes (together with the emended diagnoses) for three species of Euglenaria Karnkowska, E. W. Linton et Kwiatowski [Eu. anabaena (Mainx) Karnkowska et E. W. Linton; Eu. caudata (Hübner) Karnkowska et E. W. Linton; and Eu. clavata (Skuja) Karnkowska et E. W. Linton] and two species of Euglena Ehrenberg [E. granulata (Klebs) Schmitz and E. velata Klebs] was achieved due to literature studies, verification of morphological diagnostic features (cell size, cell shape, number of chloroplasts, the presence of mucocysts), as well as molecular characters (SSU rDNA). Now all these species are easy to identify and distinguish, despite their high morphological similarity, that is, spindle‐shaped (or cylindrically spindle‐shaped) cells and parietal, lobed chloroplasts with a single pyrenoid, accompanied by bilateral paramylon caps located on both sides of the chloroplast. E. granulata is the only species in this group that has spherical mucocysts. E. velata is distinguished by the largest cells (90–150 μm) and has the highest number of chloroplasts (>30). Eu. anabaena has the fewest chloroplasts (usually 3–6), and its cells are always (whether the organism is swimming or not) spindle‐shaped or cylindrically spindle‐shaped, in contrast to the cells of Eu. clavata, which are club‐shaped (clavate) while swimming and only after stopping change to resemble the shape of a spindle or a cylindrical spindle; Eu. clavata has numerous chloroplasts (15–20). Eu. caudata is characterized by asymmetrical spindle‐shaped (fusiform) cells, that is, with an elongated rear section and a shorter front section; the number of chloroplasts normally ranges from 7 to 15.     

Observations on Purpureofilum apyrenoidigerum gen. et sp. nov. from Australia and Bangiopsis subsimplex from India (Stylonematales, Bangiophyceae, Rhodophyta)

Purpureofilum apyrenoidigerum gen et sp. nov. was obtained from a mangrove habitat in New South Wales, Australia. It had unbranched uniseriate to multiseriate filaments less than 1 mm tall, with a unicellular base. Each cell had a single multilobed parietal chloroplast without a pyrenoid. During reproduction vegetative cells were discharged directly as monospores that remained motile for several hours after release. Spores with long tails moved more slowly (0.053–0.195 μm sχ) than spores without tails (0.43–1.76 μm s′¹). Phylo‐genetic analysis of sequences of the small subunit of the nuclear‐encoded rRNA and plastid‐encoded ribu‐lose bisphosphate carboxylase/oxygenase genes revealed that Purpureofilum is a member of the Stylonematales and is most closely related to the filamentous genus Bangiopsis. Bangiopsis differs from Purpureofilum by having longer (to 5 mm) multiseriate filaments, cells containing a stellate chloroplast, a conspicuous central pyrenoid, and monospores often formed in packets. Monospores of Bangiopsis were also motile. Transmission electron microscopy investigation of Purpureofilum and Bangiopsis revealed that the Golgi complexes are associated only with rough endo‐plasmic reticulum and that the plastid contains a peripheral thylakoid; this combination of features being the same as in all other multicellular members of the Stylonematales. The low molecular weight carbohydrates of Purpureofilum and Bangiopsis were digenea‐side and sorbitol, which were present in most other Stylonematales.     

Morphology and phylogeny of a new wall‐less freshwater volvocalean flagellate,Hapalochloris nozakii gen. et sp. nov. (Volvocales,Chlorophyceae)

New strains of a wall‐less unicellular volvocalean flagellate were isolated from a freshwater environment in Japan. Observations of the alga, described here as Hapalochloris nozakii Nakada, gen. et sp. nov., were made using light, fluorescence, and electron microscopy. Each vegetative cell had two flagella, four contractile vacuoles, and a spirally furrowed cup‐shaped chloroplast with an axial pyrenoid, and mitochondria located in the furrows. Based on the morphology, H. nozakii was distinguished from other known wall‐less volvocalean flagellates. Under electron microscopy, fibrous material, instead of a cell wall and dense cortical microtubules, was observed outside and inside the cell membrane, respectively. Based on the phylogenetic analyses of 18S rRNA gene sequences, H. nozakii was found to be closely related to Asterococcus, Oogamochlamys, Rhysamphichloris, and “Dunaliella” lateralis and was separated from other known wall‐less flagellate volvocaleans, indicating independent secondary loss of the cell wall in H. nozakii. In the combined 18S rRNA and chloroplast gene tree, H. nozakii was sister to Lobochlamys.     

STRUCTURE AND ASEXUAL REPRODUCTION OF THE ENIGMATIC CHAROPHYCEAN GREEN ALGA ENTRANSIA FIMBRIATA (KLEBSORMIDIALES,CHAROPHYCEAE)1

As the closest relatives of embryophytes, the charophycean green algae (sensu Mattox and Stewart) may reveal the evolutionary history of characters in this lineage. Recent molecular phylogenetic analysis indicates that the little‐known species Entransia fimbriata Hughes is a member of the charophycean order Klebsormidiales. In this study LM and EM were used to identify and describe additional structural characters of Entransia so that comparisons could be made with Klebsormidium and with other charophycean algae outside the order Klebsormidiales. Features that Entransia shares with various members of the genus Klebsormidium include cylindrical cells in unbranched filaments that may spiral, parietal chloroplasts that cover only part of the circumference of the cell, H‐shaped cross walls, and vegetative reproduction by both fragmentation and formation of zoospores or aplanospores. Among the characteristics that distinguish Entransia from Klebsormidium are a highly lobed chloroplast with multiple pyrenoids; a single large vacuole; short cells that die and collapse, apparently facilitating filament fragmentation; and germinating filaments with condensed adhesive at the base and a tapering spine at the tip. Although Entransia has sometimes been tentatively considered to be a member of the Zygnemataceae, the presence of a flagellate life history stage distinguishes Entransia from this group. The pyrenoids of Entransia are typical of those of charophycean algae in having traversing membranes and surrounding starch. Presence of multiple such pyrenoids in each chloroplast of Entransia supports the hypothesis that the common ancestor of charophycean algae and embryophytes had a single chloroplast with multiple pyrenoids.     

Production of paramylon,a β‐1,3‐glucan,by heterotrophic growth of Euglena gracilis on potato liquor in fed‐batch and repeated‐batch mode of cultivation

Recently, it had been shown that Euglena gracilis was able to grow heterotrophically not only on synthetic media, but also on media based on potato liquor. Supplementation with glucose in both cases led to the accumulation of paramylon, a β‐1,3‐glucan. Thus, such a process may yield a valuable product accompanied by the revaluation of an otherwise annoying waste stream of the potato‐starch industry. Actually, process strategies have been evaluated in order to optimise the concentration of paramylon obtained at the end of the cultivation process. Therefore, cultivation processes based on fed‐batch and in particular repeated‐batch strategies have been studied. It is shown that repeated‐batch operation maybe particularly suited for such a process since E. gracilis seems to adapt gradually to the cultivation medium so that the concentration of media components may be increased step by step. Repeated‐batch cultivation of E. gracilis leads to biomass concentrations in access of 20 g/L with a consistent paramylon mass fraction of about 75%. Cultivations have been carried out at an operating temperature of 27.5°C. As had been found earlier already, pH control is not required during cultivation. On the basis of these results it is clear that repeated‐batch cultivation represent a simple and economic way for the production of paramylon by heterotrophic cultivation of E. gracilis.     

Comparative assessment of the Euglena gracilis var. saccharophila variant strain as a producer of the β‐1,3‐glucan paramylon under varying light conditions

Euglena gracilis Z and a “sugar loving” variant strain E. gracilis var. saccharophila were investigated as producers of paramylon, a β‐1,3‐glucan polysaccharide with potential medicinal and industrial applications. The strains were grown under diurnal or dark growth conditions on a glucose–yeast extract medium supporting high‐level paramylon production. Both strains produced the highest paramylon yields (7.4–8 g · L^?1, respectively) while grown in the dark, but the maximum yield was achieved faster by E. gracilis var. saccharophila (48 h vs. 72 h). The glucose‐to‐paramylon yield coefficient Y_par/glu = 0.46 ± 0.03 in the E. gracilis var. saccharophila cultivation, obtained in this study, is the highest reported to date. Proteomic analysis of the metabolic pathways provided molecular clues for the strain behavior observed during cultivation. For example, overexpression of enzymes in the gluconeogenesis/glycolysis pathways including fructokinase‐1 and chloroplastic fructose‐1,6‐bisphosphatase (FBP ) may have contributed to the faster rate of paramylon accumulation in E. gracilis var. saccharophila . Differentially expressed proteins in the early steps of chloroplastogenesis pathway including plastid uroporphyrinogen decarboxylases, photoreceptors, and a highly abundant (68‐fold increase) plastid transketolase may have provided the E. gracilis var. saccharophila strain an advantage in paramylon production during diurnal cultivations. In conclusion, the variant strain E. gracilis var. saccharophila seems to be well suited for producing large amounts of paramylon. This work has also resulted in the identification of molecular targets for future improvement of paramylon production in E. gracilis , including the FBP and phosophofructokinase 1, the latter being a key regulator of glycolysis.     

Chloroplast Genome Evolution in the Euglenaceae

Over the last few years multiple studies have been published outlining chloroplast genomes that represent many of the photosynthetic euglenid genera. However, these genomes were scattered throughout the euglenophyceaean phylogenetic tree, and focused on comparisons with Euglena gracilis. Here, we present a study exclusively on taxa within the Euglenaceae. Six new chloroplast genomes were characterized, those of Cryptoglena skujai, E. gracilis var. bacillaris, Euglena viridis, Euglenaria anabaena, Monomorphina parapyrum, and Trachelomonas volvocina, and added to six previously published chloroplast genomes to determine if trends existed within the family. With this study: at least one genome has now been characterized for each genus, the genomes of different strains from two taxa were characterized to explore intraspecific variability, and a second taxon has been characterized for the genus Monomorphina to examine intrageneric variability. Overall results showed a large amount of variability among the genomes, though a few trends could be identified both within Euglenaceae and within Euglenophyta. In addition, the intraspecific analysis indicated that the similarity of a genome sequence between strains was taxon dependent, and the intrageneric analysis indicated that the majority of the evolutionary changes within the Euglenaceae occurred intergenerically.     

CRYPTOGLENA PIGRA: A EUGLENOID WITH ONE CHLOROPLAST12

The taxonomic status of Cryptoglena pigra Ehrb., interpreted from observations based on bright-field microscopy, has been uncertain. Examination with the electron microscope of a clone of C pigra isolated by E. G. Pringsheim reveals certain features which, collectively, are distinctly euglenoid: periplast associated with muciferous bodies and subpellicular microtubules; canal and reservoir with microtubules; one flagellum with a swelling and emergent through a canal, and a second flagellum without a swelling and nonremergent; stigma (eyetpot) closely apprrssed to but not part of the chloroplast; nucleus with permanently condensed chromosomes attached to the inner nuclrar membrane; mitochondria with disc-shaped cristae constricted at the base; chloroplast with thylakoids often in triplets; and paramylon grains in the cytoplasm. Unlike most euglenoids, C. pigra possesses a single chloroplast that in transverse thin sections is U-shaped.     

Discovery of a novel type of body scale in the marine dinoflagellate,Amphidinium cupulatisquama sp. nov. (Dinophyceae)

A new species of Amphidinium, A. cupulatisquama Tamura et Horiguchi, from sand samples from Ikei Island, Okinawa Prefecture in subtropical Japan, is described based on light, scanning and transmission electron microscopy and the partial sequencing of the large subunit rDNA gene. The species has a typical morphology for the genus, but is distinguished from previously described species by having a combination of the following characteristics: (i) a relatively large cell (over 30 µm in length); (ii) possessing an eyespot on the dorsal side of the cingulum; (iii) the longitudinal flagellum emerging from a point close to the cingulum; (iv) cell division taking place in the motile phase; and (v) possessing body scales. This is the third species of this genus to possess body scales. The body scales of A. cupulatisquama are uniform and cup‐shaped in side view and elliptical in face view. Their dimensions are 136.4 nm by 91.0 nm by 81.8 nm high. In side view, the scale is seen to have a thick lower half and a thin upper half. This scale type is very different from those of previously reported Amphidinium species (HG114 and HG115). The molecular tree indicated that A. cupulatisquama and the two other strains of body scale‐bearing Amphidinium are distantly related within the Amphidinium clade.