Re-examining alveolate evolution using multiple protein molecular phylogenies

Alveolates are a diverse group of protists that includes three major lineages: ciliates, apicomplexa, and dinoflagellates. Among these three, it is thought that the apicomplexa and dinoflagellates are more closely related to one another than to ciliates. However, this conclusion is based almost entirely on results from ribosomal RNA phylogeny because very few morphological characters address this issue and scant molecular data are available from dinoflagellates. To better examine the relationships between the three major alveolate groups, we have sequenced six genes from the non-photosynthetic dinoflagellate, Crypthecodinium cohnii: actin, beta-tubulin, hsp70, BiP, hsp90, and mitochondrial hsp10. Beta-tubulin, hsp70, BiP, and hsp90 were found to be useful for intra-alveolate phylogeny, and trees were inferred from these genes individually and in combination. Trees inferred from individual genes generally supported the apicomplexa-dinoflagellate grouping, as did a combined analysis of all four genes. However, it was also found that the outgroup had a significant effect on the topology within alveolates when using certain methods of phylogenetic reconstruction, and an alternative topology clustering dinoflagellates and ciliates could not be rejected by the combined data. Altogether, these results support the sisterhood of apicomplexa and dinoflagellates, but point out that the relationship is not as strong as is often assumed.     

A Transcriptome-based Perspective of Meiosis in Dinoflagellates

There is increasing interest in the possibility of sexual recombination in dinoflagellates, especially those symbiotic with coral, since recombination may be able to augment genetic diversity and reduce levels of coral bleaching. Several previous studies have addressed this in Symbiodinium by querying sequence databanks with a list of 51 genes termed a meiosis detection toolkit. Here, we have constructed an expanded list of 307 genes involved in meiosis in budding yeast. We find the genes involved in the major regulatory steps in yeast meiosis are also found in dinoflagellates, as are many of the genes involved in recombination. In contrast, few genes involved in forming the synaptonemal complex or forming spores are conserved. We further note that the meiosis-related genes absent in dinoflagellates are also as a general rule absent from other protists in the closely related apicomplexa and the ciliates. We conclude the symbiotic dinoflagellates are as able to undergo meiosis as are other protists.     

Ciliate pellicular proteome identifies novel protein families with characteristic repeat motifs that are common to alveolates

The pellicles of alveolates (ciliates, apicomplexans, and dinoflagellates) share a common organization, yet perform very divergent functions, including motility, host cell invasion, and armor. The alveolate pellicle consists of a system of flattened membrane sacs (alveoli, which are the defining feature of the group) below the plasma membrane that is supported by a membrane skeleton as well as a network of microtubules and other filamentous elements. We recently showed that a family of proteins, alveolins, are common and unique to this pellicular structure in alveolates. To identify additional proteins that contribute to this structure, a pellicle proteome study was conducted for the ciliate Tetrahymena thermophila. We found 1,173 proteins associated with this structure, 45% (529 proteins) of which represented novel proteins without matches to other functionally characterized proteins. Expression of four newly identified T. thermophila pellicular proteins as green fluorescent protein-fusion constructs confirmed pellicular location, and one new protein located in the oral apparatus. Bioinformatic analysis revealed that 21% of the putative pellicular proteins, predominantly the novel proteins, contained highly repetitive regions with strong amino acid biases for particular residues (K, E, Q, L, I, and V). When the T. thermophila novel proteins were compared with apicomplexan genomic data, 278 proteins with high sequence similarity were identified, suggesting that many of these putative pellicular components are shared between the alveolates. Of these shared proteins, 126 contained the distinctive repeat regions. Localization of two such proteins in Toxoplasma gondii confirmed their role in the pellicle and in doing so identified two new proteins of the apicomplexan invasive structure--the apical complex. Screening broadly for these repetitive domains in genomic data revealed large and actively evolving families of such proteins in alveolates, suggesting that these proteins might underpin the diversity and utility of their unique pellicular structure.     

Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic

Plantae (as defined by Cavalier-Smith, 1981) plastids evolved via primary endosymbiosis whereby a heterotrophic protist enslaved a photosynthetic cyanobacterium. This "primary" plastid spread into other eukaryotes via secondary endosymbiosis. An important but contentious theory in algal evolution is the chromalveolate hypothesis that posits chromists (cryptophytes, haptophytes, and stramenopiles) and alveolates (ciliates, apicomplexans, and dinoflagellates) share a common ancestor that contained a red-algal-derived "secondary" plastid. Under this view, the existence of several later-diverging plastid-lacking chromalveolates such as ciliates and oomycetes would be explained by plastid loss in these lineages. To test the idea of a photosynthetic ancestry for ciliates, we used the 27,446 predicted proteins from the macronuclear genome of Tetrahymena thermophila to query prokaryotic and eukaryotic genomes. We identified 16 proteins of possible algal origin in the ciliates Tetrahymena and Paramecium tetraurelia. Fourteen of these are present in other chromalveolates. Here we compare and contrast the likely scenarios for algal-gene origin in ciliates either via multiple rounds of horizontal gene transfer (HGT) from algal prey or symbionts, or through endosymbiotic gene transfer (EGT) during a putative photosynthetic phase in their evolution.     

Ellobiopsids of the genus Thalassomyces are alveolates

Ellobiopsids are multinucleate protist parasites of aquatic crustaceans that possess a nutrient absorbing 'root' inside the host and reproductive structures that protrude through the carapace. Ellobiopsids have variously been affiliated with fungi, 'colorless algae', and dinoflagellates, although no morphological character has been identified that definitively allies them with any particular eukaryotic lineage. The arrangement of the trailing and circumferential flagella of the rarely observed bi-flagellated 'zoospore' is reminiscent of dinoflagellate flagellation, but a well-organized 'dinokaryotic nucleus' has never been observed. Using small subunit ribosomal RNA gene sequences from two species of Thalassomyces, phylogenetic analyses robustly place these ellobiopsid species among the alveolates (ciliates, apicomplexans, dinoflagellates and relatives) though without a clear affiliation to any established alveolate lineage. Our trees demonstrate that Thalassomyces fall within a dinoflagellate + apicomplexa + Perkinsidae + "marine alveolate group 1" clade, clustering most closely with dinoflagellates. However, the poor statistical support for branches within this region indicates that additional data will be needed to resolve relationships among these taxa.     

Molecular evolution of ciliates (Ciliophora) and some related groups of protozoans

The review summarizes current evidence, including the findings related to molecular phylogeny of ciliates (type Ciliophora) and some related groups of protozoans. Based on comparison of the sequences of genes encoding various ribosomal RNAs (rRNAs), the phylogenetic relationships in seven out of eight known classes of ciliates are discussed. The events related to early branching of the eukaryotic tree are briefly presented. The evolutionary history of amitochondrial protists ids considered with regard to reductionistic evolution and archeozoic hypothesis. The phylogenetic relationships among ciliates and sister groups of apicomplexans and dinoflagellates are considered.     

Evolution of the glucose-6-phosphate isomerase: the plasticity of primary metabolism in photosynthetic eukaryotes

Glucose-6-phosphate isomerase (GPI) has an essential function in both catabolic glycolysis and anabolic gluconeogenesis and is universally distributed among Eukaryotes, Bacteria, and some Archaea. In addition to the cytosolic GPI, land plant chloroplasts harbor a nuclear encoded isoenzyme of cyanobacterial origin that is indispensable for the oxidative pentose phosphate pathway (OPPP) and plastid starch accumulation. We established 12 new GPI sequences from rhodophytes, the glaucophyte Cyanophora paradoxa, a ciliate, and all orders of complex algae with red plastids (haptophytes, diatoms, cryptophytes, and dinoflagellates). Our comprehensive phylogenies do not support previous GPI-based speculations about a eukaryote-to-prokaryote horizontal gene transfer from metazoa to gamma-proteobacteria. The evolution of cytosolic GPI is largely in agreement with small subunit analyses, which indicates that it is a specific marker of the host cell. A distinct subtree comprising alveolates (ciliates, apicomplexa, Perkinsus, and dinoflagellates), stramenopiles (diatoms and Phytophthora [oomycete]), and Plantae (green plants, rhodophytes, and Cyanophora) might suggest a common origin of these superensembles. Finally, in contrast to land plants where the plastid GPI is of cyanobacterial origin, chlorophytes and rhodophytes independently recruited a duplicate of the cytosolic GPI that subsequently acquired a transit peptide for plastid import. A secondary loss of the cytosolic isoenzyme and the plastid localization of the single GPI in chlorophycean green algae is compatible with physiological studies. Our findings reveal the fundamental importance of the plastid OPPP for Plantae and document the plasticity of primary metabolism.     

Fine structure of the dorsal bristle complex and pellicle of Euplotes

The fine structure of the dorsal bristle complex and pellicle of non-developing Euplotes eurystomus is described in detail by scanning and transmission electron microscopy. The bristle-pit unit is a highly differentiated complex of organelles. The bristle complex is composed of a pair of kinetosomes (basal bodies) joined by a connective. The anterior kinetosome bears the bristle cilium, which contains a polarized network of particles (“lasiosomes”). The posterior kinetosome bears a very short, knob-like “condylocilium,” and has an associated striated fiber. Accessory ribbons of microtubules are also associated with the kinetosome couplets. Parasomal sacs, a septum connecting the bristle cilium to the anterior wall of the pit, core granules of the kinetosomes, and large membranous ampules are described. The organization of the bristle complex bears many similarities to the somatic ciliature of other ciliates. The pellicle of Euplotes is composed of a continucus outer cell membrane subtended by membranous alveoli, which contain a “fibrous mat.” Two sheets of subpellicular microtubules (longitudinal and transverse) are located just beneath the alveoli. The “epiplasm” seen in some other ciliates is apparently absent in Euplotes. The texture of the cell surface is a pattern of folds or rugae composed of the outer cell membrane and the upper membrane of the alveolus. The pattern of rugae probably defines the “silverline-system” of light microscopy.     

Molecular phylogenetic evidence that the phylum Haplosporidia has an alveolate ancestry

The phylogenetic position of the phylum Haplosporidia among other protists was investigated with the complete 16S-like rRNA gene sequences from two species in the phylum: Haplosporidium nelsoni, a parasite of oysters, and Minchinia teredinis, a parasite of shipworms. Because the lack of obvious morphological homologies with other protists hampered decisions regarding taxonomic composition for sequence alignment and phylogenetic analysis, the complete sequences for these two haplosporidians were directed as search queries to the blast/ncbi.nlm.nih.gov electronic mail server. The results of this heuristic similarity search provided a basis for constructing a preliminary higher-taxonomic-level analysis comparing the haplosporidians with species from the slime molds, fungi, algae, amoebae, ciliates, dinoflagellates, and apicomplexans. Maximum parsimony yielded equivocal results, whereas transversionally weighted parsimony suggested an affinity with the alveolates (i.e., the ciliates, dinoflagellates, and apicomplexans). Multiple alignment of the two haplosporidian sequences against 17 taxa in a secondary analysis focusing on the alveolates and subsequent parsimony analysis placed the phylum Haplosporidia as a monophyletic group within the Alveolata and as a taxon of equal rank with the other three alveolate phyla. The precise placement within the Alveolata was sensitive to weighting.      

Mixotrophic Protists In Marine and Freshwater Ecosystems

ABSTRACT Some protists from both marine and freshwater environments function at more than one trophic level by combining photosynthesis and panicle ingestion. Photosynthetic algae from several taxa (most commonly chrysomonads and dinoflagellates) have been reported to ingest living prey or nonliving particles, presumably obtaining part of their carbon and/or nutrients from phagocytosis. Conversely, some ciliates and sarcodines sequester chloroplasts after ingestion of algal prey. Plastid retention or "chloroplast symbiosis" by protists was first demonstrated < 20 years ago in a benthic foraminiferan. Although chloroplasts do not divide within these mixotrophic protists, they continue to function photosynthetically and may contribute to nutrition. Sarcodines and ciliates that harbor endosymbiotic algae could be considered mixotrophic but are not covered in detail here. the role of mixotrophy in the growth of protists and the impact of their grazing on prey populations have received increasing attention. Mixotrophic protists vary in their photosynthetic and ingestion capabilities, and thus, in the relative contribution of photosynthesis and phagotrophy to their nutrition. Abundant in both marine and freshwaters, they are potentially important predators of algae and bacteria in some systems. Mixotrophy may make a stronger link between the microbial and classic planktonic food webs by increasing trophic efficiency.     

Protist Biogeography1

Autecology (cellular organelles and secretions, encystment and dispersal abilities), environmental conditions (physiological tolerances and interaction with other organisms), and evolutionary history contribute to protist biogeography, which manifests ecological and historical aspects. Ecological biogeography is seen in the influence of geochemistry on the distribution of fresh-water phytoflagellates and algae, and of moisture and vegetation type on soil-litter protists. A temporal feature is often present because many protists encyst and respond only to certain ranges of temperature and organic content. Historical biogeography has occurred by radiative host evolution on symbiotic protozoa (e.g., termite flagellates and rumen ciliates), and by the isolating effects of water currents, temperature, and density gradients on oceanic protists (coccoliths, dinoflagellates, foraminifera, radiolaria, and tintinnines). These two aspects combine in protists living on animal surfaces. Humans affect protist biogeography by increasing parasite ranges through human migrations and by water pollution. They can diminish these situations by disease control and exploiting appropriate ciliates in sewage disposal. Many free-living protozoa appear to be cosmopolitan, but mating types and isoenzyme studies suggest that speciation with its geographic connotations may be more widespread than presently appreciated.     

Evolving lineages of Symbiodinium-like dinoflagellates based on ITS1 rDNA

Symbiodinium-like dinoflagellates have been shown to be a diverse group of endosymbionts that associate mutualistically with many kinds of coral reef dwellers, including cnidarians, molluscs, and protists. A high number of genetically ITS types of symbionts have been reported to date. However, whether these recently identified Symbiodinium ITS types indeed represent independent evolutionary lineages is still unsettled. Here I tested the null hypothesis that certain group of symbionts sampled from different geographical locations are derived from a single evolutionary lineage using a nested clade analysis (NCA). I analyzed a total of 174 ITS1 sequences from GenBank and pooled them into 74 ITS1 distinct haplotypes. Using these haplotypes, the statistical parsimony criterion produced 23 independent network trees, each one corresponding to a genetically independent evolving lineage. Some of these lineages revealed certain degree of specificity with some host groups at least at the phylum level. Within the previously described 28S-rDNA phylotype A, five ITS1 lineages were resolved. Phylotypes B and C resolved each in two ITS1 lineages. The highest ITS1 symbiont diversity was observed within the phylotype F, in which 11 lineages were resolved. Moreover, most of these lineages were associated uniquely with protist hosts from the group of foraminiferans. Here it is suggested that this high genetic diversity of endosymbionts associated with foraminiferans is linked with the evolution of soritacean foraminifera, which seems to have been driven by endosymbiosis. Lastly, the absence of genetic recombination presented in this study, suggest a lack of hybridisation at least among the major 28S-rDNA phylotypes within Symbiodinium-like dinoflagellates. This supports highly the idea that these phylotypes are indeed independent evolutionary units, which should be considered at least as different species. Whether they belong to the same genus or to different higher taxa still needs to be revised.     

Characterization of TtALV2, an Essential Charged Repeat Motif Protein of the Tetrahymena thermophila Membrane Skeleton

Alveolins are a recently described class of proteins common to all members of the superphylum Alveolata that are characterized by conserved charged repeat motifs (CRMs) but whose exact function remains unknown. We have analyzed the smaller of the two alveolins of Tetrahymena thermophila, TtALV2. The protein localizes to dispersed, broken patches arranged between the rows of the longitudinal microtubules. Macronuclear knockdown of Ttalv2 leads to multinuclear cells with no apparent cell polarity and randomly occurring cell protrusions, either by interrupting pellicle integrity or by disturbing cytokinesis. Correct association of TtALV2 with the alveoli or the pellicle is complex and depends on both the termini as well as the charged repeat motifs of the protein. Proteins containing similar CRMs are a dominant part of the ciliate membrane cytoskeleton, suggesting that these motifs may play a more general role in mediating membrane attachment and/or cytoskeletal association. To better understand their integration into the cytoskeleton, we localized a range of CRM-based fusion proteins, which suggested there is an inherent tendency for proteins with CRMs to be located in the peripheral cytoskeleton, some nucleating as filaments at the basal bodies. Even a synthetic protein, mimicking the charge and repeat pattern of these proteins, directed a reporter protein to a variety of peripheral cytoskeletal structures in Tetrahymena. These motifs might provide a blueprint for membrane and cytoskeleton affiliation in the complex pellicles of Alveolata.     

A New Way to Investigate Living Flagellated/Ciliated Cells in the Light Microscope: Immobilization of Cells in Agarose

A method for cell immobilization of living flagellated/ciliated cells in agarose has been developed that allows single cells to be viewed for prolonged periods of time using high resolution light microscopy. Embedding in ultralow gelling, soft agarose preserves cellular functions of various flagellated/ciliated protists including delicate species, marine dinoflagellates, cryptomonads, contractile ciliates, etc. for days. Cell division, morphogenesis of cell organelles and intracellular movements can thus be studied for the first time in great detail. The method may also be useful for the isolation of flagellated/ciliated protists from nature and for the establishment of axenic clonal cultures in a single step.     

An analysis of protists in Pacific oxygen deficient zones: implications for Prochlorococcus and N2-producing bacteria

Ocean oxygen deficient zones (ODZs) host 30%–50% of marine N₂ production. Cyanobacteria photosynthesizing in the ODZ create a secondary chlorophyll maximum and provide organic matter to N₂-producing bacteria. This chlorophyll maximum is thought to occur due to reduced grazing in anoxic waters. We first examine ODZ protists with long amplicon reads. We then use non-primer-based methods to examine the composition and relative abundance of protists in metagenomes from the Eastern Tropical North and South Pacific ODZs and compare these data to the oxic Hawaii Ocean Time-series (HOT) in the North Pacific. We identify and quantify protists in proportion to the total microbial community. From metagenomic data, we see a large drop in abundance of fungi and protists such as choanoflagellates, radiolarians, cercozoa and ciliates in the ODZs but not in the oxic mesopelagic at HOT. Diplonemid euglenozoa were the only protists that increased in the ODZ. Dinoflagellates and foraminifera reads were also present in the ODZ though less abundant compared to oxic waters. Denitrification has been found in foraminifera but not yet in dinoflagellates. DNA techniques cannot separate dinoflagellate cells and cysts. Metagenomic analysis found taxonomic groups missed by amplicon sequencing and identified trends in abundance.     

Bacterivory and herbivory: Key roles of phagotrophic protists in pelagic food webs

Research on microbial loop organisms, heterotrophic bacteria and phagotrophic protists, has been stimulated in large measure by Pomeroy's seminal paper published in BioScience in 1974. We now know that a significant fate of bacterioplankton production is grazing by < 20-µm-sized flagellates. By selectively grazing larger, more rapidly growing and dividing cells in the bacterioplankton assemblage, bacterivores may be directly cropping bacterial production rather than simply the standing stock of bacterial cells. Protistan herbivory, however, is likely to be a more significant pathway of carbon flow in pelagic food webs than is bacterivory. Herbivores include both < 20-µm flagellates as well as > 20-µm ciliates and heterotrophic dinoflagellates in the microzooplankton. Protists can grow as fast as, or faster than their phytoplankton prey. Phototrophic cells grazed by protists range from bacterial-sized prochlorophytes to large diatom chains (which are preyed upon by extracellularly-feeding dinoflagellates). Recent estimates of microzooplankton herbivory in various parts of the sea suggest that protists routinely consume from 25 to 100% of daily phytoplankton production, even in diatom-dominated upwelling blooms. Phagotrophic protists should be viewed as a dominant biotic control of both bacteria and of phytoplankton in the sea.     

Architecture and evolution of dinoflagellate chromosomes: an enigmatic origin

Dinoflagellates are a highly diversified group of unicellular protists that present fascinating nuclear features which have intrigued researchers for many years. As examples, a dense nuclear matrix accommodates permanently condensed chromosomes that are composed of fibers organized without histones and nucleosomes in stacked rows of parallel nested arches. The macromolecular chromosome structure corresponds to cholesteric liquid crystals with a constant left-handed twist. RNA acts to maintain the chromosome structure. Whole mounted chromosomes have a left-handed screw-like configuration with coils which progressively increase their pitch. This helical arrangement seems to be the result of a couple of narrow strands coiling together. Chromosomes do not show Q, G and C banding patterns. However, a roughly spherical differentiated upper end (primitive kinetochore?) and two differentiated coiling regions, the upper one composed of two to three coils where a couple of sister strands run together and parallel to each other, and the lower one where sister strands run out of phase by 180 degrees angular difference along the immediate next turns, can be distinguished. The chromosome segregation into two daughter chromatids begins at the telomere that attaches to the nuclear envelope, follows along the chromosome axis constituting first a Y-shaped and afterwards a V-shaped chromosome, which packs the newly synthesized DNA inside the "old" chromosome. Dividing chromosomes remain highly condensed, and the diameters of the new chromatids and the undivided chromosome are similar, but the number of arches is twice as large in G1 as in G2. The nuclear envelope remains through the cell cycle and shows spindle fibers, which penetrate intranuclear cytoplasmic channels during mitosis constituting an extra nuclear spindle. These and other cytogenetic features suggest that dinoflagellates are a group of enigmatic protists, unique and different from the usual eukaryotes. In contrast, DNA sequence studies propose that dinoflagellates are true eukaryotes, closely related to Apicomplexa, and ciliates (Alveolata), suggesting that the unusual features of chromosome and nuclear organization are not primitive but derived characters. Nevertheless, dinoflagellates have reached enigmatic specific nuclear and chromosome solutions, extremely far from those of other living beings.     

The flagellar apparatus and cytoskeleton of the dinoflagellates

Summary Modern microscopical approaches have allowed more accurate investigations of the three-dimensional nature of the dinoflagellate flagellar apparatus (FA) and several other cytoskeletal protein complexes. Our presentation overviews the nature of the dinoflagellate FA and cytoskeleton in a number of taxa and compares them with those of other protists. As with other protists, the FA of the dinoflagellates can be characterized by the presence of fibrous and microtubular components. Our studies and others indicate that the dinoflagellate FA can be expected to possess a striated fibrous root on the basal body of the transverse flagellum and a multimembered microtubular root on the basal body of the longitudinal flagellum. Two other features that appear widespread in the group are the transverse striated root associated microtubule (tsrm) and the transverse microtubular root (tmr). The tsrm extends at least half the length of the transverse striated root while the tmr extends from the transverse basal body toward the exit aperture of the transverse flagellum. In most cases, the tmr gives rise to several cytoplasmic microtubules at a right angle. The apparent conserved nature of these roots leads us to the conclusion that the dinoflagellate FA can be compared to the FA of the cryptomonads, chrysophytes, and the ciliates for phylogenetic purposes. Of these groups, the chrysophytes possess an FA with the most structures in common with the dinoflagellates. Our immunomicroscopical investigations of the microtubular, actin and centrin components of the dinoflagellate cytoskeleton point to the comparative usefulness of these cytological features.Abbreviations aptb apical transverse microtubular band - FA flagellar apparatus - Imr longitudinal microtubular root - mls multilayered structure - tmr transverse microtubular root - tmre transverse microtubular root extension - tsr transverse striated fibrous root - tsrm transverse striated root associated microtubule     

Molecular evolution of the 5'-terminal domain of large-subunit rRNA from lower eukaryotes. A broad phylogeny covering photosynthetic and non-photosynthetic protists

This paper summarizes the present status of an analysis of protist phylogeny using rapid partial sequencing of 28S rRNA. Data from 12 protistan phyla are now available and have been used to construct a tentative dendrogram based on a distance matrix method. The tree is robust and has considerable internal consistency. The following salient points are observed: a number of flagellate groups (particularly Euglenozoa) emerge very early among eukaryotes, whereas ciliates and dinoflagellates emerge late, suggesting that some characteristics that had been considered as primitive may in fact be derived. Both chlorophytic and chromophytic photosynthetic protists emerge very late in the tree, close to the Metazoa-Metaphyta-Fungi radiation, suggesting relatively late occurrence of the photosynthetic symbiosis. Taxonomic and phylogenetic information is also obtained within a phylum where rRNA of enough species are sequenced. A deep trichotomy is thus observed within the ciliates. The data are discussed with respect to classical protist phylogenies.