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Phylogeny of Heterokonta: Incisomonas marina, a uniciliate gliding opalozoan related to Solenicola (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes

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Abstract

Environmental rDNA sequencing has revealed many novel heterokont clades of unknown morphology. We describe a new marine heterotrophic heterokont flagellate, Incisomonas marina, which most unusually lacks an anterior cilium. It glides and swims with its cilium trailing behind, but is predominantly sedentary on the substratum, with or without a cilium. 18S rDNA sequence phylogeny groups Incisomonas strongly within clade MAST-3; with others it forms a robust sister clade to Solenicola, here grouped with it as new order Uniciliatida, placed within new class Nanomonadea encompassing MAST-3. Our comprehensive maximum likelihood heterokont phylogeny shows Nanomonadea as sister to MAST-12 plus Opalinata within Opalozoa, and that Actinophryida are not Opalozoa (previously suggested by distance trees), but highly modified raphidomonads, arguably related to Heliorapha (formerly Ciliophrys) azurina gen., comb. n. We discuss evolution of Actinophryida from photosynthetic raphidophytes. Clades MAST-4,6-11 form one early-branching bigyran clade. Olisthodiscus weakly groups with Hypogyristea not Raphidomonadea. Phylogenetic analysis shows that MAST-13 is all Bicosoeca. Some gliding uniciliates similar to Incisomonas marina seem to have been misclassified: therefore we establish Incisomonas devorata comb. n. for Rigidomastix devoratum, revise the genus Rigidomastix, transfer Clautriavia parva to Kiitoksia. We make 17 new familes (13 heterokont (three algal), two cercozoan, two amoebozoan).

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... Also, a parallel classification was proposed soon after the first study ( Richards and Bass, 2005). With only one exception (Cavalier-Smith and Scoble, 2013), this diversity remains uncultured, so determining their cell physiology and ecological attributes is one of the main challenges for future ecological studies. Some groups were investigated in detail, mainly by FISH using group-specific oligonucleotide probes, and MAST cells turned out to be small (2-5 mm) heterotrophic flagellates, widely distributed and active bacterial grazers ( Massana et al., 2006;Lin et al., 2012;Piwosz et al., 2013). ...
... The placement of the remaining groups shifted in different trees. Non-ochrophyta stramenopiles were separated into three phylogenetic regions, following Cavalier-Smith and Scoble (2013). First, the Pseudofungi formed a set of separate lineages basal to Ochrophyta that included Pirsonia, Peronosporomyctes, Hyphochytriales, Developayella, and several MASTs. ...
... Each of these phylogenetic units deserves a careful inspection, which can be based on FISH probes or targeted sequencing as has been recently done for MAST-4 to evaluate its genetic structure ( Rodríguez-Martínez et al., 2012) and biogeography ( Rodríguez-Martínez et al., 2013). Also, culturing attempts should be continued (Cavalier-Smith and Scoble, 2013;del Campo et al., 2013), and the potential of genomes obtained from single cells should be exploited by phylogenomics and genome reconstructions (Yoon et al., 2011). The ecological attributes and putative specialization of the different clades is an intriguing aspect to be analyzed. ...
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Molecular surveys in planktonic marine systems have unveiled a large novel diversity of small protists. A large part of this diversity belongs to basal heterotrophic stramenopiles and is distributed in a set of polyphyletic ribogroups (described from rDNA sequences) collectively named as MAST (MArine STramenopiles). In the few groups investigated, MAST cells are globally distributed and abundant bacterial grazers, therefore having a putatively large impact on marine ecosystem functioning. The main aim of this study is to reevaluate the MAST ribogroups described so far and to determine whether additional groups can be found. For this purpose, we used traditional and state-of-the-art molecular tools, combining 18S rDNA sequences from publicly available clone libraries, single amplified genomes (SAGs) of planktonic protists, and a pyrosequencing survey from coastal waters and sediments. Our analysis indicated a final set of 18 MAST groups plus 5 new ribogroups within Ochrophyta (named as MOCH). The MAST ribogroups were then analyzed in more detail. Seven were typical of anoxic systems and one of oxic sediments. The rest were clearly members of oxic marine picoplankton. We characterized the genetic diversity within each MAST group and defined subclades for the more diverse (46 subclades in 8 groups). The analyses of sequences within subclades revealed further ecological specializations. Our data provide a renovated framework for phylogenetic classification of the numerous MAST ribogroups and support the notion of a tight link between phylogeny and ecological distribution. These diverse and largely uncultured protists are widespread and ecologically relevant members of marine microbial assemblages.The ISME Journal advance online publication, 7 November 2013; doi:10.1038/ismej.2013.204.
... These two groups, Ochrophyta and Pseudofungi, form the clade Gyrista (Cavalier-Smith 1998). Ochrophyta are most often divided in the two groups Khakista (diatoms and bolidophytes) and Phaeista (including the remaining photosynthetic groups) (Brown and Sorhannus 2010;Gomez et al. 2011;Cavalier-Smith and Scoble 2013;Massana et al. 2014), although this classification has been challenged by several phylogenetic studies based on different markers (Riisberg et al. 2009;Yang et al. 2012;Sev c ıkov a et al. 2015). The relationships among the rest of stramenopile groups, all of them heterotrophic (e.g., labyrinthulomycetes and thraustochytrids, bicosoecids, the parasite Blastocystis, and most MAST lineages), are still unclear as they vary from one phylogenetic analysis to another. ...
... Bayesian and ML analyses converged to the same primary dichotomy of ochrophytes, in all cases with maximal statistical support: Pelagophyceae, Dictyochophyceae, Bolidophyceae and diatoms on one side, and all other ochrophytes on the other side (see fig. 1 and supplementary file S2, Supplementary Material online). This result was in contradiction with the commonly observed, but weakly supported, dichotomy between Khakista (Bolidophyceae plus diatoms) and Phaeista (all other ochrophytes) found in SSU rDNAbased trees (Brown and Sorhannus 2010;Gomez et al. 2011;Cavalier-Smith and Scoble 2013;Massana et al. 2014). By contrast, it agreed with previous multigene phylogenetic analyses (Riisberg et although, since our tree was based on a much larger gene sampling than those previously used, we were able to retrieve maximal support for all branches within this group ( fig. 1). ...
... The second important result emerging from our study concerns the relationships among Ochrophyte lineages. While all phylogenies based on SSU rDNA have shown the Khakista-Phaeista dichotomy (Brown and Sorhannus 2010;Gomez et al. 2011;Cavalier-Smith and Scoble 2013;Massana et al. 2014), our Bayesian and ML analyses all converge with maximal support to the paraphyly of Phaeista, with Pelagophyceae and Dictyochophyceae branching as sister group of the Khakista. Interestingly, a possible relationship between diatoms, pelagophytes and dictyochophytes had already been proposed based on their reduced flagellar apparatus (Saunders et al. 1995). ...
Article
Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of protists. It includes ecologically important algae (such as diatoms or large multicellular brown seaweeds), as well as heterotrophic (e.g. bicosoecids, MAST groups) and parasitic (e.g. Blastocystis, oomycetes) species. Despite their evolutionary and ecological relevance, deep phylogenetic relationships among stramenopile groups, inferred mostly from small-subunit (SSU) rDNA phylogenies, remain unresolved, especially for the heterotrophic taxa. Taking advantage of recently released stramenopile transcriptome and genome sequences, as well as data from the genomic assembly of the MAST-3 species Incisomonas marina generated in our laboratory, we have carried out the first extensive phylogenomic analysis of stramenopiles, including representatives of most major lineages. Our analyses, based on a large dataset of 339 widely distributed proteins, strongly support a root of stramenopiles lying between two clades, Bigyra and Gyrista (Pseudofungi plus Ochrophyta). Additionally, our analyses challenge the Phaeista-Khakista dichotomy of photosynthetic stramenopiles (ochrophytes) as two groups previously considered to be part of the Phaeista (Pelagophyceae and Dictyochophyceae), branch with strong support with the Khakista (Bolidophyceae and Diatomeae). We propose a new classification of ochrophytes within the two groups Chrysista and Diatomista to reflect the new phylogenomic results. Our stramenopile phylogeny provides a robust phylogenetic framework to investigate the evolution and diversification of this group of ecologically relevant protists.
... Furthermore, the extended sample of heterokont sequences studied here highlights the problems of reconstruction an accurate rDNAbased tree, and as yet insufficient sampling of the heterokont diversity, especially in close relatives of ochrophytes. At the same time, our results support the monophyly of a large group of heterokonts discovered earlier (Cavalier-Smith and Scoble, 2013), which includes Ochrophyta, Pirsonia and related environmental clones, Developea, Pseudofungi (oomycetes plus hyphochytriomycetes), MAST-1, MAST-23, another 3-4 isolated clades of environmental sample sequences, and MAST-2 as the first branch of the assemblage. Cavalier-Smith and Scoble (2013) referred to this large group as Gyrista, introduced earlier as a superphylum to accommodate Ochrophyta and "Bigyra, " and as a likely sister group to Sagenista, which includes Labyrinthulea and its closest relatives (Cavalier-Smith, 1997). ...
... At the same time, our results support the monophyly of a large group of heterokonts discovered earlier (Cavalier-Smith and Scoble, 2013), which includes Ochrophyta, Pirsonia and related environmental clones, Developea, Pseudofungi (oomycetes plus hyphochytriomycetes), MAST-1, MAST-23, another 3-4 isolated clades of environmental sample sequences, and MAST-2 as the first branch of the assemblage. Cavalier-Smith and Scoble (2013) referred to this large group as Gyrista, introduced earlier as a superphylum to accommodate Ochrophyta and "Bigyra, " and as a likely sister group to Sagenista, which includes Labyrinthulea and its closest relatives (Cavalier-Smith, 1997). The Sagenista were later included in the paraphyletic "Bigyra" (Cavalier-Smith and Chao, 2006;Cavalier-Smith and Scoble, 2013). ...
... Cavalier-Smith and Scoble (2013) referred to this large group as Gyrista, introduced earlier as a superphylum to accommodate Ochrophyta and "Bigyra, " and as a likely sister group to Sagenista, which includes Labyrinthulea and its closest relatives (Cavalier-Smith, 1997). The Sagenista were later included in the paraphyletic "Bigyra" (Cavalier-Smith and Chao, 2006;Cavalier-Smith and Scoble, 2013). In the ML tree from an earlier work (Cavalier-Smith and Scoble, 2013), Opalozoa, a part of the paraphyletic "Bigyra, " is sister to Gyrista. ...
Article
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Heterotrophic lineages of Heterokonta (or stramenopiles), in contrast to a single monophyletic group of autotrophs, Ochrophyta, form several clades that independently branch off the heterokont stem lineage. The nearest neighbors of Ochrophyta in the phylogenetic tree appear to be almost exclusively bacterivorous, whereas the hypothesis of plastid acquisition by the ancestors of the ochrophyte lineage suggests an ability to engulf eukaryotic alga. In line with this hypothesis, the heterotrophic predator at the base of the ochrophyte lineage may be regarded as a model for the ochrophyte ancestor. Here, we present a new genus and species of marine free-living heterotrophic heterokont Develorapax marinus, which falls into an isolated heterokont cluster, along with the marine flagellate Developayella elegans, and is able to engulf eukaryotic cells. Together with environmental sequences D. marinus and D. elegans form a class-level clade Developea nom. nov. represented by species adapted to different environmental conditions and with a wide geographical distribution. The position of Developea among Heterokonta in large-scale phylogenetic tree is discussed. We propose that members of the Developea clade represent a model for transition from bacterivory to a predatory feeding mode by selection for larger prey. Presumably, such transition in the grazing strategy is possible in the presence of bacterial biofilms or aggregates expected in eutrophic environment, and has likely occurred in the ochrophyte ancestor.
... Several changes to Raphidophycean taxonomy have recently been suggested, including the description of three marine genera: Chlorinimonas (Yamaguchi et al. 2010) from Japan, Viridilobus (Demir-Hilton et al. 2012) from USA and Psammamonas (Grant et al. 2013) from Australia. Olisthodiscus was traditionally treated as a raphidophyte but previously published ultrastructure (Hara et al. 1985;Inouye et al. 1992) and recently published phylogenetic analysis (Cavalier-Smith & Scoble 2013) indicates it belongs outside Raphidophyceae. ...
... The main objective of this study was to shed new light on the genetic and morphological diversity of Heterosigma akashiwo and examine whether this widely distributed species consists of more than one species. Because of recent additions and suggested changes to Raphidophyceae (Yamaguchi et al. 2010;Demir-Hilton et al. 2012;Cavalier-Smith & Scoble 2013;Grant et al. 2013), we also reconstructed the phylogeny of the class including all currently described taxa. Further, we analysed genetic variation within the rDNA of 24 Heterosigma strains, resulting in the description of a novel species of Heterosigma, Heterosigma minor sp. ...
... Chattonella The current hierarchy of Raphidophyceae was updated in Table 5. We omitted the change suggested by Cavalier-Smith & Scoble (2013) to include Actinosphaerium in Raphidophyceae because in their study it was represented by only one 18S rDNA sequence. Both multiple gene phylogenetic analysis and a morphological study are in our opinion required to draw conclusions of such consequence. ...
Article
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Heterosigma akashiwo is one of the smallest raphidophytes and is known for its ability to form dense, fishkilling blooms. In many parts of the world, H. akashiwo is a permanent resident of the algal community, and blooms have caused extensive financial losses for the aquaculture industry. Different aspects of its biology have been the focus of numerous investigations over the last two decades but, perhaps because of its small size and fragile nature, few morphological studies have been carried out. We conducted phylogenetic and morphological studies of 24 strains of Heterosigma from the coastal waters of Europe, North America, Australia and New Zealand. Complete 18S, ITS region and the D1'D2 region of 28S rDNA were sequenced and compared with all available raphidophyte sequences, revealing a novel species of Heterosigma, Heterosigma minor sp. nov. All strains of H. akashiwo were genetically very similar across the rDNA region (. 99.8% similarity) and morphologically very similar in light microscopy and scanning electron microscopy. Heterosigma minor shared only 98.2% similarity with H. akashiwo, and there were several morphological differences: it was smaller, rounder and had fewer mucocysts than H. akashiwo. The secondary structure of ITS2 was reconstructed, revealing three compensatory base changes between the two species, further indicating that H. minor is a sister to H. akashiwo. The phylogeny of Raphidophyceae was reconstructed to include all currently described raphidophytes.
... The Ochrophyta, a monophyletic phylum within the Stramenopiles (or Heterokonta), are the most diverse algal group with secondary plastids of algal origin in terms of morphology, pigmentation and phylogeny 3,4 . Diatoms (Bacillariophyceae) and multicellular brown algae (Phaeophyceae) are the best characterized ochrophytes, but at least 15 separate "classes", plus several isolated smaller lineages of uncertain taxonomic status exist [4][5][6][7][8] . Several groups within the ochrophytes have important ecological roles, particularly in terms of marine photosynthesis and uptake of CO 2 9 . ...
... Understanding relationships among the ochrophytes is important for both ecological and evolutionary studies. Phylogenetic studies of nuclear SSU rRNA gene sequences proposed the existence of several higher-order clades, specifically: diatoms plus the Bolidophyceae; the Chrysophyceae plus the Synchromophyceae; and the large "PX" clade comprising brown algae, the Xanthophyceae and other less well-known groups [4][5][6][7][8] . Multi-gene datasets including various combinations of nuclear, plastid and mitochondrial genes have improved resolution of ochrophyte phylogenetic relationships, yet some relationships are still unresolved 5,7,10 . ...
... While some analyses have supported such a grouping 5,7 , others have not 10 . Although our analysis does not include data from the other proposed Limnista lineages (i.e., synchromophytes and Picophagus), their affinity to the Chrysophyceae is consistently supported by other phylogenetic analyses 7,8,41,42 . Thus, our results can be interpreted as direct evidence for the monophyly of the Limnista sensu Cavalier-Smith and Chao 11 . ...
Article
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Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae). A shared split of the clpC gene as well as phylogenomic analyses of concatenated protein sequences demonstrated that chrysophytes and eustigmatophytes form a clade, the Limnista, exhibiting an unexpectedly elevated rate of plastid gene evolution. Our analyses also indicate that the root of the ochrophyte phylogeny falls between the recently redefined Khakista and Phaeista assemblages. Taking advantage of the expanded sampling of plastid genome sequences, we revisited the phylogenetic position of the plastid of Vitrella brassicaformis, a member of Alveolata with the least derived plastid genome known for the whole group. The results varied depending on the dataset and phylogenetic method employed, but suggested that the Vitrella plastids emerged from a deep ochrophyte lineage rather than being derived vertically from a hypothetical plastid-bearing common ancestor of alveolates and stramenopiles. Thus, we hypothesize that the plastid in Vitrella, and potentially in other alveolates, may have been acquired by an endosymbiosis of an early ochrophyte.
... A similar co-occurrence of MAST-3 and diatoms was observed at Station 5 ( Figure 6). MAST-3 has poor mobility, and it was speculated that epiphytism or parasitism should be one of its lifestyles (Cavalier-Smith and Scoble, 2013;Goḿez et al., 2010;Massana et al., 2014;Seeleuthner et al., 2018). Solenicola setigera (MAST-3I) has been confirmed to be parasitic to diatoms (Goḿez et al., 2011). ...
... Solenicola setigera (MAST-3I) has been confirmed to be parasitic to diatoms (Goḿez et al., 2011). Although relative evidence is still lacking, Incisomonas marina (OTU-244) (MAST-3J) was suggested to also follow the same life strategy (Cavalier-Smith and Scoble, 2013;Seeleuthner et al., 2018). The cooccurrence of MAST-1C or MAST-3 accompanied diatoms implied that diatom abundance in the flooded summer should be controlled by these parasitic flagellates at this time. ...
Article
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The transient impact of flooding on the community composition of marine picoeukaryotes (PEs, cell size ≤5 μm) in the East China Sea (ECS) was revealed in this study. In a summer without flooding (i.e., July 2009), photosynthetic picoeukaryotes (PPEs) were more abundant in the area covered by the Changjiang River diluted water (CDW, salinity ≤31) than in the non-CDW affected area. According to the 18S ribosomal RNA phylogeny, Alveolata (all from the superclass Dinoflagellata) was the main community component accounting for 72 to 99% of the community at each sampling station during the nonflooded summer. In addition to Dinoflagellata, diatoms or Chlorophyta also contributed a considerable proportion to the PE assemblage at the stations close to the edge of CDW coverage. In July 2010, an extreme flooding event occurred in the Changjiang River basin and led to the CDW covering nearly half of the ECS. In the flooded summer, the abundance of PPEs in the CDW-covered area decreased significantly to less than 1 × 10 ⁴ cells ml ⁻¹ . Compared to that during the nonflooded summer, the diversity of the PE composition was increased. While Dinophyceae still dominated the surface waters, Syndiniophyceae, which were represented by the uncultured Marine Alveolata Group (MALV)-I and MALV-II, accounted for a substantial amount in the Dinoflagellata superclass relative to this community composition in the nonflooded summer. Furthermore, a variety of plankton, including Cryptophyta, Haptophyta, Picobiliphyta, the uncultured Marine Stramenopiles (MASTs) and heterotrophic nanoflagellates, were observed. The nutrition modes of these PEs have been reported to be mixotrophic or heterotrophic. Therefore, it was inferred that the potentially mixotrophic and heterotrophic PE compositions might be favored in the marginal sea in the flooded summer.
... Molecular phylogenetic evidence demonstrates that the most recent ancestor of stramenopiles was likely a free-living bacterivorous biflagellate [55]. Parasitic stramenopiles have a polyphyletic distribution within the group and therefore evolved independently several times [14]. Oomycetes (or Peronosporomycetes), for instance, are fungus-like rhizoidal organisms with a flagellated zoospore stage (e.g., the infamous potato pathogen Phytophthora infestans). ...
... Slopalinids are either small biflagellated cells (around 15 m) with one nucleus or large multiflagellated cells (up to several millimeter) with multiple nuclei. Blastocystis plus the slopalinids form one of the earliest branching lineages of the stramenopiles along with the freeliving bicosoecida, the free-living placididea, and the saprotrophic Labyrinthulomycetes [14]; the branching order among those lineages still remains unclear. ...
... p0020 The photosynthetic stramenopiles form a largely monophyletic group (Dorrell et al., 2017;Walker et al., 2011), with most of the major nonphotosynthetic lineages (e.g. oomycetes, labyrinthulomycetes, and slopalinids, which include the important human pathogen Blastocystis) branching paraphyletically at the base of the stramenopile clade ( Fig. 1) (Cavalier-Smith & Scoble, 2013;Derelle et al., 2016;Dorrell et al., 2017). Although the exact branching order and phylogenetic utility of specific photosynthetic stramenopile clades remain debated, the general consensus from recent multigene phylogenies is for a basal division between a cladecontaining diatoms and Bolidomonas (together forming the "Khakista"), and pelagophytes and dictyochophytes (the "Hypogyristea"), and a separate clade containing all remaining lineages (the "Chrysista") ( Fig. 1) (Derelle et al., 2016;Dorrell et al., 2017;Riisberg et al., 2009;Yang et al., 2012). ...
... In contrast to the situation for oomycetes and other basal lineages, these groups clearly branch with photosynthetic relatives, hence must have once had plastids, and in some of them leucoplasts have been visualised (Kamikawa, Yubuki, et al., 2015;Mylnikov, Mylnikova, & Tikhonenkov, 2008;Sekiguchi, Moriya, Nakayama, & Inouye, 2002). The secondarily nonphotosynthetic lineages include members of the chrysophytes and synurophytes (Paraphysomonas, Apoikia, Spumella) (Kim, Yubuki, Leander, & Graham, 2010;Mangot et al., 2017;Mylnikov et al., 2008); Leukarachnion, which forms a sister-group to synchromophytes (Grant, Tekle, Anderson, Patterson, & Katz, 2009); the actinophryids, which resolve with the raphidophytes (Cavalier- Smith & Scoble, 2013); the dictyochophytes Pteridomonas and Ciliophrys (Sekiguchi et al., 2002); and several pennate diatom species within the Nitzschia clade (Kamikawa, Tanifuji, et al., 2015). All of the above lineages are believed to be free-living osmotrophs or phagotrophs, rather than obligate parasites of other lineages, and may constitute major heterotrophic components of freshwater and marine ecosystems (Mangot et al., 2017). ...
Chapter
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The stramenopiles encompass an incredible diversity of organisms, including ecologically fundamental single-celled algae such as diatoms, giant macroalgae such as kelps, as well as photo-mixotrophic and heterotrophic species. The photosynthetic species possess plastids of secondary or higher red algal origin. The diversity of stramenopile species provides an ideal system for exploring the fundamental features underpinning plastid establishment in eukaryotes, and also how plastid metabolism has diversified following endosymbiosis. In this chapter, we present an overview of stramenopile diversity and explore the chimeric origins of the stramenopile plastid, which utilises a combination of pathways derived from red algae and other sources to support its function. Next, we discuss unusual features of stramenopile plastid metabolism, some of which, responses to acute nutrient limitation and metabolic crosstalk with the mitochondria, may be specific to the diatoms and underpin their relative success in the contemporary ocean. Finally, we discuss even more dramatic transitions in the evolutionary history and life strategies of individual stramenopile groups, including evidence that stramenopiles may have given rise to some of the other major plastid lineages observed today, such as those of haptophytes and dinoflagellates, thus majorly contributing to the spread of photosynthesis through the tree of life.
... With the aid of molecular biology, S. setigera has been reported as the first morphologically identified member of a ubiquitous and diverse clade of environmental sequences known as MAST3 (Marine Stramenopiles III) (Gómez et al. 2011). A second member of this clade was further identified, confirming the nature of this group as represented by unicellular heterotrophic organisms with a flagellum used to capture picoplankton and small nanoplanktonic prey (Cavalier-Smith & Scoble 2013). ...
... Solenicola setigera is an independent organism phylogenetically unrelated to the diatoms (Gómez et al. 2011;Cavalier-Smith & Scoble 2013). In this study, we contributed new data on the diatom to elucidate the nature of this enigmatic symbiotic consortium. ...
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The consortium between the colonial stramenopile Solenicola setigera and the centric chain-forming diatom Leptocylindrus mediterraneus is cosmopolitan throughout the world ocean yet rarely abundant. However, the nature of the association remains enigmatic. A mutualistic symbiosis requires a live diatom host, but the frustule of L. mediterraneus is apparently empty, lacking protoplasm and plastids. The parasitism requires free-living host cells to be infected, but there is no evidence of populations of the free-living diatom. During experiments attempting to culture the heterotrophic S. setigera, we successfully obtained a strain of the host diatom. In the small-subunit (SSU) rDNA phylogeny, L. mediterraneus was closely related to Dactyliosolen blavyanus and to a new sequence of Dactyliosolen sp. while distantly related to the genus Leptocylindrus. We proposed the reinstatement of L. mediterraneus in the genus Dactyliosolen as D. mediterraneus. Even under optimal growth conditions, the frustule was nearly empty with reduced protoplasm concentrated in the middle. When compared with congeneric species, D. mediterraneus showed a doublelayered structure that acts as substrate for Solenicola. The free-living diatom lacked the convex walls that D. mediterraneus showed as host of Solenicola. The diatom in consortium with Solenicola maintained the photosynthetic machinery to eventually proliferate as a free-living organism. The ecological and morphological observations suggested that the diatom was successfully adapted to the mutualistic symbiosis with Solenicola. We discarded a parasitic relationship in this exceptional example of symbiosis.
... If Chromista were polyphyletic, sharing former red algal chloroplasts with the same novel protein-import machinery (Cavalier-Smith, 1999;Stork et al., 2012) might in theory be attributed to serial tertiary transfers of descendants of the singly enslaved red algal chloroplast from an early cryptophyte to Haptophyta and from them to Harosa after the first photosynthetic chromist evolved that new machinery (Cavalier-Smith et al., 1994;Baurain et al., 2010). Conversely, if chromists are holophyletic and ancestrally photophagotrophic, a single red algal enslavement produced the ancestral chromist, subsequent plastid losses yielding ancestrally heterotrophic chromist groups like ciliates, Rhizaria, and Heliozoa (Cavalier-Smith, 1999, 2010aCavalier-Smith and Scoble, 2013). ...
... Axopodia carry granules ('extrusomes') that entrap prey and secrete immobilizing and digestive enzymes. Axopodial protists are polyphyletic, comprising subphylum Radiozoa (within the rhizarian phylum Retaria), rhizarian infraclass Phaeodaria of Cercozoa, phylum Heliozoa (with Haptophyta forming infrakingdom Haptista (Cavalier-Smith, 2003b), and a less speciose array of diverse pseudoheliozoa that evolved independently within Cercozoa and Ochrophyta (an ancestrally and predominantly algal heterokont phylum that includes pseudoheliozoan pedinellids and actinophryids (Cavalier-Smith and Scoble, 2013)). Axopodial skeletons and extrusomes of each group have characteristic ultrastructure, consistent with sequence evidence assigning them to very different places in the chromist tree (reviewed by Cavalier- ). ...
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Heliozoan protists have radiating cell projections (axopodia) supported by microtubular axonemes nucleated by the centrosome and bearing granule-like extrusomes for catching prey. To clarify previously confused heliozoan phylogeny we sequenced partial transcriptomes of two tiny naked heliozoa, the endohelean Microheliella maris and centrohelid Oxnerella marina, and the cercozoan pseudoheliozoan Minimassisteria diva. Phylogenetic analysis of 187 genes confirms that all are chromists; but centrohelids (microtubules arranged as hexagons and triangles) are not sisters to Endohelea having axonemes in transnuclear cytoplasmic channels (triangular or square microtubular arrays). Centrohelids are strongly sister to haptophytes (together phylum Haptista); we explain the common origins of their axopodia and haptonema. Microheliella is sister to new superclass Corbistoma (zooflagellate Telonemea and Picomonadea, with asymmetric microfilamentous pharyngeal basket), showing that these axopodial protists evolved independently from zooflagellate ancestors. We group Corbistoma and Endohelea as new cryptist subphylum Corbihelia with dense fibrillar interorganellar connections; endohelean axopodia and Telonema cortex are ultrastructurally related. Differently sampled trees clarify why corticate multigene eukaryote phylogeny is problematic: long-branch artefacts probably distort deep multigene phylogeny of corticates (Plantae, Chromista); basal radiations may be contradictorily reconstructed because of their extreme closeness and the Bayesian star-tree paradox. Haptista and Hacrobia are holophyletic, and Chromista probably are. Copyright © 2015. Published by Elsevier Inc.
... Stramenopiles includes a wide range of photosynthetic forms as well as many heterotrophs (see Cavalier-Smith and Scoble 2013). Photosynthetic stramenopiles, also known as ochrophytes, have plastids derived ultimately from a red algal donor and form a monophyletic group (Cavalier-Smith and Scoble 2013;Derelle et al. 2016). The best known are the diatoms (▶ Bacillariophyta), which are unicellular/colonial forms with bipartite siliceous "cell walls" that are of huge ecological importance in the marine microplankton (e.g.), and the filamentous or genuinely multicellular ▶ Phaeophyta, informally known as brown algae. ...
... Furthermore, environmental sequencing studies have shown that the oceans contain a wide diversity of undescribed lineages of stramenopiles, collec- tively called "MASTs" (MArine STramenopiles; though some are also found in freshwater), which appear to be largely or entirely heterotrophic flagellates ( Massana et al. 2014). In recent years, a couple of species that belong to one MAST lineage have been cultivated or reinvestigated (Incisomonas and Solenicola), and this group is now known as Nanomonadea (Cavalier-Smith and Scoble 2013). None of these various heterotrophic flagellate groups is covered in the Handbook; a summary of MAST diversity is given by Massana et al. (2014). ...
Chapter
The last quarter century has seen dramatic changes in our understanding of the phylogenetic relationships among protist groups and their evolutionary history. This is due in large part to the maturation of molecular phylogenetics, to genomics and transcriptomics becoming widely used tools, and to ongoing and accelerating progress in characterizing the major lineages of protists in the biosphere. As an introduction to the Handbook of the Protists, Second Edition, we provide a brief account of the diversity of protistan eukaryotes, set within the context of eukaryote phylogeny as currently understood. Most protist lineages can be assigned to one of a handful of major groupings (“supergroups”). These include Archaeplastida (which also includes land plants), Sar (including Stramenopiles/Heterokonta, Alveolata, and Rhizaria), Discoba, Metamonada, Amoebozoa, and Obazoa. This last group in turn contains Opisthokonta, the clade that includes both animals and fungi. Many, but not all, of the deeper-level phylogenetic relationships within these groups are now resolved. Additional well-known groups that are related to Archaeplastida and/or Sar include Cryptista (cryptophyte algae and their relatives), Haptophyta, and Centrohelida, among others. Another set of protist lineages are probably most closely related to Amoebozoa and Obazoa, including Ancyromonadida and perhaps Malawimonadidae (though the latter may well be more closely related to Metamonada). The bulk of the known diversity of protists is covered in the following 43 chapters of the Handbook of the Protists; here we also briefly introduce those lineages that are not covered in later chapters. The Handbook is both a community resource and a guidebook for future research by scientists working in diverse areas, including protistology, phycology, microbial ecology, cell biology, and evolutionary genomics.
... When the first phylogenetic trees that included the available 18S rRNA gene sequence (AY788937. 1) from Olisthodiscus luteus NIES-15 were finally published by others, this organism appeared as an isolated branch outside Raphidophyceae or any other conventionally defined ochrophyte class (P ribyl et al. 2012, Cavalier-Smith andScoble 2013). Based on this, Cavalier-Smith assigned O. luteus to a newly erected subclass Sulcophycidae and placed it along with pelagophytes and dictyochophytes (treated together as the subclass Alophycidae) into his class Hypogyristea, despite the arguably insignificant bootstrap support for the monophyly of this class (Cavalier-Smith and Scoble 2013). ...
... This shows that the different Olisthodiscus strains have a special cell covering not known in other ochrophytes. The SEM data showed that Olisthodiscus does not have a sulcus confining the posterior flagellum, as previously claimed by Cavalier-Smith and Scoble (2013). Our data confirmed that the two flagella indeed arise from a ventral depression as originally described (Carter 1937). ...
Article
The phylogenetic diversity of Ochrophyta, a diverse and ecologically important radiation of algae, is still incompletely understood even at the level of the principal lineages. One taxon that has eluded simple classification is the marine flagellate genus Olisthodiscus. We investigated O. luteus K‐0444, and documented its morphological and genetic differences from the NIES‐15 strain, which we described as O. tomasii sp. nov. Phylogenetic analyses of combined 18S and 28S rRNA sequences confirmed that Olisthodiscus constitutes a separate, deep, ochrophyte lineage, but its position could not be resolved. To overcome this problem, we sequenced the plastid genome of O. luteus K‐0444 and used the new data in multigene phylogenetic analyses, which suggested that Olisthodiscus is a sister lineage of the class Pinguiophyceae within a broader clade additionally including Chrysophyceae, Synchromophyceae, and Eustigmatophyceae. Surprisingly, the Olisthodiscus plastid genome contained three genes, ycf80, cysT, and cysW, inherited from the rhodophyte ancestor of the ochrophyte plastid yet lost from all other ochrophyte groups studied so far. Combined with nuclear genes for CysA and Sbp proteins, Olisthodiscus is the only known ochrophyte possessing a plastidial sulfate transporter SulT. In addition, the finding of a cemA gene in the Olisthodiscus plastid genome and an updated phylogenetic analysis ruled out the previously proposed hypothesis invoking horizontal cemA transfer from a green algal plastid into Synurales. Altogether, Olisthodiscus clearly represents a novel phylogenetically distinct ochrophyte lineage, which we have proposed as a new class, Olisthodiscophyceae.
... Actinophryidae includes enigmatic eukaryvorous, heterotrophic protists belonging to the Stramenopiles (Adl et al. 2019). Their spherical cells lack cilia, but possess a number of microtubule-supported, radiating axopodia (Ockleford and Tucker 1973;Suzaki et al. 1980;Sakaguchi et al. 1998;Mikrjukov and Patterson 2001;Cavalier-Smith and Scoble 2013). Ultrastructural studies have not detected any plastid or plastid-like structures. ...
... Ultrastructural studies have not detected any plastid or plastid-like structures. The phylogenetic position of Actinophryidae remains unclear, despite its detailed morphological characterization and molecular phylogenetic analyses based on genes for 18S rRNA and actin have been conducted (Ockleford and Tucker 1973;Suzaki et al. 1980;Sakaguchi et al. 1998;Mikrjukov and Patterson 2001;Nikolaev et al 2004;Cavalier-Smith and Scoble 2013). ...
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Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (non-photosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRS) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened prior to the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually-targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host-plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions.
... Prior to this study, eleven Rhizomastix species, both freeliving and endobiotic, had been described. The endobiotic species were isolated from insects, namely crane flies, cockroaches and mole crickets (R. dastagiri, R. gracilis, R. gryllotalpae, R. murthii, R. periplanetae) (Bhaskar Rao 1963, 1970Ludwig 1946;Mackinnon 1913;Mali et al. 2002;Sultana 1976), amphibians (R. biflagellata, R. gracilis, R. ranae) (Alexeieff 1911;Cepicka 2011;Jim enez et al. 2001;Krishnamurthy 1969) and reptiles (R. scincorum) (Bovee and Telford 1962;Cavalier-Smith and Scoble 2013). Rhizomastix hominis was isolated from human faeces (Yakimoff and Kolpakoff 1921). ...
Article
The genus Rhizomastix is a poorly-known group of amoeboid heterotrophic flagellates living as intestinal commensals of insects, amphibians or reptiles, and as inhabitants of organic freshwater sediments. Eleven Rhizomastix species have been described so far, but DNA sequences from only a single species have been published. Recently, phylogenetic analyses confirmed a previous hypothesis that the genus belongs to the Archamoebae; however, its exact position therein remains unclear. In this study we cultured nine strains of Rhizomastix, both endobiotic and free-living. According to their light-microscopic morphology and SSU rRNA and actin gene analyses, the strains represent five species, of which four are newly described here: R. bicoronata sp. nov., R. elongata sp. nov., R. vacuolata sp. nov. and R. varia sp. nov. In addition, R. tipulae sp. nov., living in the intestine of crane flies, is separated from the type species, R. libera. We also examined the ultrastructure of R. elongata sp. nov., which revealed that it is more complicated than the previously-described R. libera. Our data show that either the endobiotic lifestyle of some Rhizomastix species has arisen independently from other endobiotic archamoebae, or the free-living members of this genus represent a secondary switch from the endobiotic lifestyle. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
... For a much better understanding of their origins we need multigene trees for all lineages of Variosea and Mycetozoa, as previous 18S rDNA trees suggested that protosteloids (non-social amoebae whose resting cysts are born on stalks and thus are called spores by analogy with those of slime mould fruiting bodies, and which were formerly lumped in class Protostelea) and Variosea are phylogenetically partially overlapping (Shadwick et al., 2009). Prior to the present paper Variosea comprised four morphologically distinct orders, three ciliated: uniciliate Phalansteriida (Phalansterium, Rhizomonas and three other largely sedentary and non-amoeboid genera: Cavalier-Smith, 2013; Cavalier-Smith and Scoble, 2013); Holomastigida, (the only minimally amoeboid Multicilia); and putatively multiciliate but not highly mobile Artodiscida (no sequences available). The non-ciliate Varipodida are unfortunately the only variosean order with available transcriptomes, making it very hard to establish their relationships and to decide whether Variosea are the paraphyletic ancestors of all Conosa or the earliest diverging clade or clarify phenotypic evolutionary patterns within the class. ...
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Monophyly of protozoan phylum Amoebozoa, and subdivision into subphyla Conosa and Lobosa each with different cytoskeletons, are well established. However early diversification of non-ciliate lobose amoebae (Lobosa) is poorly understood. To clarify it we used recently available transcriptomes to construct a 187-gene amoebozoan tree for 30 species, the most comprehensive yet. This robustly places new genus Atrichosa (formerly lumped with Trichosphaerium) within lobosan class Tubulinea, not Discosea as previously supposed. We identified an earliest diverging lobosan clade comprising marine amoebae armoured by porose scaliform cell-envelopes, here made a novel class Cutosea with two pseudopodially distinct new families. Cutosea comprise Sapocribrum, ATCC PRA-29 misidentified as ‘Pessonella’, plus from other evidence Squamamoeba. We confirm that Acanthamoeba and ATCC 50982 misidentified as Stereomyxa ramosa are closely related. Discosea have a strongly supported major subclade comprising Thecamoebida plus Glycostylida (suborders Dactylopodina, Stygamoebina; Vannellina) phylogenetically distinct from Centramoebida. Himatismenida (now including new suborder Pellitina) are either sister to Centramoebida or deeper branching. Discosea usually appear holophyletic (rarely paraphyletic). Paramoeba transcriptomes include prokinetoplastid Perkinsela-like endosymbiont sequences. Cunea, misidentified as Mayorella, is closer to Paramoeba than Vexillifera within holophyletic Dactylopodina. Taxon-rich site-heterogeneous rDNA trees confirm cutosan distinctiveness, allow improved conosan taxonomy, and reveal previous dictyostelid tree misrooting.
... Their joint clade is robustly (90% support) part of a major radiation of terrestrial gregarines that includes Monocystis, Steinina ctenocephali, and Syncystis. This strongly supported clade also includes 19 aspen rhizosphere soil DNA gregarine clones previously misannotated as Eimeriidae or Cryptosporidiidae (Lesaulnier et al. 2008); previously we and others showed that other sequences called Eimeriidae in that study actually come from many different phyla all across the neozoan part of the eukaryotic tree Chao 2010, 2012;Cavalier-Smith and Scoble 2013;Howe et al. 2011;Kudryavtsev et al. 2011;Lara et al. 2011). This large clade of terrestrial gregarines was made a new superfamily Actinocephaloidea in Cavalier-Smith (2014) and is strongly sister to the gregarine family Stylocephalidae (Fig. 1). ...
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Contradictory and confusing results can arise if sequenced 'monoprotist' samples really contain DNA of very different species. Eukaryote-wide phylogenetic analyses using five genes from the amoeboflagellate culture ATCC 50646 previously implied it was an undescribed percolozoan related to percolatean flagellates (Stephanopogon, Percolomonas). Contrastingly, three phylogenetic analyses of 18S rRNA alone, did not place it within Percolozoa, but as an isolated deep-branching excavate. I resolve that contradiction by sequence phylogenies for all five genes individually, using up to 652 taxa. Its 18S rRNA sequence (GQ377652) is near-identical to one from stained-glass windows, somewhat more distant from one from cooling-tower water, all three related to terrestrial actinocephalid gregarines Hoplorhynchus and Pyxinia. All four protein-gene sequences (Hsp90; α-tubulin; β-tubulin; actin) are from an amoeboflagellate heterolobosean percolozoan, not especially deeply branching. Contrary to previous conclusions from trees combining protein and rRNA sequences or rDNA trees including Eozoa only, this culture does not represent a major novel deep-branching eukaryote lineage distinct from Heterolobosea, and thus lacks special significance for deep eukaryote phylogeny, though the rDNA sequence is important for gregarine phylogeny. α-tubulin trees for over 250 eukaryotes refute earlier suggestions of lateral gene transfer within eukaryotes, being largely congruent with morphology and other gene trees. Copyright © 2015. Published by Elsevier GmbH.
... Subsequent studies have propagated the double meaning for MAST-13. On one hand, Kolodziej and Stoeck (2007), Park and Simpson (2010), Orsi et al. (2011), Cavalier-Smith andScoble (2013), and Massana et al. (2014) has been subsequently excluded from the MAST clades (Massana et al. 2014) because of its clear affiliation with the Bicosoecida. On the other hand, Takishita et al.'s (2010) analysis of environmental DNA sequences included only their version of MAST-13 (NA-MAKO-31), but not Zuendorf et al.'s version of MAST-13 lineages. ...
Article
Although environmental DNA surveys improve our understanding of biodiversity, interpretation of unidentified lineages is limited by the absence of associated morphological traits and living cultures. Unidentified lineages of marine stramenopiles are called “MAST clades”. Twenty-five MAST clades have been recognized: MAST-1 through MAST-25; seven of these have been subsequently discarded because the sequences representing those clades were found to either (1) be chimeric or (2) affiliate within previously described taxonomic groups. Eighteen MAST clades remain without a cellular identity. Moreover, the discarded “MAST-13” has been used in different studies to refer to two different environmental sequence clades. After establishing four cultures representing two different species of heterotrophic stramenopiles and then characterizing their morphology and molecular phylogenetic positions, we determined that the two different species represented the two different MAST-13 clades: (1) a lorica-bearing Bicosoeca kenaiensis and (2) a microaerophilic flagellate previously named “Cafeteria marsupialis”. Both species were previously described with only light microscopy; no cultures, ultrastructural data or DNA sequences were available from these species prior to this study. The molecular phylogenetic position of three different “C. marsupialis” isolates was not closely related to the type species of Cafeteria; therefore, we established a new genus for these isolates, Cantina gen. nov.This article is protected by copyright. All rights reserved.
... The pelagophyte Au. anophagefferens lacks genes for the aspartate pathway and instead encodes genes for the kynurenine pathway, whereas all other photosynthetic Stramenopiles appear to contain the aspartate pathway. This is especially puzzling, as the lineages of Pelagophyceae and brown algae (Phaeophyceae) are supposed to have split after the Oomycota (water molds or downy mildew) and diatoms (Bacillariophyceae) formed separate lineages ( fig. 2) (Brown and Sorhannus 2010;Cavalier-Smith and Scoble 2013). Although the early diverging stramenopile clade Labyrinthulomycetes probably reflects the ancient state, that is, inherited the kynurenine pathway from the last common ancestor of all eukaryotes, this does not seem to be a valid explanation for Au. ...
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NAD+ is an essential molecule for life, present in each living cell. It can function as an electron carrier or cofactor in redox biochemistry and energetics, and serves as substrate to generate the secondary messenger cyclic ADP ribose and nicotinic acid adenine dinucleotide phosphate. Although de novo NAD+ biosynthesis is essential, different metabolic pathways exist in different eukaryotic clades. The kynurenine pathway starting with tryptophan was most likely present in the last common ancestor of all eukaryotes, and is active in fungi and animals. The aspartate pathway, detected in most photosynthetic eukaryotes, was probably acquired from the cyanobacterial endosymbiont that gave rise to chloroplasts. An evolutionary analysis of enzymes catalyzing de novo NAD+ biosynthesis resulted in evolutionary trees incongruent with established organismal phylogeny, indicating numerous gene transfers. Endosymbiotic gene transfers probably introduced the aspartate pathway into eukaryotes and may have distributed it among different photosynthetic clades. In addition, several horizontal gene transfers substituted eukaryotic genes with bacterial orthologs. Although horizontal gene transfer is accepted as a key mechanism in prokaryotic evolution, it is supposed to be rare in eukaryotic evolution. The essential metabolic pathway of de novo NAD+ biosynthesis in eukaryotes was shaped by numerous gene transfers.
... Two environmental sequences were misannotated as thaumatomonads, from the same soil study (Lesaulnier et al. 2008) from which many previous papers found numerous misannotations affecting other groups (e.g. Cavalier-Smith and Chao 2012;Cavalier-Smith and Scoble 2013;Howe et al. 2011a): Amb 18S 1199 (EF023758) is maximally supported as sister to Nudifila, placed below in the new family Nudifilidae: environmental sequence Elev 18S 823 (EF024516) is not even an imbricate or ventrifilosan sequence, but belongs to the deep-branching probable glissomonad clade Te that also includes a sequence (EF023937) even more bizarrely annotated as an apicomplexan eimeriid (Lesaulnier et al. 2008). Fig. 1.1 does, however, reveal three distinct environmental clades lacking cultured representatives that are genuinely within Thaumatomonadidae, two from soil (AB534345, EF023728), one from marine sand (AY620317). ...
Article
We describe 11 new species of Thaumatomonadida using light and electron microscopy and rDNA gene sequences (18S, ITS1, 5.8S, ITS2). We found clear distinctions between major clades in molecular and morphological traits that support now splitting Thaumatomastix into three genera: new marine genera Ovaloplaca (oval plate-scales) and Thaumatospina (triangular plate-scales), both with distinctive radially-symmetric bobbin-based spine-scales, restricting Thaumatomastix to freshwater species with putatively non-homologous eccentric-spine scales and thicker triangular plate-scales. New genus Scutellomonas lacks spine-scales, having oval plate-scales with deeply-dished upper tier as in Ovaloplaca, with which it forms a clade having short/absent anterior cilium. Cowlomonas gen. n. is possibly naked. We describe two new Allas species, two new Thaumatomonas, and one new Reckertia species, and transfer R. hindoni to Thaumatomonas. Triangular-scaled Reckertia has varied plate-scales and ciliary scales. Thaumatomonas rDNA trees reveal two clades: zhukovi/seravini (predominantly triangular scales); coloniensis/oxoniensis/lauterborni/constricta/solis (scales mostly oval). We hypothesize that the ancestor of Thaumatomonadidae had radially-symmetric bobbin-based spine-scales and triangular plate-scales, bobbin-based spine-scales being lost in one lineage and eccentric-spine scales evolving in Thaumatomastix. Bobbin-based spine-scales arguably evolved from triangular plate-scales and single-tier ciliary scales (Ovaloplaca and Reckertia only) from plate-scale rudiments. We present a unified scheme for scale evolution and development in Imbricatea.
... An improved taxonomy for Paraphysomonas will improve our understanding of ecological studies, especially those concerned with microbial food-webs, seasonality, and biogeography. Also, the benefi t of knowing the genetic distance of silica-scaled protists like Paraphysomonas will give a more unifi ed picture of their evolution and might also help us better interpret the genetic diversity of scaleless protists, especially ones like Spumella, which branch in several parts of the chrysophyte tree and obviously had polyphyletic origins from algal ancestors entirely independently of Paraphysomonas (Cavalier-Smith & Chao 2006, Cavalier-Smith & Scoble 2013. Though Spumella were once included in Leucophycidae and Paraphysomonadida , they are now fi rmly excluded (Cavalier-Smith & Chao 2006) and must be classifi ed in at least three separate places within Ochromonadales, and at least two new genera established. ...
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*I have purchased preprints if you would like a copy of my article - limited number available.* The chrysophyte genus Paraphysomonas has over 50 species, distinguished by a remarkably diverse array of scale morphology – from simple spine scales to complex basket or mesh-work scales. Only a few species are commonly found in environmental surveys, often by examining crude water and silt samples. Despite the commonness of those few species, only limited sequence data are publicly avail- able for known species. The few sequences that are available are not helpful in resolving the taxonomic or evolutionary relationship amongst all these morphologically diverse Paraphysomonas species, partly because different strains identified as the same species have such divergent sequences that misidentification must have been frequent, and partly because sequences are available for only two major scale types and four nominal species. There is much need for clonal cultures of Paraphysomonas on which sequencing and electron microscopy can be carried out in parallel, in order to shed light on the taxonomy of this ‘genus’. This short review attempts to highlight mistakes in the literature that have led to the confusion of a few common Paraphysomonas species and thus propose new ways to scrutinize scale data by listing key spine- scale features, thus rejuvenating research on a common ‘genus’ and revealing its previously overlooked diversity. A more critical approach is expected to subdivide Paraphysomonas into several genera according to their contrasting scale morphologies.
... Thus, our study highlights the importance of metabarcoding analyses. Using short fragments of the 18S rRNA gene is an important first step toward detecting novel eukaryotic diversity, paving the way for further isolation and description of new taxa (del Campo and Gómez et al., 2011;Cavalier-Smith and Scoble, 2013;Shiratori et al., 2017;López-Escardó et al., 2018). ...
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Opisthokonta represents a major lineage of eukaryotes and includes fungi and metazoans, as well as other less known unicellular groups. The latter are paraphyletic assemblages that branch in between the former two groups, and thus are important for understanding the origin and early diversification of opisthokonts. The full range of their diversity, however, has not yet been explored from diverse ecological habitats. Freshwater environments are crucial sources for new diversity; they are considered even more heterogeneous than marine ecosystems. This heterogeneity implies more ecological niches where local eukaryotic communities are located. However, knowledge of the unicellular opisthokont diversity is scarce from freshwater environments. Here, we performed an 18S rDNA metabarcoding study in the Middle Paraná River, Argentina, to characterize the molecular diversity of microbial eukaryotes, in particular unicellular members of Opisthokonta. We identified a potential novel clade branching as a sister-group to Fungi. We also detected in our data that more than 60% operational taxonomic units classified as unicellular holozoans (animals and relatives) represent new taxa at the species level. Of the remaining, the majority was assigned to the newly described holozoan species, Syssomonas multiformis. Together, our results show that a large hidden diversity of unicellular members of opisthokonts still remain to be uncovered. We also found that the geographical and ecological distribution of several taxa considered exclusive to marine environments is wider than previously thought.
... Curators can incorporate relevant information from diverse sources such as traditional classification schemes, phylogenomic studies, historical literature, morphological observations, and distribution data from high-throughput sequencing studies [22]. Such expert knowledge enables researchers to generate robust classification schemes for lineages known only from sequences, such as the diverse marine stramenopiles (MASTs [23]), and can provide a mechanism for workers to link described organisms to proposed environmental MAST lineages (e.g., Solenicola setigera and Incisomonas marina, which belong to the MAST-3 [24,25] clade, or Pseudophyllomitus vesiculosus, which belongs to the MAST-6 clade [26]). Many parts of the eukaryotic tree of life are currently known either from sequences or from morphological records, but not both [27,28], so enabling morphological data to inform molecular classification is crucial [21]. ...
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Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef ( eukref.org ) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.
... Oomycetes superficially resemble fungi in appearance, but phylogenetically belong to the stramenopile (or heterokont) lineage, that includes brown algae and diatoms [1]. Phytophthora infestans is an exemplar oomycete that has been a focus of sustained investigation owing to its devastating global impact on potato and tomato production, as the causative organism of late blight [2]. ...
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In eukaryotes, two sources of Ca2+ are accessed to allow rapid changes in the cytosolic levels of this second messenger: the extracellular medium and intracellular Ca2+ stores, such as the endoplasmic reticulum. One class of channel that permits Ca2+ entry is the transient receptor potential (TRP) superfamily, including the polycystic kidney disease (PKD) proteins, or polycystins. Channels that release Ca2+ from intracellular stores include the inositol 1,4,5-trisphosphate/ryanodine receptor (ITPR/RyR) superfamily. Here, we characterise a family of proteins that are only encoded by oomycete genomes, that we have named PKDRR, since they share domains with both PKD and RyR channels. We provide evidence that these proteins belong to the TRP superfamily and are distinct from the ITPR/RyR superfamily in terms of their evolutionary relationships, protein domain architectures and predicted ion channel structures. We also demonstrate that a hypothetical PKDRR protein from Phytophthora infestans is produced by this organism, is located in the cell-surface membrane and forms multimeric protein complexes. Efforts to functionally characterise this protein in a heterologous expression system were unsuccessful but support a cell-surface localisation. These PKDRR proteins represent potential targets for the development of new “fungicides”, since they are of a distinctive structure that is only found in oomycetes and not in any other cellular organisms.
... Pteridomonas;Patterson 1985) are the only vegetatively flagellate chromists to have entirely lost centriolar roots when losing the posterior cilium and evolving periciliary axopodial feeding; I suggest they were able to do so by using the multiply duplicated noncentriolar BBs to make a circlet of 3-mt axopodia around the remaining anterior cilium whose water currents drew in prey to them. I earlier suggested that actinophryid axopodia evolved independently by multiplying raphidophyte rhizostyle mts (Cavalier-Smith and Scoble 2013), arguing that the rhizostyle is a composite of a standard root R2 and a non-root (nucleus-and PM-associated) mt structure perhaps antiparallel to it, which I now suggest is a BB (see fuller supplementary discussion SD10). Of the four main chromist lineages, only alveolates never use BB-derived axopodia in that way: Ciliophora lost BB through focusing on multiplying kinetids to make giant multiciliate predators, whereas Myzozoa used BB as ancillary to a novel feeding mode-myzocytosis, which in Apicomplexa became the apicomonad pseudoconoid and sporozoan conoid. ...
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In 1981 I established kingdom Chromista, distinguished from Plantae because of its more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. Plantae originated by converting a cyanobacterium to chloroplasts with Toc/Tic translocons; most evolved cell walls early, thereby losing phagotrophy. Chromists originated by enslaving a phagocytosed red alga, surrounding plastids by two extra membranes, placing them within the endomembrane system, necessitating novel protein import machineries. Early chromists retained phagotrophy, remaining naked and repeatedly reverted to heterotrophy by losing chloroplasts. Therefore, Chromista include secondary phagoheterotrophs (notably ciliates, many dinoflagellates, Opalozoa, Rhizaria, heliozoans) or walled osmotrophs (Pseudofungi, Labyrinthulea), formerly considered protozoa or fungi respectively, plus endoparasites (e.g. Sporozoa) and all chromophyte algae (other dinoflagellates, chromeroids, ochrophytes, haptophytes, cryptophytes). I discuss their origin, evolutionary diversification, and reasons for making chromists one kingdom despite highly divergent cytoskeletons and trophic modes, including improved explanations for periplastid/chloroplast protein targeting, derlin evolution, and ciliary/cytoskeletal diversification. I conjecture that transit-peptide-receptor-mediated ‘endocytosis’ from periplastid membranes generates periplastid vesicles that fuse with the arguably derlin-translocon-containing periplastid reticulum (putative red algal trans-Golgi network homologue; present in all chromophytes except dinoflagellates). I explain chromist origin from ancestral corticates and neokaryotes, reappraising tertiary symbiogenesis; a chromist cytoskeletal synapomorphy, a bypassing microtubule band dextral to both centrioles, favoured multiple axopodial origins. I revise chromist higher classification by transferring rhizarian subphylum Endomyxa from Cercozoa to Retaria; establishing retarian subphylum Ectoreta for Foraminifera plus Radiozoa, apicomonad subclasses, new dinozoan classes Myzodinea (grouping Colpovora gen. n., Psammosa), Endodinea, Sulcodinea, and subclass Karlodinia; and ranking heterokont Gyrista as phylum not superphylum. Electronic supplementary material The online version of this article (10.1007/s00709-017-1147-3) contains supplementary material, which is available to authorized users.
... Oomycetes were once placed within fungi in earlier classification systems, but are now widely considered as part of stramenopiles (Baldauf et al., 2000;Yoon et al., 2002). Although there are different views about the phylogenetic relationships within stramenopiles (Brown and Sorhannus, 2009;Riisberg et al., 2009;Yang et al., 2012;Cavalier-Smith and Scoble, 2013;Ševčíková et al., 2015), the most recent phylogenomic analyses suggest that oomycetes form a clade closely related to ochrophytes, a monophyletic group of photosynthetic stramenopiles (Derelle et al., 2016). Unlike ochrophytes, oomycetes do not contain plastids (Tyler et al., 2006;Derelle et al., 2016), not even vestigial ones like those in apicomplexan parasites (called apicoplast) (Maréchal and Cesbron-Delauw, 2001). ...
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The spread of photosynthesis is one of the most important but constantly debated topics in eukaryotic evolution. Various hypotheses have been proposed to explain the plastid distribution in extant eukaryotes. Notably, the chromalveolate hypothesis suggested that multiple eukaryotic lineages were derived from a photosynthetic ancestor that had a red algal endosymbiont. As such, genes of plastid/algal origin in aplastidic chromalveolates, such as oomycetes, were considered to be important supporting evidence. Although the chromalveolate hypothesis has been seriously challenged, some of its supporting evidence has not been carefully investigated. In this study, we re-evaluate the “algal” genes from oomycetes with a larger sampling and careful phylogenetic analyses. Our data provide no conclusive support for a common photosynthetic ancestry of stramenopiles, but show that the initial estimate of “algal” genes in oomycetes was drastically inflated due to limited genome data available then for certain eukaryotic lineages. These findings also suggest that the evolutionary histories of these “algal” genes might be attributed to complex scenarios such as differential gene loss, serial endosymbioses, or horizontal gene transfer.
... Curators can incorporate relevant information from diverse sources such as traditional classification schemes, phylogenomic studies, historical literature, morphological observations, and distribution data from high-throughput sequencing studies [22]. Such expert knowledge enables researchers to generate robust classification schemes for lineages known only from sequences, such as the diverse marine stramenopiles (MASTs [23]), and can provide a mechanism for workers to link described organisms to proposed environmental MAST lineages (e.g., Solenicola setigera and Incisomonas marina, which belong to the MAST-3 [24,25] clade, or Pseudophyllomitus vesiculosus, which belongs to the MAST-6 clade [26]). Many parts of the eukaryotic tree of life are currently known either from sequences or from morphological records, but not both [27,28], so enabling morphological data to inform molecular classification is crucial [21]. ...
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Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is an ongoing community-driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the eukaryotic tree of life and microbial ecologists, who use environmental sequence data to develop reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous mining and annotation of sequence data by providing protocols, guidelines, and tools. The EukRef pipeline and tools allow users interested in a particular group of microbial eukaryotes to retrieve all sequences belonging to that group from International Nucleotide Sequence Database Collaboration (INSDC) (GenBank, European Nucleotide Archive [ENA], or DBJD), to place those sequences in a phylogenetic tree, and to curate taxonomic and environmental information for the group. We provide guidelines to facilitate the process and to standardize taxonomic annotations. The final outputs of this process are (1) a reference tree and alignment, (2) a reference sequence database, including taxonomic and environmental information, and (3) a list of putative chimeras and other artifactual sequences. These products will be useful for the broad community as they become publicly available (at eukref.org) and are shared with existing reference databases.
... MAST-3 were the most diverse group, with 135 ASVs in this study (supplementary file 6). Solenicola setigera and Incisomonas marina have been identified as belonging to MAST-3I and 3 J, respectively, and Solenicola setigera was recognized as the diatom symbiont [7,27]. In the sECS, MAST-3E contributed the maximum reads in MAST-3 ( Fig. S3), whereas MAST-3I provided higher diversity (32 ASVs vs. 19 ASVs for MAST-3E, supplementary file 6). ...
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MArine STramenopiles (MASTs) have been recognized as parts of heterotrophic protists and contribute substantially to protist abundances in the ocean. However, little is known about their spatiotemporal variations with respect to environmental and biological factors. The objectives of this study are to use canonical correspondence analysis to investigate how MASTs communities are shaped by environmental variables, and co-occurrence networks to examine their potential interactions with prokaryotic communities. Our dataset came from the southern East China Sea (sECS) in the subtropical northwestern Pacific, and involved 14 cruises along a coastal-oceanic transect, each of which sampled surface water from 4 to 7 stations. MASTs communities were revealed by metabarcoding of 18S rDNA V4 region. Most notably, MAST-9 had a high representation in warm waters in terms of read number and diversity. Subclades of MAST-9C and -9D showed slightly different niches, with MAST-9D dominating in more coastal waters where concentrations of nitrite and Synechococcus were higher. MAST-1C was a common component of colder water during spring. Overall, canonical correspondence analysis showed that MASTs communities were significantly influenced by temperature, nitrite and Synechococcus concentrations. The co-occurrence networks showed that certain other minor prokaryotic taxa can influence MAST communities. This study provides insight into how MASTs communities varied with environmental and biological variables.
... A partial genome of a MAST-4 clade D was previously characterized using single-cell sequencing 8 . In this study, we present three distinct genomes from clades A, C, and E, clearly divergent from clade D. MAST-3 11 is a very diverse group of small flagellated organisms that includes a potential diatom epibiont and one cultured strain 13,14 . Heterotrophic chrysophytes from the Clade H additionally appear to be abundant in the ocean, according to environmental DNA surveys 15 . ...
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Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine p
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A novel facultative anaerobic bacterivorous nanoflagellate was isolated from the water just below the permanent oxic-anoxic interface of the meromictic Lake Suigetsu, Japan. We characterized the isolate using light and transmission electron microscopy and molecular phylogenetic analyses inferred from 18S rDNA sequences. The phylogenetic analyses showed that the isolate belonged to class Placididea (stramenopiles). The isolate showed key ultrastructural features of the Placididea, such as flagellar hairs with two unequal terminal filaments, microtubular root 2 changing in shape from an arced to an acute-angled shape, and a lack of an x-fiber in root 2. However, the isolate had a single helix in the flagellar transition region, which is a double helix in the two known placidid nanoflagellates Placidia cafeteriopsis and Wobblia lunata. Moreover, the isolate had different intracellular features compared with these two genera, such as the arrangement of basal bodies, the components of the flagellar apparatus, the number of mitochondria, and the absence (or presence) of paranuclear bodies. The 18S rDNA sequence was also phylogenetically distant from the clades of the known Placididae W. lunata and P. cafeteriopsis. Consequently, the newly isolated nanoflagellate was described as Suigetsumonas clinomigrationis gen. et sp. nov. Copyright © 2015 Elsevier GmbH. All rights reserved.
Article
We describe Diplophrys parva n. sp., a freshwater heterotroph, using fine structural and sequence evidence. Cells are small (L = 6.5 +/- 0.08 mu m, W = 5.5 +/- 0.06 mu m; mean +/- SE) enclosed by an envelope/theca of overlapping scales, slightly oval to elongated-oval with rounded ends, (1.0 x 0.5-0.7 mu m), one to several intracellular refractive granules (similar to 1.0-2.0 mu m), smaller hyaline peripheral vacuoles, a nucleus with central nucleolus, tubulo-cristate mitochondria, and a prominent Golgi apparatus with multiple stacked saccules (= 10). It is smaller than published sizes of Diplophrys archeri (similar to 10-20 mu m), modestly less than Diplophrys marina (similar to 5-9 mu m), and differs in scale size and morphology from D. marina. No cysts were observed. We transfer D. marina to a new genus Amphifila as it falls within a molecular phylogenetic clade extremely distant from that including D. parva. Based on morphological and molecular phylogenetic evidence, Labyrinthulea are revised to include six new families, including Diplophryidae for Diplophrys and Amphifilidae containing Amphifila. The other new families have distinctive morphology: Oblongichytriidae and Aplanochytriidae are distinct clades on the rDNA tree, but Sorodiplophryidae and Althorniidae lack sequence data. Aplanochytriidae is in Labyrinthulida; the rest are in Thraustochytrida; Labyrinthomyxa is excluded.
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A novel free-living heterotrophic stramenopile, Platysulcus tardus gen. nov., sp. nov. was isolated from sedimented detritus on a seaweed collected near the Ngeruktabel Island, Palau. P. tardus is a gliding flagellate with tubular mastigonemes on the anterior short flagellum and a wide, shallow ventral furrow. Although the flagellar apparatus of P. tardus is typical of stramenopiles, it shows novel ultrastructural combinations that are not applied to any groups of heterotrophic stramenopiles. Phylogenetic analysis using SSU rRNA genes revealed that P. tardus formed a clade with stramenopiles with high support. However, P. tardus did not form a subclade with any species or environmental sequences within the stramenopiles, and no close relative was suggested by the phylogenetic analysis. Therefore, we concluded that P. tardus should be treated as a new genus and species of stramenopiles and have proposed a new family, Platysulcidae fam. nov., for this phylogenetically distinct organism. Copyright © 2015 Elsevier GmbH. All rights reserved.
Chapter
The opalinids (Opalinidae: genera Opalina, Cepedea, Protoopalina, Zelleriella, and Protozelleriella) are highly unusual protists with large cells, multiple flagella, and two to hundreds of nuclei. The name Opalina is derived from the iridescent appearance when light reflects on the delicately folded surface of the cells. Opalinids are found exclusively in the intestines of frogs and some other hosts. They form the group Slopalinida together with two related genera of intestinal flagellates, Karotomorpha and Proteromonas. The former is a tetrakont flagellate that inhabits the intestines of certain amphibians, while the latter possesses only two flagella and is found in a wider spectrum of vertebrate hosts. Both morphology and molecular data suggest that Karotomorpha is phylogenetically closer to the opalinids, although both flagellates were traditionally classified in a single family, Proteromonadidae. Molecular data have shown that yet another unusual gut protist is closely related to Slopalinida: the genus Blastocystis. Unlike its relatives, it bears no flagella and is usually observed in the form of spherical cells with huge vacuoles. It is quite common in the intestines of many vertebrates (including humans) and invertebrates. Together, these organisms form Opalinata, a diverse assemblage of variously modified unicellular eukaryotes.
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Protists play a fundamental role in all ecosystems, but we are still far from estimating the total diversity of many lineages, in particular in highly diverse environments, such as freshwater. Here, we survey the protist diversity of the Paraná River using metabarcoding, and we applied an approach that includes sequence similarity and phylogeny to evaluate the degree of genetic novelty of the protists' communities against the sequences described in the reference database PR2. We observed that ~28% of the amplicon sequence variants were classified as novel according to their similarity with sequences from the reference database; most of them were related to heterotrophic groups traditionally overlooked in freshwater systems. This lack of knowledge extended to those groups within the green algae (Archaeplastida) that are well documented such as Mamiellophyceae, and also to the less studied Pedinophyceae, for which we found sequences representing novel deep‐branching clusters. Among the groups with potential novel protists, Bicosoecida (Stramenopiles) were the best represented, followed by Codosiga (Opisthokonta), and the Perkinsea (Alveolata). This illustrates the lack of knowledge on freshwater planktonic protists and also the need for isolation and/or cultivation of new organisms to better understand their role in ecosystem functioning.
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The 'big new biology' is a vision of a discipline transformed by a commitment to sharing data and with investigative practices that call on very large open pools of freely accessible data. As this datacentric world matures, biologists will be better able to manage the deluge of data arising from digitization programs, governmental mandates for data sharing, and increasing instrumentation of science. The big new biology will create new opportunities for research and will enable scientists to answer questions that require access to data on a scale not previously possible. Informatics will become the new genomics, and those not participating will become marginalized. If a traditional discipline like protistology is to benefit from this big data world, it must define, build, and populate an appropriate infrastructure. The infrastructure is likely to be modular, with modules focusing on needs within defined subject and makes it available in standard formats by an array of pathways. It is the responsibility of protistologists to build such nodes for their own discipline.
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I thoroughly discuss ciliary transition zone (TZ) evolution, highlighting many overlooked evolutionarily significant ultrastructural details. I establish fundamental principles of TZ ultrastructure and evolution throughout eukaryotes, inferring unrecognised ancestral TZ patterns for Fungi, opisthokonts, and Corticata (i.e., kingdoms Plantae and Chromista). Typical TZs have a dense transitional plate (TP), with a previously overlooked complex lattice as skeleton. I show most eukaryotes have centriole/TZ junction acorn-V filaments (whose ancestral function was arguably supporting central pair microtubule-nucleating sites; I discuss their role in centriole growth). Uniquely simple malawimonad TZs (without TP, simpler acorn) pinpoint the eukaryote tree's root between them and TP-bearers, highlighting novel superclades. I integrate TZ/ciliary evolution with the best multiprotein trees, naming newly recognised major eukaryote clades and revise megaclassification of basal kingdom Protozoa. Recent discovery of non-photosynthetic phagotrophic flagellates with genome-free plastids (Rhodelphis), the sister group to phylum Rhodophyta (red algae), illuminates plant and chromist early evolution. I show previously overlooked marked similarities in cell ultrastructure between Rhodelphis and Picomonas, formerly considered an early diverging chromist. In both a nonagonal tube lies between their TP and an annular septum surrounding their 9+2 ciliary axoneme. Mitochondrial dense condensations and mitochondrion-linked smooth endomembrane cytoplasmic partitioning cisternae further support grouping Picomonadea and Rhodelphea as new plant phylum Pararhoda. As Pararhoda/Rhodophyta form a robust clade on site-heterogeneous multiprotein trees, I group Pararhoda and Rhodophyta as new infrakingdom Rhodaria of Plantae within subkingdom Biliphyta, which also includes Glaucophyta with fundamentally similar TZ, uniquely in eukaryotes. I explain how biliphyte TZs generated viridiplant stellate-structures.
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Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of the group. This is most obvious in Bigyromonadea, which is one of four major stramenopile subgroups but represented by a single transcriptome. To examine the diversity of Bigyromonadea and how the lack of data affects the tree, we generated transcriptomes from seven novel bigyromonada species described in this study: Develocauda condao n. gen. n. sp., Develocanicus komovi n. gen. n. sp., Develocanicus vyazemskyi n. sp., Cubaremonas variflagellatum n. gen. n. sp., Pirsonia chemainus nom. prov., Feodosia pseudopoda nom. prov., and Koktebelia satura nom. prov. Both maximum likelihood and Bayesian phylogenomic trees based on a 247 gene-matrix recovered a monophyletic Bigyromonadea that includes two diverse subgroups, Developea and Pirsoniales, that were not previously related based on single gene trees. Maximum likelihood analyses show Bigyromonadea related to oomycetes, whereas Bayesian analyses and topology testing were inconclusive. We observed similarities between the novel bigyromonad species and motile zoospores of oomycetes in morphology and the ability to self-aggregate. Rare formation of pseudopods and fused cells were also observed, traits that are also found in members of labyrinthulomycetes, another osmotrophic stramenopiles. Furthermore, we report the first case of eukaryovory in the flagellated stages of Pirsoniales. These analyses reveal new diversity of Bigyromonadea, and altogether suggest their monophyly with oomycetes, collectively known as Pseudofungi, is the most likely topology of the stramenopile tree.
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Three kinds of cells exist with increasingly complex membrane-protein targeting: Unibacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacteria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved ∼1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eukaryote cells, culminating in two dissimilar cilia via a novel gliding-fishing-swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost.
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Eustigmatophyceae (Ochrophyta, Stramenopiles) is a small algal group with species of the genus Nannochloropsis being its best studied representatives. Nuclear and organellar genomes have been recently sequenced for several Nannochloropsis spp., but phylogenetically wider genomic studies are missing for eustigmatophytes. We sequenced mitochondrial genomes (mitogenomes) of three species representing most major eustigmatophyte lineages, Monodopsis sp. MarTras21, Vischeria sp. CAUP Q 202, and Trachydiscus minutus, and carried out their comparative analysis in the context of available data from Nannochloropsis and other stramenopiles, revealing a number of noticeable findings. Firstly, mitogenomes of most eustigmatophytes are highly collinear and similar in the gene content, but extensive rearrangements and loss of three otherwise ubiquitous genes happened in the Vischeria lineage; this correlates with an accelerated evolution of mitochondrial gene sequences in this lineage. Secondly, eustigmatophytes appear to be the only ochrophyte group with the Atp1 protein encoded by the mitogenome. Thirdly, eustigmatophyte mitogenomes uniquely share a truncated nad11 gene encoding only the C-terminal part of the Nad11 protein, while the N-terminal part is encoded by a separate gene in the nuclear genome. Fourthly, UGA as a termination codon and the cognate release factor mRF2 were lost from mitochondria independently by the Nannochloropsis and T. minutus lineages. Finally, the rps3 gene in the mitogenome of Vischeria sp. is interrupted by the UAG codon, but the genome includes a gene for an unusual tRNA with an extended anticodon loop that we speculate may serve as a suppressor tRNA to properly decode the rps3 gene.
Chapter
The last quarter century has seen dramatic changes in our understanding of the phylogenetic relationships among protist groups and their evolutionary history. This is due in large part to the maturation of molecular phylogenetics, to genomics and transcriptomics becoming widely used tools, and to ongoing and accelerating progress in characterizing the major lineages of protists in the biosphere. As an introduction to the Handbook of the Protists, Second Edition, we provide a brief account of the diversity of protistan eukaryotes, set within the context of eukaryote phylogeny as currently understood. Most protist lineages can be assigned to one of a handful of major groupings (“supergroups”). These include Archaeplastida (which also includes land plants), Sar (including Stramenopiles/Heterokonta, Alveolata, and Rhizaria), Discoba, Metamonada, Amoebozoa, and Obazoa. This last group in turn contains Opisthokonta, the clade that includes both animals and fungi. Many, but not all, of the deeper-level phylogenetic relationships within these groups are now resolved. Additional well-known groups that are related to Archaeplastida and/or Sar include Cryptista (cryptophyte algae and their relatives), Haptophyta, and Centrohelida, among others. Another set of protist lineages are probably most closely related to Amoebozoa and Obazoa, including Ancyromonadida and perhaps Malawimonadidae (though the latter may well be more closely related to Metamonada). The bulk of the known diversity of protists is covered in the following 43 chapters of the Handbook of the Protists; here we also briefly introduce those lineages that are not covered in later chapters. The Handbook is both a community resource and a guidebook for future research by scientists working in diverse areas, including protistology, phycology, microbial ecology, cell biology, and evolutionary genomics.
Conference Paper
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The Oomycota represent a peculiar chromalveolate group which evolving to osmo-heterotrophic life direction. The most primitive representatives of this group are holocapric and parasitizing the algae and nematodes. They are devoid of specific fungus-like features and have rather complex an extrusion apparatus reminiscent those of parasitic alveolates. In a phylogenetic aspect, the Oomycota form together with Ochrophyta and Hyphochytriomycota a monophyletic HOOF clade (Hypochytriomycota, Oomycota, Ochrophyta), the sister to clade BOL (Bicosoecida, Opalinata, Labyrhintulida). Inside the HOOF clade, the Oomycota are clustered with sequences known as MAST (marine stramenopiles). Some common features of Oomycota with autotrophic protists (in particular, some plastid genes, delegated to the nuclear genome) represent an evidence of a common autotrophic ancestor of chromalveolates, whereas ancestral forms of Oomycota were heterotrophic, having plastids lost at amoeboid level. Alike the true fungi, the polar hyphal growth in Oomycota could be realized according to the scheme of fixation of «unidirectional outflow» during colonizing plant filaments and pseudoparenchymas. The class Peronosporomycetes represents a certain limit of Oomycota evolution, reaching developed mycelial forms with a strengthened cell wall, which makes to possible the colonization of terrestrial habitats as destructive plant parasites. However, the features of cell proliferation, as well as cell wall composition, did not allow these organisms to develop in the way of aerial mycelium differentiation.
Chapter
The free-living heterotrophic flagellates are phylogenetically very diverse, and their phylogenetic diversity is nearly equal to that of all eukaryotes. They constitute the microbial loop together with bacteria and other protists, and play an indispensable and important role in aquatic ecosystems. However, their diversity has not been fully understood. In addition, recent environmental DNA studies suggest that there are many unidentified heterotrophic flagellate lineages in nature. This chapter describes the current knowledge on the diversity, biology and ecology of various groups of free-living heterotrophic flagellates.
Chapter
Marine protists include a heterogeneous collection of phototrophic and heterotrophic unicells covering a wide cell size range and belonging to virtually all eukaryotic lineages. They have been identified by microscopy, which allows a reasonable level of resolution for the larger specimens but is clearly insufficient for the smallest ones. Moreover, as occurs with their prokaryotic counterparts, a large majority of marine protists are uncultivable. Molecular tools have revolutionized field studies of protists’ diversity, allowing exhaustive species inventories especially when combined with high-throughput sequencing technologies. These surveys have shown that natural assemblages are very diverse, including novel phylogenetic lineages that had remained uncharacterized despite their evident ecological significance. The extent of diversity and novelty is largest within the assemblage of the smallest protists, the picoeukaryotes. The information gathered by sequencing phylogenetic marker genes has been combined with an array of complementary molecular methods such as fingerprinting tools to study diversity changes along spatial and temporal gradients, fluorescence in situ hybridization (FISH) to put a face on the novel lineages and perform specific cell counts, and metagenomics to explore ecological adaptations on the basis of the genetic potential. This chapter presents an overview of the molecular approaches currently applied to gain knowledge on the diversity and function of protists in the environment.
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Despite their diversity and ecological importance, many areas of the SAR—Stramenopila, Alveolata, and Rhizaria—clade are poorly understood as the majority (90%) of SAR species lack molecular data and only 5% of species are from well-sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the “dark area” of SAR: the morphologically described species that are missing molecular data. The majority of molecular data for SAR lineages are characterized from marine samples and vertebrate hosts, highlighting the need for additional research effort in areas such as freshwater and terrestrial habitats and “non-vertebrate” hosts. We also describe the paucity of data on the biogeography of SAR species, and point to opportunities to illuminate diversity in this major eukaryotic clade. See also the video abstract here: https://youtu.be/_VUXqaX19Rw.
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Free-living amoebae of the genus Acanthamoeba are potentially pathogenic protozoa widespread in the environment. The detection/diagnosis as well as environmental survey strategies is mainly based on the identification of the 18S rDNA sequences of the strains that allow the recovery of various distinct genotypes/subgenotypes. The accurate recording of such data is important to better know the environmental distribution of distinct genotypes and how they may be preferentially associated with disease. Recently, a putative new acanthamoebal genotype T99 was introduced, which comprises only environmental clones apparently with some anomalous features. Here, we analyze these sequences through partial treeing and BLAST analyses and find that they are actually chimeras. Our results show that the putative T99 genotype is very likely formed by chimeric sequences including a middle fragment from acanthamoebae of genotype T13, while the 5′- and 3′-end fragments came from a nematode and a cercozoan, respectively. Molecular phylogenies of Acanthamoeba including T99 are consequently erroneous as genotype T99 does not exist in nature. Careful identification of Acanthamoeba genotypes is therefore critical for both phylogenetic and diagnostic applications.
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The study of cultured strains has a long tradition in protistological research and has greatly contributed to establishing the morphology, taxonomy and ecology of many protist species. However, cultivation-independent techniques, based on 18S rRNA gene sequences, have demonstrated that natural protistan assemblages mainly consist of hitherto uncultured protist lineages. This mismatch impedes the linkage of environmental diversity data with the biological features of cultured strains. Thus, novel taxa need to be obtained in culture to close this knowledge gap. In this study, traditional cultivation techniques were applied to samples from coastal surface waters and from deep oxygen-depleted waters of the Baltic Sea. Based on 18S rRNA gene sequencing, 126 monoclonal cultures of heterotrophic protists were identified. The majority of the isolated strains were affiliated with already cultured and described taxa, mainly chrysophytes and bodonids. This was likely due to "culturing bias" but also to the eutrophic nature of the Baltic Sea. Nonetheless, ~12% of the isolates in our culture collection showed highly divergent 18S rRNA gene sequences compared to those of known organisms and thus may represent novel taxa, either at the species or the genus level. Moreover, we also obtained evidence that some of the isolated taxa are ecologically relevant, under certain conditions, in the Baltic Sea. This article is protected by copyright. All rights reserved.
Chapter
Members of the Archamoebae comprise free-living and endobiotic amoeboid flagellates, amoeboflagellates, and amoebae, with distinctive hyaline cytoplasm and bulging pseudopodia. They live in anoxic or microoxic habitats and are anaerobes, lacking typical mitochondria, as well as Golgi stacks, plastids, and normal peroxisomal microbodies. They have a distinctive flagellar apparatus present in all flagellated members of the group. Life cycles of individual species can include flagellates, amoebae of various sizes, and cysts. In recent years, the group has been divided into five separate families, Mastigamoebidae, Entamoebidae, Pelomyxidae, Tricholimacidae, and Rhizomastixidae, whose interrelationships have not been completely resolved. Here, we clarify the composition of these groups and the circumscription of genera in the Archamoebae.
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Complete mitochondrion-related organelle (MRO) genomes of several subtypes (STs) of the unicellular stramenopile Blastocystis are presented. Complete conservation of gene content and synteny in gene order is observed across all MRO genomes, comprising 27 protein coding genes, 2 ribosomal RNA genes and 16 transfer RNA (tRNA) genes. Despite the synteny, differences in the degree of overlap between genes was observed between subtypes and also between isolates within the same subtype. Other notable features include unusual base-pairing mismatches in the predicted secondary structures of some tRNAs. Intriguingly, the rps4 gene in some MRO genomes is missing a start codon and, based on phylogenetic relationships among STs, this loss has happened twice independently. One unidentified open reading frame (orf160) is present in all MRO genomes. However, with the exception of ST4 where the feature has been lost secondarily, orf160 contains variously one or two in-frame stop codons. The overall evidence suggests that both the orf160 and rps4 genes are functional in all STs, but how they are expressed remains unclear.
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Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features >74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.
Chapter
Members of the Archamoebae comprise free-living and endobiotic amoeboid flagellates, amoeboflagellates, and amoebae, with distinctive hyaline cytoplasm and bulging pseudopodia. They live in anoxic or microoxic habitats and are anaerobes, lacking typical mitochondria, as well as Golgi stacks, plastids, and normal peroxisomal microbodies. They have a distinctive flagellar apparatus present in all flagellated members of the group. Life cycles of individual species can include flagellates, amoebae of various sizes, and cysts. In recent years, the group has been divided into five separate families, Mastigamoebidae, Entamoebidae, Pelomyxidae, Tricholimacidae, and Rhizomastixidae, whose interrelationships have not been completely resolved. Here, we clarify the composition of these groups and the circumscription of genera in the Archamoebae.
Chapter
The opalinids (Opalinidae: genera Opalina, Cepedea, Protoopalina, Zelleriella, and Protozelleriella) are highly unusual protists with large cells, multiple flagella, and two to hundreds of nuclei. The name Opalina is derived from the iridescent appearance when light reflects on the delicately folded surface of the cells. Opalinids are found exclusively in the intestines of frogs and some other hosts. They form the group Slopalinida together with two related genera of intestinal flagellates, Karotomorpha and Proteromonas. The former is a tetrakont flagellate that inhabits the intestines of certain amphibians, while the latter possesses only two flagella and is found in a wider spectrum of vertebrate hosts. Both morphology and molecular data suggest that Karotomorpha is phylogenetically closer to the opalinids, although both flagellates were traditionally classified in a single family, Proteromonadidae. Molecular data have shown that yet another unusual gut protist is closely related to Slopalinida: the genus Blastocystis. Unlike its relatives, it bears no flagella and is usually observed in the form of spherical cells with huge vacuoles. It is quite common in the intestines of many vertebrates (including humans) and invertebrates. Together, these organisms form Opalinata, a diverse assemblage of variously modified unicellular eukaryotes.
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The diversity, relationships and classification of the actinophryid heliozoa (protists) are reviewed. Descriptions of two new species (Acrinophrys salsuginosa and Ciliophrys azurina) are presented. The actinophryid heliozoa are revised to include six species: Acrinophrys sol (Muller, 1773) Ehrenberg, 1830, A. pontica Valkanov, 1940, A. tauryanini Mikrjukov et Patterson, 2000, A. salsuginosa sp. n., Actinosphaerium eichhornii (Ehrenberg, 1840) Stein, 1857, and A. nucleofilum Barrett, 1958. Echinosphoerium /Echinosphaerium Hovasse, 1965 and Camptonema Schaudinn, 1894 are regarded as junior subjective synonyms of Actinosphaerium Stein, 1857. The relatedness between actinophryid heliozoa and pedinellid helioflagellates is discussed. The new species, Ciliophrys azurina, exhibiting characters (tapering axonemes and peripheral location of heterochromatin) previously only reported in the actinophryids. This allows a proposition for the sequence of character acquisition and a new group of stramenopiles - the actinodines - uniting pedinellids, ciliophryids and actinophryids.
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Heterotrophic flagellates (protozoa) occurring in the marine sediments at Botany Bay, Australia are reported. Among the 87 species from 43 genera encountered in this survey are 13 new taxa: Cercomonas granulatus n. sp., Clautriavia cavus n. sp., Heteronema larseni n. sp., Notosolenus adamas n. sp., Notosolenus brothernis n. sp., Notosolenus hemicircularis n. sp., Notosolenus lashue n. sp., Notosolenus pyriforme n. sp., Petalomonas intortus n. sp., Petalomonas iugosus n. sp., Petalomonas labrum n. sp., Petalomonas planus n. sp. and Petalomonas virgatus n. sp.; and seven new combinations, Carpediemonas bialata n. comb., Dinema platysomum n. comb., Petalomonas calycimonoides nom. nov., Petalomonas christeni nom. nov., Petalomonas physaloides n. comb., Petalomonas quinquecarinata n. comb. and Petalomonas spinifera n. comb. Most flagellates described here appear to be cosmopolitan. We are unable to assess if the new species are endemic because of the lack of intensive studies elsewhere.
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As increasing attention has recently been paid to the structure and function of the water ecosystems, the ecological function of free-living heterotrophic flagellates in water ecosystems has emerged as a central issue in water ecological research. Researches have shown that heterotrophic flagellates are being important members of microbial food webs. Strengthen and expand the researches on heterotrophic flagellate diversity, community structure and their function in nutrient recycling will contribute to understanding on the structure, function and the process of water ecosystems. In this paper, species diversity, community structure and feeding ecology of heterotrophic flagellate were summarized. The mechanism in nutrient recycling and the function in water ecosystem of heterotrophic flagellate were also discussed.
Chapter
Introduction Functional Roles, Classification, and Biological Traits Environmental Diversity and Molecular Phylogenetics Distribution, Abundance, and Activities Genomic Approaches to Picoeukaryote Ecology Integration of Picoeukaryotes to the Microbial Food Web: Research Directions Summary Acknowledgments References
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We describe Diplophrys parva n. sp., a freshwater heterotroph, using fine structural and sequence evidence. Cells are small (L = 6.5 +/- 0.08 mu m, W = 5.5 +/- 0.06 mu m; mean +/- SE) enclosed by an envelope/theca of overlapping scales, slightly oval to elongated-oval with rounded ends, (1.0 x 0.5-0.7 mu m), one to several intracellular refractive granules (similar to 1.0-2.0 mu m), smaller hyaline peripheral vacuoles, a nucleus with central nucleolus, tubulo-cristate mitochondria, and a prominent Golgi apparatus with multiple stacked saccules (= 10). It is smaller than published sizes of Diplophrys archeri (similar to 10-20 mu m), modestly less than Diplophrys marina (similar to 5-9 mu m), and differs in scale size and morphology from D. marina. No cysts were observed. We transfer D. marina to a new genus Amphifila as it falls within a molecular phylogenetic clade extremely distant from that including D. parva. Based on morphological and molecular phylogenetic evidence, Labyrinthulea are revised to include six new families, including Diplophryidae for Diplophrys and Amphifilidae containing Amphifila. The other new families have distinctive morphology: Oblongichytriidae and Aplanochytriidae are distinct clades on the rDNA tree, but Sorodiplophryidae and Althorniidae lack sequence data. Aplanochytriidae is in Labyrinthulida; the rest are in Thraustochytrida; Labyrinthomyxa is excluded.
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Recent molecular and ultrastructural discoveries necessitate major changes in the higher level classification of the kingdom Protozoa. A new class Anaeromonadea and subphylum Anaeromonada are created for the anaerobic tetrakont flagellate Trimastix, which is grouped with Parabasala, ranked as a subphylum, to form the new protozoan phylum Trichozoa. To simplify the supraphyletic classification of Protozoa I dispense with the category parvkingdom by increasing Neozoa in rank from infrakingdom to subkingdom and creating a new subkingdom Eozoa for the eokaryote phyla Trichozoa, Percolozoa and Euglenozoa.
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The cell morphology and ultrastructure of Fibrocapsa japonica were examined and compared with those of related taxa. The results suggested that Fibrocapsa must be treated as an autonomous genus separate from Chattonella, and its circumscription should follow the description of Toriumi and Takano (1975) with some amendments based on the new criteria presented in this study.ZusammenfassungZellmorphologie und Ultrastruktur von Fibrocapsa japonica wurden untersucht und mit verwandten Formen verglichen. Die Ergebnisse zeigen, daß Fibrocapsa als eine eigene, von Chattonella abgegrenzte Gattung betrachtet werden muß. Ihre Beschreibung folgt der von Torittmi und Takano (1975), mit einigen Verbesserungen, die durch die neuen, in dieser Arbeit vorgestellten Merkmale begründet sind.
Article
SUMMARYA marine ‘chrysophyte’ species Polypodochrysis teissieri Magne having distinctive lorica was re-examined using both light and electron microscopy. Light microscopic observations were basically identical to Magne's descriptions (Magne 1975), except that the aplanospore in that paper was shown to be a distinctive uniflagellate zoospore. General ultrastructure of both chloroplast and mitochondria was typical of the photosynthetic stramenopiles (chromophytes). An embedded pyrenoid was found in the center of chloroplast and was penetrated by the chloroplast envelope. Two Golgi bodies were always located adjacent to the nucleus; they were arranged perpendicularly in vegetative cells, but had a parallel arrangement in zoospores. Thin sections of the lorica resembled siliceous structures such as diatom frustules, but energy dispersive X-ray analysis did not show any significant amount of silicon. Naked zoospores have a single emergent flagellum that lacked mastigonemes; a flagellar swelling and an eyespot were also absent. Zoospores showed gliding motion on the surface of substrate. Two different cytoplasmic extensions (pseudopods) were observed in the zoospore. One lingulate pseudopod originated from the base of the flagellum and was always associated with the flagellum, and the second pseudopod formed only when the cell changed direction. Investigations of the flagellar apparatus showed a single transitional plate in the transitional region of the emergent flagellum, a second basal body closely located to the flagellum-bearing basal body, three microtubular roots and a set of cytoskeletal microtubules, and a small rhizoplast that connected the non-flagellum-bearing basal body and the nucleus. Many features of the zoospore of Polypodochrysis show a similarity with that of Glossomastix chrysoplasta (Pinguiophyceae), suggesting that the single emergent flagellum of Polypodochrysis and Glossomastix is homologous. This single flagellum may correspond to the mature flagellum that is generally recognized as the short posterior flagellum in stramenopiles, and it represents a unique flagellar arrangement within stramenopiles. Based on the morphological features, in addition to the other data (18S rRNA and rbcL genes and biochemical features) published elsewhere, Polypodochrysis was removed from the class Chrysophyceae and transferred to a new class, the Pinguiophyceae.
Article
Glossomastix chrysoplasta gen. et sp. nov. is described from cultures isolated from sandstone rubble, Sorrento Back Beach, Mornington Peninsula, Victoria, Australia. The alga forms wall-less, coccoidal vegetative cells that congregate in mucilaginous colonies and reproduce by successive bipartition. Plastids have girdle lamellae and partially embedded pyrenoids that are traversed by cytoplasmic channels. Zoospores are uniflagellate and swim poorly; a narrow lingulate pseudopod provides their primary form of motion. The single flagellum, which lacks hairs, a flagellar swelling, and autofluorescence, is the equivalent of the posterior flagellum in other golden algae. The anterior flagellum is absent; the basal body with which it would normally be associated is blind. The flagellar apparatus has two basal bodies, three microtubular roots, and a rhizoplast. The posterior (elder) basal body has a transitional helix that is proximal to the basal plate. Glossomastix chrysoplasta, placed in the Pinguiophyceae on the basis of molecular sequence and biochemical data, shares some ultrastructural features with other members of the class, especially Polypodochrysis teissieri, which has similar zoospores, but it also differs from other pinguiophytes in many respects. Glossomastix chrysoplasta is the pinguiophyte with, on average, the largest cells (exclusive of external materials), and it is the only one with a colonial habit.
Article
Summary A new, marine, sand-dwelling raphidophyte from Sylt, Germany, Haramonas viridis Horiguchi et Hoppenrath sp. nov. is described. This represents a second species in the previously monotypic genus Haramonas, which was originally described from a sand sample from a mangrove river mouth in tropical Australia, based on the type species, H. dimorpha. This new species from a cold temperate region: (i) possesses a tubular invagination in the posterior part of the cell; (ii) produces copious amounts of mucilage in culture; (iii) possesses both motile and non-motile stages in its life cycle; and (iv) has overlapping discoidal chloroplasts, all of which are diagnostic features of the genus Haramonas. Therefore, it is indisputable that this species belongs to this genus. However, the species from Sylt differs from the type species of the genus in: (i) having a larger cell size; (ii) possessing a larger number of chloroplasts; and (iii) being greenish in color. The ultrastructural study revealed that the structure of the tubular invagination was the same as that of the type species.
Article
Summary The flagellar apparatus of 3 isolates ofHeterosigma akashiwo (Hada) Hada has been studied by serial sectioning. The two basal bodies lie at almost right angles to one another, but in a different plane, and are interconnected by an extensive root system. This consists of three roots (i) a massive cross-banded fibrous root (= rhizoplast) which extends from near the proximal ends of both basal bodies to the anterior surface of the nucleus, (ii) a compound microtubular root with a layered structure, associated with the hairy anterior flagellum and extending to the anterior surface and (iii) the rhizostyle which passes between the two basal bodies leading anteriorly to a vesicle in the flagellar groove region and following the nucleus posteriorly terminating deep in the cytoplasm. Both the characteristic arrangement of the basal bodies and the presence of the complex layered structure are characteristic of theRaphidophyceae. The broad microtubular root, however, to which the layered structure is attached, appears to be characteristic of nearly all heterokont algae, fungi and protozoa so far examined. Thus, our findings have important implications on phylogenetic relationships within the heterokonts and lead us to question whether some of the present classes such as theChrysophyceae andXanthophyceae are indeed natural groups.
Article
The taxonomic position of the uniciliate, unicentriolar zooflagellate Phalansterium is problematic; its distinctive ultrastructure with a pericentriolar microtubular cone placed it in its own order and suggested phenotypic closeness to the eukaryote cenancestor. We sequenced the 18S rRNA of a unicellular Phalansterium. Phylogenetic analysis shows that it belongs to Amoebozoa, decisively rejecting a postulated relationship with the cercozoan Spongomonas; Phalansterium groups with Varipodida ord. nov. (Gephyramoeba/Filamoeba) or occasionally Centramoebida emend. (Acanthamoebidae/Balamuthiidae fam. nov.), centrosomes of the latter suggesting flagellate ancestors. We also studied Phalansterium solitarium cyst ultrastructure; unlike previously studied P. solitarium, this strain has pentagonally symmetric walls like P. consociatum. We also sequenced 18S rRNA genes of further isolates of Hyperamoeba, an aerobic unicentriolar amoeboflagellate with conical microtubular skeleton; both group strongly with myxogastrid Mycetozoa. However, the four Hyperamoeba strains do not group together, suggesting that Hyperamoeba are polyphyletic derivatives of myxogastrids that lost fruiting bodies independently. We revise amoebozoan higher-level classification into seven classes, establishing Stelamoebea cl. nov. for Protosteliida emend. plus Dictyosteliida (biciliate former ‘protostelids’ comprise Parastelida ord. nov. within Myxogastrea), and new subphylum Protamoebae to embrace Variosea cl. nov. (Centramoebida, Phalansteriida, Varipodida), Lobosea emend., Breviatea cl. nov. for ‘Mastigamoeba invertens’ and relatives, and Discosea cl. nov. comprising Glycostylida ord. nov. (vannellids, vexilliferids, paramoebids, Multicilia), Dermamoebida ord. nov. (Thecamoebidae) and Himatismenida. We argue that the ancestral amoebozoan was probably unikont and that the cenancestral eukaryote may have been also.
Article
When specimens of Actinosphaerium nucleofilum are placed at 4°C, the axopodia retract and the birefringent core (axoneme) of each axopodium disappears. In fixed specimens, it has been shown that this structure consists of a highly patterned bundle of microtubules, each 220 A in diameter; during cold treatment these microtubules disappear and do not reform until the organisms are removed to room temperature. Within a few minutes after returning the specimens to room temperature, the axonemes reappear and the axopodia begin to reform reaching normal length 30–45 min later. In thin sections of cells fixed during the early stages of this recovery period, microtubules, organized in the pattern of the untreated specimens, are found in each reforming axopodium. Reforming axopodia without birefringent axonemes (and thus without microtubules) are never encountered. From these observations we conclude that the microtubules may be instrumental not only in the maintenance of the axopodia but also in their growth. Thus, if the microtubules are destroyed, the axopodia should retract and not reform until these tubular units are reassembled. During the cold treatment short segments of a 340-A tubule appeared; when the organisms were removed from the cold, these tubular segments disappeared. It seems probable that they are one of the disintegration products of the microtubules. A model is presented of our interpretation of how a 220-A microtubule transforms into a 340-A tubule and what this means in terms of the substructure of the untreated microtubules.
Article
Commation gen. nov. is a genus of planktonic, unicellular protists characterized by a circular to oval (sometimes flattened) cell body and a proboscis. Cells move predominantly by gliding. The mitochondria are tubulocristate and the two flagellar basal bodies are furnished with microtubular roots as well as a rhizoplast. The single emerging flagellum, which is rarely observed, apparently carries tripartite hairs. These features suggest that Commation should be listed among the genera and groups of organisms assembled in the informal group stramenopiles. Two species, C. eposianum sp. nov. (previously referred to as the "comma-shaped amoeba") and C. cryoporinum sp. nov., are described from Antarctic waters. The species are distinguished by differences in, e.g., the morphology of the proboscis, the complexity and details of the cytoskeleton, and the number of types of extrusomes present. Commation spp. appear to be ubiquitous in Antarctic waters at cell abundancies typically ranging from 10(3)-10(4) cells per litre.
Article
A new algal class, the Phaeothamniophyceae classis nova, is established from genera formerly classified in the Chrysophyceae (e.g., Chrysapion, Chrysoclonium, Chrysodictyon, Phaeobotrys, Phaeogloea, Phaeoschizochlamys, Phaeothamnion, Selenophaea, Sphaeridiothrix, Stichogloea, Tetrachrysis, Tetrapion and Tetrasporopsis) as well as one genus previously assigned to the Xanthophyceae (Pleurochloridella). HPLC analysis revealed the presence of fucoxanthin, diadinoxanthin, diatoxanthin, β-carotene and heteroxanthin, in addition to chlorophylls a and c, in four genera (Phaeoschizochlamys, Phaeothamnion, Stichogloea, Pleurochloridella). The combination of fucoxanthin and heteroxanthin is known only for these organisms. The rbcL sequences of the same four genera, along with representatives of other chromophyte classes, were analyzed phylogenetically and provided independent support for recognition of the Phaeothamniophyceae as a distinct taxon. These data indicate that the Phaeothamniophyceae are more closely related to the classes Xanthophyceae and Phaeophyceae than to the Chrysophyceae. Electron microscopy revealed that Phaeoschizochlamys, Phaeothamnion and Stichogloea possess electron opaque vesicles at the cell periphery, have a cell wall that often appears laminate, form new daughter cell walls via eleutheroschisis, and have plastids with girdle lamellae and a ring-shaped genophore. The flagellar apparatus of Phaeothamnion zoospores (described in a previous study) is chosen as representative of the new class. The flagella are inserted laterally, basal bodies form an angle of ca. 145° or more, a multi-gyred flagellar transitional helix is present and tripartite flagellar hairs lack lateral filaments. Genera placed in the Phaeothamniophyceae are assigned to the orders Phaeothamniales and Pleurochloridellales, each with a single family.
Article
The diversity of heterotrophic nanoflagellates and other protists was examined at various sites around Southampton Water (U.K.) between 1991 and 1994. Observations were made on species occurring in enrichment cultures, in freshly collected material concentrated by gentle centrifugation, and on electron microscope whole mounts. The species described belong to the apusomonads, cercomonads, dinoflagellates, euglenids, stramenopiles and thaumatomonads or else are of uncertain taxonomic affinities (Protista incertae sedis). Choanoflagellate species found during the study are described elsewhere (Tong 1997). Five new species are described: Luffisphaera hamatus n. sp., Ministeria vibrans n. sp., Pendulomonas adriperis n. gen., n. sp., Rigidomastix devoratum n. sp., and Thaumatomastix thomseni n. sp.