On the Organization of the Naked Filose Amoeba,Nuclearia moebiusiFrenzel, 1897 (Sarcodina, Filosea) and Its Implications1

A first account of the heterotrophic eukaryote Rabdiophrys Rainer from the fossil record and description of a new species from an ancient Eocene Arctic freshwater lake

Rotosphaerids are unicellular, heterotrophic, eukayotic protists that have filopodia, an exterior covering consisting of highly ornamented siliceous scales, and are classified in the Rotosphaerida within the opistokont lineage. Given their appearance as relatively large spherical cells with protruding filopodia and a silica scale covering, they are often mistaken for centrohelid heliozoans. Even though these organisms are widely distributed in both marine and freshwater environments, many species are rarely reported, and none have been reported from the fossil record. We report extensive remains of a new species of Rabdiophrys, R. giraffensis, from an ancient waterbody that was situated near the Arctic Circle in northern Canada during the Eocene. The new species has both plate and spine scales that are similar in morphology, but significantly larger than its closest modern congeners, R. monopora and R. anulifera. The waterbody in which the new species grew and thrived is inferred to have been a moderately deep, circumneutral pond, with moderate concentrations of nutrients and dissolved humic material.

Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi

Nucleariid amoebae (Opisthokonta) have been known since the nineteenth century but their diversity and evolutionary history remain poorly understood. To overcome this limitation, we have obtained genomic and transcriptomic data from three Nuclearia, two Pompholyxophrys and one Lithocolla species using traditional culturing and single-cell genome (SCG) and single-cell transcriptome amplification methods. The phylogeny of the complete 18S rRNA sequences of Pompholyxophrys and Lithocolla confirmed their suggested evolutionary relatedness to nucleariid amoebae, although with moderate support for internal splits. SCG amplification techniques also led to the identification of probable bacterial endosymbionts belonging to Chlamydiales and Rickettsiales in Pompholyxophrys. To improve the phylogenetic framework of nucleariids, we carried out phylogenomic analyses based on two datasets of, respectively, 264 conserved proteins and 74 single-copy protein domains. We obtained full support for the monophyly of the nucleariid amoebae, which comprise two major clades: (i) Parvularia-Fonticula and (ii) Nuclearia with the scaled genera Pompholyxophrys and Lithocolla. Based on these findings, the evolution of some traits of the earliest-diverging lineage of Holomycota can be inferred. Our results suggest that the last common ancestor of nucleariids was a freshwater, bacterivorous, non-flagellated filose and mucilaginous amoeba. From the ancestor, two groups evolved to reach smaller (Parvularia-Fonticula) and larger (Nuclearia and related scaled genera) cell sizes, leading to different ecological specialization. The Lithocolla + Pompholyxophrys clade developed exogenous or endogenous cell coverings from a Nuclearia-like ancestor. This article is part of a discussion meeting issue 'Single cell ecology'.

Shedding light on vampires: the phylogeny of vampyrellid amoebae revisited

With the advent of molecular phylogenetic techniques the polyphyly of naked filose amoebae has been proven. They are interspersed in several supergroups of eukaryotes and most of them already found their place within the tree of life. Although the ‘vampire amoebae’ have attracted interest since the middle of the 19th century, the phylogenetic position and even the monophyly of this traditional group are still uncertain. In this study clonal co-cultures of eight algivorous vampyrellid amoebae and the respective food algae were established. Culture material was characterized morphologically and a molecular phylogeny was inferred using SSU rDNA sequence comparisons. We found that the limnetic, algivorous vampyrellid amoebae investigated in this study belong to a major clade within the Endomyxa Cavalier-Smith, 2002 (Cercozoa), grouping together with a few soil-dwelling taxa. They split into two robust clades, one containing species of the genus Vampyrella Cienkowski, 1865, the other containing the genus Leptophrys Hertwig & Lesser, 1874, together with terrestrial members. Supported by morphological data these clades are designated as the two families Vampyrellidae Zopf, 1885, and Leptophryidae fam. nov. Furthermore the order Vampyrellida West, 1901 was revised and now corresponds to the major vampyrellid clade within the Endomyxa, comprising the Vampyrellidae and Leptophryidae as well as several environmental sequences. In the light of the presented phylogenetic analyses morphological and ecological aspects, the feeding strategy and nutritional specialization within the vampyrellid amoebae are discussed.

The ultrastructural identity of Stephanopogon apogon and the relatedness of the genus to other kinds of protists

The ultrastructural organization of the marine benthic protist Stephanopogon apogon is presented. Emphasis is placed on the structure of the mouth, the cortex, and the locomotor flagella. Viewed with a light-microscope, individuals of this species closely resemble members of the phylum Ciliophora (in terms of ciliation, body form, and presence of a discrete mouth), but Stephanopogon cells are ultrastructurally unlike all ciliophora in respect of the oral apparatus, cortical organization, and locomotor systems. The proposition that Stephanopogon is related to Euglenozoa is discussed, and is found to be supported by a single character, the form of the mitochondrial cristae. Placement of Stephanopogon in the Euglenozoa is therefore deemed to be premature.

Nuclearia thermophila sp. nov. (Nucleariidae), a new nucleariid species isolated from Yunoko Lake in Nikko (Japan)

A new species of unicellular opisthokont protist, Nuclearia thermophila sp. nov., was isolated from the warm spring water of Yunoko Lake, Japan, and has been described using light and electron microscopy. It exists as a spherical floating form and a flattened amoeboid form showing various shapes. The cells occasionally extended as branches or knobbed filopodia. The spherical form when suspended in medium measured 20-40microm in diameter (excluding filopodia). The amoeboid form may exceed 65microm along the longest axis. A nucleus with an obvious spherical nucleolus, dictyosomes, mitochondria with flat cristae, food vacuoles, and lipid droplet-like vacuoles with homogeneous contents were observed; no extracellular matrix or bacterial endosymbionts were present. The cells ingested flour particles. No cysts were seen. The molecular phylogenetic tree constructed on the basis of the small subunit ribosomal DNA revealed the novelty of N. thermophila and its relationships with previously known nucleariids.

Multiple isolations of a culturable, motile Ichthyosporean (Mesomycetozoa, Opisthokonta), Creolimax fragrantissima n. gen., n. sp., from marine invertebrate digestive tracts

A fragrant, spherical, osmotrophic eukaryote was isolated 27 times from the digestive tracts of marine invertebrates collected from the Northeast Pacific. The isolates were cultured from 7 animal collections over a 2-year period, most from the peanut worm, Phascolosoma agassizii. A small subunit ribosomal DNA phylogeny placed the spherical organism within the ichthyosporea, closest to Sphaeroforma arctica and Pseudoperkinsus tapetis. Supporting the close relationship of isolates, the sequences of ribosomal gene internal transcribed spacers determined for 26 isolates were identical, as were the elongation factor 1-alpha-like gene fragments from 7 isolates. Dispersal via amoeboid cells distinguished this species from its closest relatives and led to the erection of a new genus and species, "Creolimax fragrantissima." Vegetative cells reproduced asexually in vitro after they reached 30-60 microm in diameter by producing amoebae or endospores, which escaped through openings in the parent cell wall. Ultrathin sections of vegetative cells prepared by high-pressure-freeze substitution provided some of the first images of ichthyosporean spindle pole bodies and document, for the first time, tubular extensions of the plasma membrane into an electron-translucent inner layer of the cell wall. Ichthyosporeans are parasites and commensals of animals and culturable species are few. Because "C. fragrantissima" can be isolated regularly and repeatedly from nature and then grown easily through cycles of asexual reproduction, it has the potential to serve as a model organism for further research into marine ichthyosporeans.

The nucleariid amoebae: more protists at the animal-fungal boundary

Nucleariid amoebae are naked amoebae, generally characterized by a spherical or sometimes flattened body with radiating filopodia. Most species preferentially consume algal prey or cyanobacteria. Phylogenetic analyses of the small-subunit rRNA coding regions from four nucleariid amoebae place these species near the origin of the animal-fungal divergence, together with the choanoflagellate-Corallochytrium and the ichthyosporean clades. The species Nuclearia delicatula, N. moebiusi, and N. simplex form a monophyletic group, while ATCC 30864, tentatively but possibly incorrectly assigned to Nuclearia sp., represents a separate line of descent. These nucleariids are unrelated to the lineage containing the testate filose amoebae (Testaceafilosia). Our findings expand the morphological and phylogenetic diversity of protists at the animal-fungal divergence.

The Diversity of Eukaryotes

The discipline of evolutionary protistology has emerged in the past 30 yr. There is as yet no agreed view of how protists are interrelated or how they should be classified. The foundations of a stable taxonomic superstructure for the protists and other eukaryotes lie in cataloging the diversity of the major monophyletic lineages of these organisms. The use of common patterns of cell organization (ultrastructural identity) seems to provide us with the most robust hypotheses of such lineages. These lineages are placed in 71 groups without identifiable sister taxa. These groups are here referred to as "major building blocks." For the first time, the compositions, ultrastructural identities, synapomorphies (where available), and subgroups of the major building blocks are summarized. More than 200 further lineages without clear identities are listed. This catalog includes all known major elements of the comprehensive evolutionary tree of protists and eukaryotes. Different approaches among protistologists to issues of nomenclature, ranking, and definitions of these groups are discussed, with particular reference to two groups-the stramenopiles and the Archezoa. The concept of "extended in-group" is introduced to refer to in-groups and the most proximate sister group and to assist in identifying the hierarchical location of taxa.