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Dziani Dzaha is a hypersaline lake (Mayotte island), whose microbial community is dominated by photosynthetic microorganisms. Here, we describe two new free-living heteroloboseans. One belonging to the Pharyngomonas genus and the other, whose 18S rRNA gene sequence shares only 85% homology to its closest relatives Euplaesiobystra hypersalinica, was proposed as a new species of this genus being called Euplaesiobystra dzianiensis. Both strains were salt tolerant to 75‰ and grew between 25 and 37°C. Their distribution patterns varied seasonally and depended also on depth. Noticeably, both free-living amoebae isolates were able to graze on Arthrospira filaments, which are found within the same water layer. In conclusion, we document for the first time the presence and ecology of free-living amoebae in the thalassohaline lake Dziani Dzaha, and describe a new species of the Euplaesiobystra genus., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Morphological features are often the only characteristics suitable for identification of taxa in testate amoebae, especially in ecological and palaeoecological studies. However, whereas the morphology of some species is rather stable it may vary considerably in others. Within the order Arcellinida the genus Trigonopyxis with the type species Trigonopyxis arcula is morphologically highly variable. To identify reliable characteristics for morphology-based taxon delineation we investigated variations in shell size, pseudostome diameter and pseudostome form in T. arcula from three different sites of the Ecuadorian Andes, where these characteristics vary even more than previously described. Further, we investigated if morphological characteristics in Trigonopyxis varied with changes in environmental factors. We studied 951 shells of Trigonopyxis collected along an altitudinal gradient with varying abiotic factors. We established a method for characterization of the pseudostome form, which lead to five different morphotypes. Our results suggest that shell size alone is not an appropriate character for taxon delineation but can be used as an indicator for changes in environmental conditions. In contrast, the pseudostome form might be used for taxon delineation, but likely also varies considerably within taxa. Overall, the study provides an overview of the morphological variability of the genus Trigonopyxis., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

Amoebae able to form cytoplasmic networks or displaying a multiply branching morphology remain very poorly studied. We sequenced the small-subunit ribosomal RNA gene of 15 new amoeboid isolates, 14 of which are branching or network-forming amoebae (BNFA). Phylogenetic analyses showed that these isolates all group within the poorly-known and weakly-defined class Variosea (Amoebozoa). They are resolved into six lineages corresponding to distinct new morphotypes; we describe them as new genera Angulamoeba (type species Angulamoeba microcystivorans n. gen., n. sp.; and A. fungorum n. sp.), Arboramoeba (type species Arboramoeba reticulata n. gen., n. sp.), Darbyshirella (type species Darbyshirella terrestris n. gen., n. sp.), Dictyamoeba (type species Dictyamoeba vorax n. gen., n. sp.), Heliamoeba (type species Heliamoeba mirabilis n. gen., n. sp.), and Ischnamoeba (type species Ischnamoeba montana n. gen., n. sp.). We also isolated and sequenced four additional variosean strains, one belonging to Flamella, one related to Telaepolella tubasferens, and two members of the cavosteliid protosteloid lineage. We identified a further 104 putative variosean environmental clone sequences in GenBank, comprising up to 14 lineages that may prove to represent additional novel morphotypes. We show that BNFA are phylogenetically widespread in Variosea and morphologically very variable, both within and between lineages., (Copyright © 2015 Elsevier GmbH. All rights reserved.)

High microbial diversity is revealed by environmental DNA surveys. However, nothing is known about the morphology and function of these potentially new organisms. In the course of an environmental soil diversity study, we found for the first time environmental sequences that reveal the presence of Paulinellidae (a mostly marine and marginally freshwater family of euglyphid testate amoebae) in samples of forest litter from different geographic origins. The new sequences form a basal, robust clade in the family. We used fluorescent in situ hybridization (FISH) to detect the organisms from which these sequences derived. We isolated the cells and documented them with light and scanning electron microscopy. Based on these observations, we described these organisms as Micropyxidiella edaphonis gen. nov. sp. nov. The organisms were very small testate amoebae (generally less than 10μm) with an irregular proteinaceous test. This suggests an unknown diversity in testate amoebae, and calls for extending this type of investigations to other protist groups which are known only as environmental DNA sequences., (Copyright © 2015 Elsevier GmbH. All rights reserved.)

Arcellacea (testate lobose amoebae) are important lacustrine environmental indicators that have been used in paleoclimatic reconstructions, assessing the effectiveness of mine tailings pond reclamation projects and for studying the effects of land use change in rural, industrial and urban settings. Recognition of ecophenotypically significant infra-specific 'strains' within arcellacean assemblages has the potential to enhance the utility of the group in characterizing contemporary and paleoenvironments. We present a novel approach which employs statistical tools to investigate the environmental and taxonomic significance of proposed strains. We test this approach on two identified strains: Difflugia protaeiformis Lamarck strain 'acuminata' (DPA), characterized by fine grained agglutination, and Difflugia protaeiformis Lamarck strain 'claviformis' (DPC), characterized by coarse grained agglutination. Redundancy analysis indicated that both organisms are associated with similar environmental variables. No relationship was observed between substrate particle size and abundance of DPC, indicating that DPC has a size preference for xenosomes during test construction. Thus DPC should not be designated as a distinct strain but rather form a species complex with DPA. This study elucidates the need to justify the designation of strains based on their autecology in addition to morphological stability., (Copyright © 2014 Elsevier GmbH. All rights reserved.)

To date only five partial and two complete SSU rRNA gene sequences are available for the lobose testate amoebae (Arcellinida). Consequently, the phylogenetic relationships among taxa and the definition of species are still largely dependant on morphological characters of uncertain value, which causes confusion in the phylogeny, taxonomy and the debate on cosmopolitanism of free-living protists. Here we present a SSU rRNA-based phylogeny of the Hyalospheniidae including the most common species. Similar to the filose testate amoebae of the order Euglyphida the most basal clades have a terminal aperture; the ventral position of the pseudostome appears to be a derived character. Family Hyalospheniidae appears paraphyletic and is separated into three clades: (1) Heleopera sphagni, (2) Heleopera rosea and Argynnia dentistoma and (3) the rest of the species from genera Apodera, Hyalosphenia, Porosia and Nebela. Our data support the validity of morphological characters used to define species among the Hyalospheniidae and even suggest that taxa described as varieties may deserve the rank of species (e.g. N. penardiana var. minor). Finally our results suggest that the genera Hyalosphenia and Nebela are paraphyletic, and that Porosia bigibbosa branches inside the main Nebela clade.

We combine a morphological description with a multigene analysis to assess the phylogenetic placement of a poorly known amoeboid taxon Corallomyxa within the eukaryotic tree of life. A detailed morphological analysis including transmission electron microscopy and light microscopy of Corallomyxa sp. ATCC 50975 demonstrates that this isolate is a new species, herein designated, Corallomyxa tenera sp. nov. This species possesses features of the genus, such as a multinucleate, reticulate plasmodium with localized bidirectional streaming and occasional formation of surface buds, but is differentially characterized from other species by its delicate appearance, short duration of the anastomosing reticulate network and production of round smooth-walled cysts. The new species also lacks some features found in some Corallomyxa species, including cytoplasmic condensation and an electron dense "chromocenter". A Bayesian analysis of four concatenated genes (SSU-rDNA, actin, alpha- and beta-tubulin) from a wide diversity of eukaryotes places the new species together with taxa placed in the putative supergroup 'Rhizaria'. All molecular loci refute the traditional placement of Corallomyxa within the supergroup 'Amoebozoa', which includes other Mycetozoidea and Lobosea. Maximum likelihood and Bayesian analyses of the two well-sampled genes, SSU-rDNA and actin, with increased taxon sampling of 'Rhizaria' show a close affinity of Corallomyxa with Foraminifera, Gromia and, for SSU-rDNA, Haplosporidia. We further identify a novel stem, herein designated E23-13-1, in the predicted SSU-rDNA secondary structure that supports this relationship. A hypothesis is presented for the evolution of morphological and molecular synapomorphies in a clade containing Gromia, Corallomyxa, Foraminifera and Haplosporidia.

We sequenced 18S rRNA genes from 21 vannellid amoebae (Amoebozoa; Vannellidae), including nearly all available type cultures, and performed a comprehensive phylogenetic analysis for 57 Vannellidae sequences. The results show that species of Vannella and Platyamoeba are completely mixed and do not form distinct clades. Several very closely related species pairs exist, each with a Vannella and a Platyamoeba species differing in only a few nucleotides. Therefore, presence (Vannella) or absence (Platyamoeba) of glycostyles in the cell surface coat is an invalid generic distinction; the genera must be merged. As Vannella has priority, we formally transferred Platyamoeba species into Vannella, except for the non-vannellid P. stenopodia, here renamed Stenamoeba stenopodia gen. n. comb. n. and transferred to the family Thecamoebidae. Our trees show that Vannella glycostyles were probably easily and repeatedly evolutionarily lost. We have established a new genus Ripella, with distinct morphology and sequence signatures for Vannella platypodia and morphologically similar species that form a clearly separate clade, very distant from other Vannellidae. Vannellids form four well-separated single-genus clades: Vannella sensu stricto, Ripella, Clydonella, and Lingulamoeba. Species of the revised genus Vannella comprise four closely related, well-supported subclades: one marine and three freshwater. Here, we provide an illustrated checklist for all 40 known Vannellidae species.

The existing data on the molecular phylogeny of filose testate amoebae from order Euglyphida has revealed contradictions between traditional morphological classification and SSU rRNA phylogeny and, moreover, the position of several important genera remained unknown. We therefore carried out a study aiming to fill several important gaps and better understand the relationships among the main euglyphid testate amoebae and the evolutionary steps that led to the present diversity at a higher level. We obtained new SSU rRNA sequences from five genera and seven species. This new phylogeny obtained shows that (1) the clade formed by species of genera Assulina and Placocista branches unambiguously at the base of the subclade of Euglyphida comprising all members of the family Trinematidae and genus Euglypha, (2) family Trinematidae (Trachelocorythion, Trinema, and Corythion) branches as a sister group to genus Euglypha, (3) three newly sequenced Euglypha species (E. cf. ciliata, E. penardi, and E. compressa) form a new clade within the genus. Since our results show that Assulina and Placocista do not belong to the Euglyphidae (unless the Trinematidae are also included in this family), we propose the creation of a new family named Assulinidae. Consequently, we give a family status to the genera Euglypha and (tentatively) Scutiglypha, which become the new family Euglyphidae. The evolutionary pattern suggested by SSU rRNA phylogeny shows a clear tendency towards increasing morphological complexity of the shell characterised by changes in the symmetry (migration of the aperture to a ventral position and/or compression of the shell) and the appearance of specialised scales at the aperture (in families Trinematidae and Euglyphidae).

One of the major steps in the evolution of life was the origin of photosynthesis in nucleated cells underpinning the evolution of plants. It is well accepted that this evolutionary process was initiated when a photosynthetic bacterium (a cyanobacterium) was taken up by a colorless host cell, probably more than a billion years ago, and transformed into a photosynthetic organelle (a plastid) during a process known as primary endosymbiosis. Here, we use sequence comparisons and phylogenetic analyses of the prokaryotic rDNA operon to show that the thecate, filose amoeba Paulinella chromatophora Lauterborn obtained its photosynthetic organelles by a similar but more recent process, which involved a different cyanobacterium, indicating that the evolution of photosynthetic organelles from cyanobacteria was not a unique event, as is commonly believed, but may be an ongoing process.

Testate lobose amoebae (order Arcellinida Kent, 1880) are common in all aquatic and terrestrial habitats, yet they are one of the last higher taxa of unicellular eukaryotes that has not found its place in the tree of life. The morphological approach did not allow to ascertain the evolutionary origin of the group or to prove its monophyly. To solve these challenging problems, we analyzed partial small-subunit ribosomal RNA (SSU rRNA) genes of seven testate lobose amoebae from two out of the three suborders and seven out of the 13 families belonging to the Arcellinida. Our data support the monophyly of the order and clearly establish its position among Amoebozoa, as a sister-group to the clade comprising families Amoebidae and Hartmannellidae. Complete SSU rRNA gene sequences from two species and a partial actin sequence from one species confirm this position. Our phylogenetic analyses including representatives of all sequenced lineages of lobose amoebae suggest that a rigid test appeared only once during the evolution of the Amoebozoa, and allow reinterpretation of some morphological characters used in the systematics of Arcellinida.

We have determined the internal transcribed spacer (ITS) sequences (including the 5.8S ribosomal DNA) of 30 strains of 14 species belonging to eight vahlkampfiid genera. Each previously described species has a specific ITS sequence, except for Tetramitus aberdonicus, Tetramitus thorntoni, and Tetramitus jugosus, which have identical ITS sequences. The latter three may therefore constitute a single species despite their apparent phenotypic differences. The ITS sequence appears to be conserved within a species. The species Willaertia magna appears to be ubiquitous. The 5.8S rDNA sequences of Singhamoeba horticola and Learamoeba waccamwensis indicate that they do not represent different genera, but both belong to the genus Tetramitus. The ITS sequences of 16 undescribed vahlkampfiid isolates were determined. Based on these sequences, seven isolates were identified as belonging to described species, while nine probably represent seven new species. Five of these presumed new species belong to the genus Tetramitus, and one each to the genera Vahlkampfia and Paravahlkampfia.

Leptomyxid amoebae encompass a diverse assemblage of amoeboid protists that have been implicated as encephalitis-causing agents. This characteristic is attributed to recent studies identifying new members of the Leptomyxidae, in particular, Balamuthia mandrillaris, that cause the disease. Their morphologies range from limax to plasmodial, as well as reticulated and polyaxial. Although systematic studies have identified B. mandrillaris as a new member of the Leptomyxidae, its precise placement within the leptomyxids is uncertain. To further assess the taxonomic placement of Balamuthia among the leptomyxid amoebae and to determine whether the members of the Leptomyxida form a monophyletic assemblage, we have sequenced 16S-like rRNA genes from representatives of three leptomyxid families. Our phylogenetic analyses revealed that current members of the order Leptomyxida do not constitute a monophyletic assemblage. Our analyses clearly show that Gephyramoeba, as well as Balamuthia do not belong in the order Leptomyxida. We highlight where molecular data give differing insights than taxonomic schemes based on traditional characters.