717 research outputs found
Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., two new alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and their contributions to reconstructing the ancestral state of alveolates and eukaryotes.
No full textThe evolutionary and ecological importance of predatory flagellates are too often overlooked. This is not only a gap in our understanding of microbial diversity, but also impacts how we interpret their better-studied relatives. A prime example of these problems is found in the alveolates. All well-studied species belong to three large clades (apicomplexans, dinoflagellates, and ciliates), but the predatory colponemid flagellates are also alveolates that are rare in nature and seldom cultured, but potentially important to our understanding of alveolate evolution. Recently we reported the first cultivation and molecular analysis of several colponemid-like organisms representing two novel clades in molecular trees. Here we provide ultrastructural analysis and formal species descriptions for both new species, Colponema vietnamica n. sp. and Acavomonas peruviana n. gen. n. sp. Morphological and feeding characteristics concur with molecular data that both species are distinct members of alveolates, with Acavomonas lacking the longitudinal phagocytotic groove, a defining feature of Colponema. Based on ultrastructure and molecular phylogenies, which both provide concrete rationale for a taxonomic reclassification of Alveolata, we establish the new phyla Colponemidia nom. nov. for the genus Colponema and its close relatives, and Acavomonidia nom. nov. for the genus Acavomonas and its close relatives. The morphological data presented here suggests that colponemids are central to our understanding of early alveolate evolution, and suggest they also retain features of the common ancestor of all eukaryotes
The morphology, ultrastructure and SSU rRNA gene sequence of a new freshwater flagellate, Neobodo borokensis n. sp (Kinetoplastea, Excavata)
No full textThe Morphology, Ultrastructure and Molecular Phylogeny of a New Freshwater Heterolobose Amoeba <em>Parafumarolamoeba stagnalis</em> n. sp. (Vahlkampfiidae; Heterolobosea)
No full textHeterolobose amoebae are important members of marine, freshwater, and soil microbial communities, but their diversity remains under-explored. We studied the diversity of Vahlkampfiidae to improve our understanding of heterolobosean relationships and their representation in aquatic benthos. Using light and electron microscopy, and molecular phylogenies based on the SSU rRNA and ITS loci, we describe the fine morphology and evolutionary relationships of a new heterolobosean Parafumarolamoeba stagnalis n. sp. from a small pond in European Russia. Cells of P. stagnalis possess a clearly distinguishable anterior hyaline pseudopodium, eruptive movement, several thin and sometimes branched uroidal filaments, spherical cysts without pores and plugs, and mitochondria that have discoid cristae and are surrounded by cisternae of the endoplasmic reticulum. The genus Parafumarolamoeba has so far included a single species, Parafumarolamoeba alta from high-altitude soil in Tibet, which is morphologically distinct from P. stagnalis. Taxonomic description for a new Parafumarolamoeba species is therefore provided
Predatory colponemids are the sister group to all other alveolates
No full textAlveolates are a major supergroup of eukaryotes encompassing more than ten thousand free-living and parasitic species, including medically, ecologically, and economically important apicomplexans, dinoflagellates, and ciliates. These three groups are among the most widespread eukaryotes on Earth, and their environmental success can be linked to unique innovations that emerged early in each group. Understanding the emergence of these well-studied and diverse groups and their innovations has relied heavily on the discovery and characterization of early-branching relatives, which allow ancestral states to be inferred with much greater confidence. Here we report the phylogenomic analyses of 313 eukaryote protein-coding genes from transcriptomes of three members of one such group, the colponemids (Colponemidia), which support their monophyly and position as the sister lineage to all other known alveolates. Colponemid-related sequences from environmental surveys and our microscopical observations show that colponemids are not common in nature, but they are diverse and widespread in freshwater habitats around the world. Studied colponemids possess two types of extrusive organelles (trichocysts or toxicysts) for active hunting of other unicellular eukaryotes and potentially play an important role in microbial food webs. Colponemids have generally plesiomorphic morphology and illustrate the ancestral state of Alveolata. We further discuss their importance in understanding the evolution of alveolates and the origin of myzocytosis and plastids
Characterization of Tulamoeba bucina n. sp., an extremely halotolerant amoeboflagellate heterolobosean belonging to the Tulamoeba-Pleurostomum Clade (Tulamoebidae n. fam.)
No full textMost protozoans that have been cultivated recently from high salinity waters appear to be obligate halophiles. Phylogenetic analyses indicate that these species mostly represent independent lineages. Here, we report the cultivation, morphological characterization, and phylogenetic analysis of two strains (XLG1 and HLM-8) of a new extremely halotolerant heterolobosean amoeboflagellate. This species is closely related to the obligate halophiles Tulamoeba peronaphora and Pleurostomum flabellatum, and more specifically to the former. Like Tulamoeba, the new species has a monopodial limax amoeba stage, however, its cyst stage lacks an intrusive pore plug. The flagellate stage bears a combination of a planar spiral feeding apparatus and unequal heterodynamic flagella that discriminates it from described Pleurostomum species. Strain XLG1 grows at salinities from 35‰ to 225‰. This degree of halotolerance is uncommon in protozoa, as most species showing growth in seawater are unable to grow at 200‰ salinity. The unrelatedness of most halophilic protozoa suggested that independent colonization of the hypersaline environment is more common than speciation within it. However, this study supports the idea that the Tulamoeba–Pleurostomum clade underwent an adaptive radiation within the hypersaline environment. A new species Tulamoeba bucina n. sp. is described, with Tulamoebidae n. fam. proposed for the Tulamoeba–Pleurostomum clade
A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction
No full textThe origin of eukaryotic cells represents a key transition in cellular evolution and is closely tied to outstanding questions about mitochondrial endosymbiosis [1, 2]. For example, gene-rich mitochondrial genomes are thought to be indicative of an ancient divergence, but this relies on unexamined assumptions about endosymbiont-to-host gene transfer [3–5]. Here, we characterize Ancoracysta twista, a new predatory flagellate that is not closely related to any known lineage in 201-protein phylogenomic trees and has a unique morphology, including a novel type of extrusome (ancoracyst). The Ancoracysta mitochondrion has a gene-rich genome with a coding capacity exceeding that of all other eukaryotes except the distantly related jakobids and Diphylleia, and it uniquely possesses heterologous, nucleus-, and mitochondrion-encoded cytochrome c maturase systems. To comprehensively examine mitochondrial genome reduction, we also assembled mitochondrial genomes from picozoans and colponemids and re-annotated existing mitochondrial genomes using hidden Markov model gene profiles. This revealed over a dozen previously overlooked mitochondrial genes at the level of eukaryotic supergroups. Analysis of trends over evolutionary time demonstrates that gene transfer to the nucleus was non-linear, that it occurred in waves of exponential decrease, and that much of it took place comparatively early, massively independently, and with lineage-specific rates. This process has led to differential gene retention, suggesting that gene-rich mitochondrial genomes are not a product of their early divergence. Parallel transfer of mitochondrial genes and their functional replacement by new nuclear factors are important in models for the origin of eukaryotes, especially as major gaps in our knowledge of eukaryotic diversity at the deepest level remain unfilled
Light and electron micrographs of colponemids.
No full text<p>(a–f) <i>Colponema edaphicum</i>: a) large food vacuole is visible, b) cell division, (c, d) two heterodymanic flagella and (e, f) extrusive organelle toxicyst (TEM), ((a–c), f) from Tikhonenkov et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Tikhonenkov2" target="_blank">[64]</a>, (d, e) from Mylnikov et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Mylnikov7" target="_blank">[65]</a>; g) <i>Colponema marisrubri</i> (from Mylnikov and Tikhonenkov <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Mylnikov4" target="_blank">[25]</a>). a.f – anterior flagellum, f.v – food vacuole, p.f – posterior flagellum, c.v – contractile vacuole, ac – acronema, tc – toxicyst. Scales: (a–e), g) –10 µm; f) –1 µm.</p
Heterotrophic Flagellates from Freshwater and Soil Habitats in Subtropical China (Wuhan Area, Hubei Province)
No full textWe studied the diversity of heterotrophic flagellates from the sandy sediments of the Yangtze River, sandy and silty sediments of Donghu Lake, soil, moss and litter from the Luojiashan and Moshan hills as well as litter from the floodplain near Donghu Lake in April 2010. Sixty-seven heterotrophic flagellate species were identified by means of phase and interference contrast light microscopy and transmission electron microscopy. The majority of the observed flagellates were bacterivorous. Local species richness of river sediment communities was significantly lower than that of lake sediments and terrestrial habitats. The communities from the terrestrial habitats were more heterogeneous than those from freshwater sediments. Common species for the aquatic habitats were Rhynchomonas nasuta, Paraphysomonas sp., Neobodo designis, N. curvifilis, Bodo saltans and Spumella spp. In the soils only Spumella spp. was found in the majority of samples. Most characteristic taxa for the lake sediments were Helkesimastix faecicola, Petalomonas minuta, P. pusilla, Diphylleia rotans, Amastigomonas caudata. Amoeboflagellates such as Cercomonas angustus, C. granulifera, Paracercomonas crassicauda were specific for the terrestrial habitats. There were no specific taxa in the river sediments. The majority of the heterotrophic flagellates identified in this survey have been noted in China earlier. They are common (and usually predominant) for other regions in both freshwater and soil habitats.We studied the diversity of heterotrophic flagellates from the sandy sediments of the Yangtze River, sandy and silty sediments of Donghu Lake, soil, moss and litter from the Luojiashan and Moshan hills as well as litter from the floodplain near Donghu Lake in April 2010. Sixty-seven heterotrophic flagellate species were identified by means of phase and interference contrast light microscopy and transmission electron microscopy. The majority of the observed flagellates were bacterivorous. Local species richness of river sediment communities was significantly lower than that of lake sediments and terrestrial habitats. The communities from the terrestrial habitats were more heterogeneous than those from freshwater sediments. Common species for the aquatic habitats were Rhynchomonas nasuta, Paraphysomonas sp., Neobodo designis, N. curvifilis, Bodo saltans and Spumella spp. In the soils only Spumella spp. was found in the majority of samples. Most characteristic taxa for the lake sediments were Helkesimastix faecicola, Petalomonas minuta, P. pusilla, Diphylleia rotans, Amastigomonas caudata. Amoeboflagellates such as Cercomonas angustus, C. granulifera, Paracercomonas crassicauda were specific for the terrestrial habitats. There were no specific taxa in the river sediments. The majority of the heterotrophic flagellates identified in this survey have been noted in China earlier. They are common (and usually predominant) for other regions in both freshwater and soil habitats
Colponemids Represent Multiple Ancient Alveolate Lineages
No full textSummaryThe alveolates comprise three well-studied protist lineages of significant environmental, medical, and economical importance: apicomplexans (e.g., Plasmodium), dinoflagellates (e.g., Symbiodinium), and ciliates (e.g., Tetrahymena). These major lineages have evolved distinct and unusual characteristics, the origins of which have proved to be difficult evolutionary puzzles. Mitochondrial genomes are a prime example: all three groups depart from canonical form and content, but in different ways. Reconstructing such ancient transitions is difficult without deep-branching lineages that retain ancestral characteristics. Here we describe two such lineages and how they illuminate the ancestral state of alveolate mitochondrial genomes. We established five clonal cultures of colponemids, predatory alveolates without cultured representatives and molecular data. Colponemids represent at least two independent lineages at the phylum level in multilocus phylogenetic analysis; one sister to apicomplexans and dinoflagellates, and the other at a deeper position. A genome survey from one strain showed that ancestral state of the mitochondrial genomes in the three major alveolate lineages consisted of an unusual linear chromosome with telomeres and a substantially larger gene set than known alveolates. Colponemid sequences also identified several environmental lineages as colponemids, altogether suggesting an untapped potential for understanding the origin and evolution of apicomplexans, dinoflagellates, and ciliates
Drawings of colponemids.
No full text<p>(a–d) <i>Colponema edaphicum</i> (from Mylnikov and Tikhonenkov <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Mylnikov5" target="_blank">[43]</a>), (e–i) <i>C. marisrubri</i> (from Mylnikov and Tikhonenkov <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Mylnikov4" target="_blank">[25]</a>), (j–m) <i>C. loxodes</i> ((j, k) from Zhukov and Mylnikov <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Zhukov1" target="_blank">[41]</a>; l) from Chadefaud <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Chadefaud1" target="_blank">[42]</a>; m) from Lemmermann <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Lemmermann1" target="_blank">[38]</a>, n) <i>C. symmetricum</i> (from Sandon <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-Sandon1" target="_blank">[39]</a>), o) <i>C. globosum</i> (from De Faria et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095467#pone.0095467-deFaria1" target="_blank">[51]</a>). a.f – anterior flagellum, f.v – food vacuole, gr – longitudinal groove, n – nucleus, p.f – posterior flagellum. Scales: (a–c), (e–i) –10 µm; d) –1; (j–m) –20 µm; (n, o) –15 µm.</p
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