Diptera: Sciaroidea Incertae Sedis), with Description of Three New Species from India and Vietnam
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Ptolemeba N. Gen., a Novel Genus of Hartmannellid Amoebae (Tubulinea, Amoebozoa); with an Emphasis on the Taxonomy of Saccamoeba
The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Ptolemeba n. gen., a Novel Genus of Hartmannellid Amoebae (Tubulinea, Amoebozoa); with an Emphasis on the Taxonomy of Saccamoeba Pamela M. Watsona, Stephanie C. Sorrella & Matthew W. Browna,b a Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, 39762 b Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi, 39762 Keywords ABSTRACT 18S rRNA; amoeba; amoeboid; Cashia; cristae; freshwater amoebae; Hartmannella; Hartmannellid amoebae are an unnatural assemblage of amoeboid organisms mitochondrial morphology; SSU rDNA; SSU that are morphologically difficult to discern from one another. In molecular phy- rRNA; terrestrial amoebae; tubulinid. logenetic trees of the nuclear-encoded small subunit rDNA, they occupy at least five lineages within Tubulinea, a well-supported clade in Amoebozoa. The Correspondence polyphyletic nature of the hartmannellids has led to many taxonomic problems, M.W. Brown, Department of Biological in particular paraphyletic genera. Recent taxonomic revisions have alleviated Sciences, Mississippi State University, some of the problems. However, the genus Saccamoeba is paraphyletic and is Mississippi State, MS 39762, USA still in need of revision as it currently occupies two distinct lineages. Here, we Telephone number: +1 662-325-2406; report a new clade on the tree of Tubulinea, which we infer represents a novel FAX number: +1 662-325-7939; genus that we name Ptolemeba n. gen. This genus subsumes a clade of hart- e-mail: [email protected] mannellid amoebae that were previously considered in the genus Saccamoeba, but whose mitochondrial morphology is distinct from Saccamoeba. -
A Revised Classification of Naked Lobose Amoebae (Amoebozoa
Protist, Vol. 162, 545–570, October 2011 http://www.elsevier.de/protis Published online date 28 July 2011 PROTIST NEWS A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa) Introduction together constitute the amoebozoan subphy- lum Lobosa, which never have cilia or flagella, Molecular evidence and an associated reevaluation whereas Variosea (as here revised) together with of morphology have recently considerably revised Mycetozoa and Archamoebea are now grouped our views on relationships among the higher-level as the subphylum Conosa, whose constituent groups of amoebae. First of all, establishing the lineages either have cilia or flagella or have lost phylum Amoebozoa grouped all lobose amoe- them secondarily (Cavalier-Smith 1998, 2009). boid protists, whether naked or testate, aerobic Figure 1 is a schematic tree showing amoebozoan or anaerobic, with the Mycetozoa and Archamoe- relationships deduced from both morphology and bea (Cavalier-Smith 1998), and separated them DNA sequences. from both the heterolobosean amoebae (Page and The first attempt to construct a congruent molec- Blanton 1985), now belonging in the phylum Per- ular and morphological system of Amoebozoa by colozoa - Cavalier-Smith and Nikolaev (2008), and Cavalier-Smith et al. (2004) was limited by the the filose amoebae that belong in other phyla lack of molecular data for many amoeboid taxa, (notably Cercozoa: Bass et al. 2009a; Howe et al. which were therefore classified solely on morpho- 2011). logical evidence. Smirnov et al. (2005) suggested The phylum Amoebozoa consists of naked and another system for naked lobose amoebae only; testate lobose amoebae (e.g. Amoeba, Vannella, this left taxa with no molecular data incertae sedis, Hartmannella, Acanthamoeba, Arcella, Difflugia), which limited its utility. -
Conicocassis, a New Genus of Arcellinina (Testate Lobose Amoebae)
Palaeontologia Electronica palaeo-electronica.org Conicocassis, a new genus of Arcellinina (testate lobose amoebae) Nawaf A. Nasser and R. Timothy Patterson ABSTRACT Superfamily Arcellinina (informally known as thecamoebians or testate lobose amoebae) are a group of shelled benthic protists common in most Quaternary lacus- trine sediments. They are found worldwide, from the equator to the poles, living in a variety of fresh to brackish aquatic and terrestrial habitats. More than 130 arcellininid species and strains are ascribed to the genus Centropyxis Stein, 1857 within the family Centropyxidae Jung, 1942, which includes species that are distinguished by having a dorsoventral-oriented and flattened beret-like test (shell). Conicocassis, a new arcel- lininid genus of Centropyxidae differs from other genera of the family, specifically genus Centropyxis and its type species C. aculeata (Ehrenberg, 1932), by having a unique test comprised of two distinct components; a generally ovoid to subspherical, dorsoventral-oriented test body, with a pronounced asymmetrically positioned, funnel- like flange extending from a small circular aperture. The type species of the new genus, Conicocassis pontigulasiformis (Beyens et al., 1986) has previously been reported from peatlands in Germany, the Netherlands and Austria, as well as very wet mosses and aquatic environments in High Arctic regions of Europe and North America. The occurrence of the species in lacustrine environments in the central Northwest Ter- ritories extends the known geographic distribution of the genus in North America con- siderably southward. Nawaf A. Nasser. Department of Earth Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada. [email protected] R. Timothy Patterson. -
Protists – a Textbook Example for a Paraphyletic Taxon
ARTICLE IN PRESS Organisms, Diversity & Evolution 7 (2007) 166–172 www.elsevier.de/ode Protists – A textbook example for a paraphyletic taxon$ Martin Schlegela,Ã, Norbert Hu¨lsmannb aInstitute for Biology II, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany bFree University of Berlin, Institute of Biology/Zoology, Working group Protozoology, Ko¨nigin-Luise-Straße 1-3, 14195 Berlin, Germany Received 7 September 2004; accepted 21 November 2006 Abstract Protists constitute a paraphyletic taxon since the latter is based on the plesiomorphic character of unicellularity and does not contain all descendants of the stem species. Multicellularity evolved several times independently in metazoans, higher fungi, heterokonts, red and green algae. Various hypotheses have been developed on the evolution and nature of the eukaryotic cell, considering the accumulating data on the chimeric nature of the eukaryote genome. Subsequent evolution of the protists was further complicated by primary, secondary, and even tertiary intertaxonic recombinations. However, multi-gene sequence comparisons and structural data point to a managable number of such events. Several putative monophyletic lineages and a gross picture of eukaryote phylogeny are emerging on the basis of those data. The Chromalveolata comprise Chromista and Alveolata (Dinoflagellata, Apicomplexa, Ciliophora, Perkinsozoa, and Haplospora). Major lineages of the former ‘amoebae’ group within the Heterolobosa, Cercozoa, and Amoebozoa. Cercozoa, including filose testate amoebae, chlorarachnids, and plasmodiophoreans seem to be affiliated with foraminiferans. Amoebozoa consistently form the sister group of the Opisthokonta (including fungi, and with choanoflagellates as sister group of metazoans). A clade of ‘plants’ comprises glaucocystophytes, red algae, green algae, and land vascular plants. The controversial debate on the root of the eukaryote tree has been accelerated by the interpretation of gene fusions as apomorphic characters. -
Protistology Light-Microscopic Morphology and Ultrastructure Of
Protistology 13 (1), 26–35 (2019) Protistology Light-microscopic morphology and ultrastructure of Polychaos annulatum (Penard, 1902) Smirnov et Goodkov, 1998 (Amoebozoa, Tubulinea, Euamo- ebida), re-isolated from the surroundings of St. Petersburg (Russia) Oksana Kamyshatskaya1,2, Yelisei Mesentsev1, Ludmila Chistyakova2 and Alexey Smirnov1 1 Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia 2 Core Facility Center “Culturing of microorganisms”, Research park of St. Petersburg State Univeristy, St. Petersburg State University, Botanicheskaya St., 17A, 198504, Peterhof, St. Petersburg, Russia | Submitted December 15, 2018 | Accepted January 21, 2019 | Summary We isolated the species Polychaos annulatum (Penard, 1902) Smirnov et Goodkov, 1998 from a freshwater habitat in the surrounding of Saint-Petersburg. The previous re-isolation of this species took place in 1998; at that time the studies of its light- microscopic morphology were limited with the phase contrast optics, and the electron- microscopic data were obtained using the traditional glutaraldehyde fixation, preceded with prefixation and followed by postfixation with osmium tetroxide. In the present paper, we provide modern DIC images of P. annulatum. Using the fixation protocol that includes a mixture of the glutaraldehyde and paraformaldehyde we were able to obtain better fixation quality for this species. We provide some novel details of its locomotive morphology, nuclear morphology, and ultrastructure. The present finding evidence that P. annulatum is a widely distributed species that could be isolated from a variety of freshwater habitats. Key words: amoebae, Polychaos, ultrastructure, Amoebozoa Introduction Amoeba proteus). These amoebae usually have a relatively large size, exceeding hundred of microns, The largest species of naked lobose amoebae they produce broad, thick pseudopodia with (gymnamoebae) – members of the family Amoe- smooth outlines (lobopodia). -
The Evolution of Ogres: Cannibalistic Growth in Giant Phagotrophs
bioRxiv preprint doi: https://doi.org/10.1101/262378; this version posted February 12, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Bloomfield, 2018-02-08 – preprint copy - bioRχiv The evolution of ogres: cannibalistic growth in giant phagotrophs Gareth Bloomfell MRC Laboratory of Molecular Biology, Cambrilge, UK [email protected] twitter.com/iliomorph Abstract Eukaryotes span a very large size range, with macroscopic species most often formel in multicellular lifecycle stages, but sometimes as very large single cells containing many nuclei. The Mycetozoa are a group of amoebae that form macroscopic fruiting structures. However the structures formel by the two major mycetozoan groups are not homologous to each other. Here, it is proposel that the large size of mycetozoans frst arose after selection for cannibalistic feeling by zygotes. In one group, Myxogastria, these zygotes became omnivorous plasmolia; in Dictyostelia the evolution of aggregative multicellularity enablel zygotes to attract anl consume surrounling conspecifc cells. The cannibalism occurring in these protists strongly resembles the transfer of nutrients into metazoan oocytes. If oogamy evolvel early in holozoans, it is possible that aggregative multicellularity centrel on oocytes coull have precelel anl given rise to the clonal multicellularity of crown metazoa. Keyworls: Mycetozoa; amoebae; sex; cannibalism; oogamy Introduction – the evolution of Mycetozoa independently in several diverse lineages, presumably reflecting strong selection for effective dispersal [9]. The dictyostelids (social amoebae or cellular slime moulds) and myxogastrids (also known as myxomycetes and true or The close relationship between dictyostelia and myxogastria acellular slime moulds) are protists that form macroscopic suggests that they shared a common ancestor that formed fruiting bodies (Fig. -
(Amoebozoa, Discosea, Dactylopodida) — a New Freshwater Amoeba with Unusual Combination of Scales
Protistology 11 (4), 238–247 (2017) Protistology Korotnevella novazelandica n. sp. (Amoebozoa, Discosea, Dactylopodida) — a new freshwater amoeba with unusual combination of scales Ilya A. Udalov1, Eckhard Völcker2 and Alexey Smirnov1 1 Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia 2 Penard Labs, Cape Town, South Africa | Submitted November 25, 2017 | Accepted December 6, 2017 | Summary A new freshwater species of naked lobose amoebae, Korotnevella novazelandica n. sp. (Amoebozoa, Discosea, Flabellinia, Dactylopodida), from New Zealand was studied and described. This species has sombrero-shaped as well as dish-shaped scales, a combination previously not known in Korotnevella. Phylogenetic analysis based on 18S rRNA gene placed it in a clade along with Korotnevella species possessing uniform sombrero-shaped scales: K. pelagolacustris, K. jeppesenii and K. fousta. At the level of light microscopy, K. novazelandica lacks clear distinctions from the above-mentioned species, but it could be easily distinguished from them in electron microscopy by the presence of dish-shaped scales. The presence of dish-shaped scales may be considered as a primitive character for the K. pelagolacustris + K. jeppesenii + K. fousta + K. novazelandica clade, which were secondarily lost in the most of species in this clade. The sombrero-shaped scales could have evolved from basket scales or developed de novo after the loss of basket scales. Key words: 18S rRNA gene, Korotnevella, molecular phylogeny, scales, systematics, ultrastructure Introduction considered to be species-specific (Pennick and Goodfellow, 1975; Page, 1981; Smirnov, 1999; The genus Korotnevella encompasses flattened O’Kelly et al., 2001; Udalov, 2015, 2016; Udalov amoebae of dactylopodial morphotype (Smirnov et al., 2016; Zlatogursky et al., 2016; Van Wichelen and Goodkov, 1999; Smirnov and Brown, 2004), et al., 2016). -
Soil Protists in Three Neotropical Rainforests Are Hyperdiverse And
bioRxiv preprint doi: https://doi.org/10.1101/050997; this version posted November 3, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites Fred´ eric´ Mahe´ 1, Colomban de Vargas 2;3, David Bass 4;5, Lucas Czech 6, Alexandros Stamatakis 6;7, Enrique Lara 8, David Singer 8, Jordan Mayor 9, John Bunge 10, Sarah Sernaker 11, Tobias Siemensmeyer 1, Isabelle Trautmann 1, Sarah Romac 2;3,Cedric´ Berney 2;3, Alexey Kozlov 6, Edward A. D. Mitchell 8;12, Christophe V. W. Seppey 8, Elianne Egge 13, Guillaume Lentendu 1, Rainer Wirth 14, Gabriel Trueba 15 and Micah Dunthorn 1∗ 1Department of Ecology, University of Kaiserslautern, Erwin-Schrodinger-Straße,¨ 67663 Kaiserslautern, Germany. 2CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. 3Sorbonne Universites,´ UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. 4Department of Life Sciences, The Natural History Museum London, Cromwell Road, London SW7 5BD, United Kingdom. 5Centre for Environment, Fisheries & Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom. 6Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg, 69118 Heidelberg, Germany. 7Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten, 76128 Karlsruhe, Germany. 8Laboratory of Soil Biodiversity, Universite´ de Neuchatel,ˆ Rue Emile-Argand, 2000 Neuchatel,ˆ Switzerland. -
The Phagotrophic Origin of Eukaryotes and Phylogenetic Classification Of
International Journal of Systematic and Evolutionary Microbiology (2002), 52, 297–354 DOI: 10.1099/ijs.0.02058-0 The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa Department of Zoology, T. Cavalier-Smith University of Oxford, South Parks Road, Oxford OX1 3PS, UK Tel: j44 1865 281065. Fax: j44 1865 281310. e-mail: tom.cavalier-smith!zoo.ox.ac.uk Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an α-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an α-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. -
Genera of the World: an Overview and Estimates Based on the March 2020 Release of the Interim Register of Marine and Nonmarine Genera (IRMNG)
Megataxa 001 (2): 123–140 ISSN 2703-3082 (print edition) https://www.mapress.com/j/mt/ MEGATAXA Copyright © 2020 Magnolia Press Article ISSN 2703-3090 (online edition) https://doi.org/10.11646/megataxa.1.2.3 http://zoobank.org/urn:lsid:zoobank.org:pub:F4A52C97-BAD0-4FD5-839F-1A61EA40A7A3 All genera of the world: an overview and estimates based on the March 2020 release of the Interim Register of Marine and Nonmarine Genera (IRMNG) TONY REES 1, LEEN VANDEPITTE 2, 3, BART VANHOORNE 2, 4 & WIM DECOCK 2, 5 1 Private address, New South Wales, Australia. �[email protected]; http://orcid.org/0000-0003-1887-5211 2 Flanders Marine Institute/Vlaams Instituut Voor De Zee (VLIZ), Wandelaarkaai 7, 8400 Ostend, Belgium. 3 �[email protected]; http://orcid.org/0000-0002-8160-7941 4 �[email protected]; https://orcid.org/0000-0002-6642-4725 5 �[email protected]; https://orcid.org/0000-0002-2168-9471 Abstract Introduction We give estimated counts of known accepted genera of the The concept of a series of papers addressing portions of world (297,930±65,840, of which approximately 21% are the question of “all genera of the world” is a valuable one, fossil), of a total 492,620 genus names presently held for which can benefit from as much preliminary scoping as “all life”, based on the March 2020 release of the Interim may be currently available. To date, synoptic surveys of Register of Marine and Nonmarine Genera (IRMNG). A fur- biodiversity have been attempted mainly at the level of ther c. -
Molecular Phylogenetics Evidence for a Novel Lineage of Amoebae Within Discosea (Amoebozoa: Lobosa)
Acta Protozool. (2013) 52: 309–316 http://www.eko.uj.edu.pl/ap ACTA doi:10.4467/16890027AP.13.028.1320 PROTOZOOLOGICA Short communication Molecular Phylogenetics Evidence for a Novel Lineage of Amoebae Within Discosea (Amoebozoa: Lobosa) Daniele CORSARO1,2 and Danielle VENDITTI1,3 1 CHLAREAS – Chlamydia Research Association, Vandoeuvre-lès-Nancy, France; 2 Laboratory of Soil Biology, Institute of Biology, University of Neuchâtel, Switzerland; 3 TREDI R & D, Faculty of Medicine, Vandoeuvre-lès-Nancy, France Abstract. Some amoebae were recovered from freshwater samples on agar plates. Due to a fungal contamination tightly associated with these amoebae, it was impossible to correctly characterize them on a morphological base, but sequences of the small subunit ribosomal RNA gene (SSU rDNA) were successfully obtained from three strains. Phylogenetic analysis performed on these SSU rDNA allowed to identify these amoebae as members of a new lineage, related to the Dermamoebida, which includes also several other environmental SSU sequences. Key words: Amoebozoa, environmental 18S rDNA, small amoebae, Dermamoebida. INTRODUCTION tured microbial eukaryotes, along with a re-analysis of reference strains and/or of new isolates, permitted also to elucidate some evolutionary relationships (Smirnov In the past ten years, culture-independent surveys et al. 2008, 2009). We recovered from a previous study based on amplification and sequencing of 18S rRNA amoebae which appeared very small at direct obser- gene (18S rDNA), revealed an unexpected diversity of vation. Two small-sized amoebae are already known, microbial eukaryotes in many types of habitats (Behnke Parvamoeba (Rogerson 1993) and Micriamoeba (Atlan et al. 2006, Dawson and Pace 2002, López-García et et al. -
Ecology of Old Woman Creek, Ohio
Shagbark hickory (Carya ovata) on a bluff overlooking Old Woman Creek estuary (Charles E. Herdendorf). CHAPTER 1. INTRODUCTION CHAPTER 6. BIOLOGY NON-VASCULAR PLANTS The algal flora and lower plants found in the vicinity of the Research Reserve embrace four of the The non-vascular plants of the Old Woman Creek five kingdoms of living organisms (Margulis and estuary and watershed include the algal flora and the Schwartz 1988). As defined by Round (1969), this lower plants. For the purposes of the Site Profile, “algal grouping includes the major divisions (with typical flora” is considered as those chlorophyll-bearing, examples) listed in Table 6.1. aquatic organisms that lack vascular systems, true tissues, and root, stem, and leaf organs (Gray 1970) and “lower plants” include the fungi, lichens, mosses, horsetails, and ferns—those aquatic and terrestrial plant-like organisms with less complex vegetative and reproductive morphology than the gymnosperms (conifers) and angiosperms (flowering plants). In this profile, the grouping of species into divisions, classes, orders, and families follows the classification system presented in Synopsis and Classification of Living Organisms (Parker 1982), except where noted. TABLE 6.1. CLASSIFICATION OF ALGAL FLORA AND LOWER PLANTS Kingdom Monera Cyanobacteria (blue-green algae) Kingdom Protista Rhodophytes (red algae) Chrysophytes (golden & yellow-green algae) Pyrrhophytes (fire algae) Cryptophytes (crytomonads) Euglenophytes (euglenoids) Chlorophytes (green algae) Kingdom Fungi Myxomycetes (slime molds) Phycomycetes (algal fungi & water molds) Ascomysetes (yeasts, molds, & cup fungi) Figure 6.1. Phycology laboratory Basidiomycetes (mushrooms, smuts, & rusts) at the Ohio Center for Coastal Wetlands Study, Deuteromycetes (imperfect fungi) Old Woman Creek SNP & NERR (David M.