Protistology Morphology and Biometry of Arcella Intermedia (Deflandre
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Testate Amoebae from South Vietnam Waterbodies with the Description of New Species Difflugia Vietnamicasp
Acta Protozool. (2018) 57: 215–229 www.ejournals.eu/Acta-Protozoologica ACTA doi:10.4467/16890027AP.18.016.10092 PROTOZOOLOGICA LSID urn:lsid:zoobank.org:pub:AEE9D12D-06BD-4539-AD97-87343E7FDBA3 Testate Amoebae from South Vietnam Waterbodies with the Description of New Species Difflugia vietnamicasp. nov. Hoan Q. TRANa, Yuri A. MAZEIb, c a Vietnamese-Russian Tropical Center, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Ha Noi, Vietnam b Department of Hydrobiology, Lomonosov Moscow State University, Moscow, Russia c Department of Zoology and Ecology, Penza State University, Penza, Russia Abstract. Testate amoebae in Vietnam are still poorly investigated. We studied species composition of testate amoebae in 47 waterbodies of South Vietnam provinces including natural lakes, reservoirs, wetlands, rivers, and irrigation channels. A total of 109 species and subspe- cies belonging to 16 genera, 9 families were identified from 191 samples. Thirty-five species and subspecies were observed in Vietnam for the first time. New speciesDifflugia vietnamica sp. nov. is described. The most species-rich genera are Difflugia (46 taxa), Arcella (25) and Centropyxis (14). Centropyxis aculeata was the most common species (observed in 68.1% samples). Centropyxis aerophila sphagniсola, Arcella discoides, Difflugia schurmanni and Lesquereusia modesta were characterised by a frequency of occurrence >20%. Other spe- cies were rarer. The species accumulation curve based on the entire dataset of this work was unsaturated and well fitted by equation S = 19.46N0.33. Species richness per sample in natural lakes and wetlands were significantly higher than that of rivers (p < 0.001). The result of the Spearman rank test shows weak or statistically insignificant relationships between species richness and water temperature, pH, dissolved oxygen, and electrical conductivity. -
Diversity, Phylogeny and Phylogeography of Free-Living Amoebae
School of Doctoral Studies in Biological Sciences University of South Bohemia in České Budějovice Faculty of Science Diversity, phylogeny and phylogeography of free-living amoebae Ph.D. Thesis RNDr. Tomáš Tyml Supervisor: Mgr. Martin Kostka, Ph.D. Department of Parasitology, Faculty of Science, University of South Bohemia in České Budějovice Specialist adviser: Prof. MVDr. Iva Dyková, Dr.Sc. Department of Botany and Zoology, Faculty of Science, Masaryk University České Budějovice 2016 This thesis should be cited as: Tyml, T. 2016. Diversity, phylogeny and phylogeography of free living amoebae. Ph.D. Thesis Series, No. 13. University of South Bohemia, Faculty of Science, School of Doctoral Studies in Biological Sciences, České Budějovice, Czech Republic, 135 pp. Annotation This thesis consists of seven published papers on free-living amoebae (FLA), members of Amoebozoa, Excavata: Heterolobosea, and Cercozoa, and covers three main topics: (i) FLA as potential fish pathogens, (ii) diversity and phylogeography of FLA, and (iii) FLA as hosts of prokaryotic organisms. Diverse methodological approaches were used including culture-dependent techniques for isolation and identification of free-living amoebae, molecular phylogenetics, fluorescent in situ hybridization, and transmission electron microscopy. Declaration [in Czech] Prohlašuji, že svoji disertační práci jsem vypracoval samostatně pouze s použitím pramenů a literatury uvedených v seznamu citované literatury. Prohlašuji, že v souladu s § 47b zákona č. 111/1998 Sb. v platném znění souhlasím se zveřejněním své disertační práce, a to v úpravě vzniklé vypuštěním vyznačených částí archivovaných Přírodovědeckou fakultou elektronickou cestou ve veřejně přístupné části databáze STAG provozované Jihočeskou univerzitou v Českých Budějovicích na jejích internetových stránkách, a to se zachováním mého autorského práva k odevzdanému textu této kvalifikační práce. -
Marine Biological Laboratory) Data Are All from EST Analyses
TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878. -
THE THECAMOEBIAN BIBLIOGRAPHY 2Nd Edition
Palaeontologia Electronica http://palaeo-electronica.org Preamble to the 2nd Edition. Since the publication of the first edition we have collected about 1,000 new titles which are inserted in the second edition. All the remarks and caveats in the Introduction are valid for both editions. The first edition of this document was published in 1999. THE THECAMOEBIAN BIBLIOGRAPHY 2nd Edition F.S. Medioli, L. Bonnet, David B. Scott, and Barbara Elizabeth Medioli ABSTRACT The literature on thecamoebians can be rather confusing, partly because it has been published in many different languages, but mainly because these Rhizopoda have been the subject of study for a wide array of researchers with very different inter- ests. Not only has this resulted in fragmentation of the literature due to research results being published in journals specializing in different fields, but inevitably has also resulted in development of a chaotic terminology and nomenclature. For example there is even confusion as to what to call the group, as terms such as "rhizopods," "testate amoebae," and "arcellaceans" have all been used by various authors as synonyms of "Thecamoebians." Even more confusing is the nomenclature of the described the- camoebian species. Lack of access to the literature and limited interchange between the various research groups has generated many synonyms. Although only a first step this fairly complete bibliography on thecamoebians has been compiled to assist researchers become more aware of the available literature. F.S. Medioli, David B. Scott. Dalhousie University, Department of Earth Sciences, Halifax, Nova Scotia, B3H 3J5, Canada. [email protected]. [email protected]. -
Evolution of the Actin Gene Family in Testate Lobose Amoebae (Arcellinida) Is Characterized by Two Distinct Clades of Paralogs and Recent Independent Expansions
Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 1-1-2011 Evolution of the Actin Gene Family in Testate Lobose Amoebae (Arcellinida) is Characterized by Two Distinct Clades of Paralogs and Recent Independent Expansions Daniel J.G. Lahr University of Massachusetts System Truc B. Nguyen Smith College Erika Barbero Smith College Laura A. Katz Smith College, [email protected] Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Lahr, Daniel J.G.; Nguyen, Truc B.; Barbero, Erika; and Katz, Laura A., "Evolution of the Actin Gene Family in Testate Lobose Amoebae (Arcellinida) is Characterized by Two Distinct Clades of Paralogs and Recent Independent Expansions" (2011). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/124 This Article has been accepted for inclusion in Biological Sciences: Faculty Publications by an authorized administrator of Smith ScholarWorks. For more information, please contact [email protected] Evolution of the Actin Gene Family in Testate Lobose Amoebae (Arcellinida) is Characterized by Two Distinct Clades of Paralogs and Recent Independent Expansions Daniel J. G. Lahr,1 Truc B. Nguyen,2 Erika Barbero,2 and Laura A. Katz*,1,2 1Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts 2Department of Biological Sciences, Smith College *Corresponding author: E-mail: [email protected]. Associate editor: Andrew Roger Abstract Research article The evolution of actin gene families is characterized by independent expansions and contractions across the eukaryotic tree of life. Here, we assess diversity of actin gene sequences within three lineages of the genus Arcella, a free-living testate (shelled) amoeba in the Arcellinida. -
Biogeography and Dispersal of Micro-Organisms: a Review Emphasizing Protists
Acta Protozool. (2006) 45: 111 - 136 Review Article Biogeography and Dispersal of Micro-organisms: A Review Emphasizing Protists Wilhelm FOISSNER Universität Salzburg, FB Organismische Biologie, Salzburg, Austria Summary. This review summarizes data on the biogeography and dispersal of bacteria, microfungi and selected protists, such as dinoflagellates, chrysophytes, testate amoebae, and ciliates. Furthermore, it introduces the restricted distribution and dispersal of mosses, ferns and macrofungi as arguments into the discussion on the postulated cosmopolitism and ubiquity of protists. Estimation of diversity and distribution of micro-organisms is greatly disturbed by undersampling, the scarcity of taxonomists, and the frequency of misidentifications. Thus, probably more than 50% of the actual diversity has not yet been described in many protist groups. Notwithstanding, it has been shown that a restricted geographic distribution of micro-organisms occurs in limnetic, marine, terrestrial, and fossil ecosystems. Similar as, in cryptogams and macrofungi about, 30% of the extant suprageneric taxa, described and undescribed, might be morphological and/or genetic and/or molecular endemics. At the present state of knowledge, micro-organism endemicity can be proved/disproved mainly by flagship species, excluding sites (e.g., university ponds) prone to be contaminated by invaders. In future, genetic and molecular data will be increasingly helpful. The wide distribution of many micro-organisms has been attributed to their small size and their astronomical numbers. However, this interpretation is flawed by data from macrofungi, mosses and ferns, many of which occupy distinct areas, in spite of their minute and abundant means of dispersal (spores). Thus, I suggest historic events (split of Pangaea etc.), limited cyst viability and, especially, time as major factors for dispersal and provinciality of micro-organisms. -
Evaluating the Taxonomic Identity in Four Species of the Lobose Testate Amoebae Genus Arcella Ehrenberg, 1832
Acta Protozool. (2009) 48: 127–142 ACTA PROTOZOOLOGICA Evaluating the Taxonomic Identity in Four Species of the Lobose Testate Amoebae Genus Arcella Ehrenberg, 1832 Daniel J. G. LAHR1,2 and Sônia G. B. C. LOPES2 1 Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, United States of America; 2 Department of Zoology, University of Sao Paulo, Sao Paulo, Brazil Summary. The taxonomic identity in microbial eukaryotes remains an impediment to discussing ecology, biogeography and phylogeny, mainly due to a lack of standards in organism descriptions and few comparative works. The lobose testate amoebae (Arcellinida) present an ideal study system, as progress is severely hindered due to taxonomic confusion. In the present survey, we have examined the morphology, biometry and ecology of 2400 individuals in the genus Arcella Ehrenberg, 1832, collected from the Tiete River in Sao Paulo, Brazil. We then contrasted these new data with 26 previously described species, varieties and forms, looking for consistencies and trying to establish distinct entities. Using a combination of morphology and multivariate statistics we were able to determine 4 distinct taxa (Arcella hemisphaerica, Arcella discoides, Arcella gibbosa and Arcella brasiliensis), each of them encompassing a number of other non-distinct nominal taxa. We describe in detail each of the 4 taxa with notes on ecology and biogeography, and list the indistinguishable names in an effort to make iden- tification and taxonomy in the testate amoebae a more objective and precise exercise by clarifying the taxonomic identity. Key words: Taxonomic identity, Arcellinida, Arcella, Morphology, Biometry. INTRODUCTION sion and future changes with sufficient stability (see ICZN (Ride et al. -
Protozoa: Rhizopoda) Related to Water Quality? - 85
Alves Corrêa et al.: Is the periphytic structure of Testaceans (Protozoa: Rhizopoda) related to water quality? - 85 - IS THE PERIPHYTIC STRUCTURE OF TESTACEANS (PROTOZOA: RHIZOPODA) RELATED TO WATER QUALITY: A CASE STUDY IN THE CUIABÁ RIVER, BRAZIL LILIANA VICTORINO ALVES CORRÊA1 – EDNA LOPES HARDOIM 2 – PETER ZEILHOFER3* 1Department of Medicine, Federal University of Mato Grosso, Brazil Av. Fernando Corrêa da Costa nº 2.367 – Boa Esperança 78060-900 Cuiabá – MT, Brazil (phone: +55-65-3615-8854; fax: +55-65-3615-8854) 2Department of Botany and Ecology, Federal University of Mato Grosso, Brazil Av. Fernando Corrêa da Costa nº 2.367 – Boa Esperança 78060-900 Cuiabá – MT, Brazil (phone: +55-65-3615-8738; fax: +55-65-3615-8738) 3Department of Geography, Federal University of Mato Grosso, Brazil Av. Fernando Corrêa da Costa nº 2.367 – Boa Esperança 78060-900 Cuiabá – MT, Brazil (phone: +55-65-3615-8738; fax: +55-65-3615-8738) *Corresponding author e-mail: [email protected] (Received 5th Nov 2013; accepted 14th Aug 2014) Abstract. Presented study describes the periphytic community of Testaceans of the Cuiabá River, Central Brazil and evaluates its relationships to physical, chemical and biological water characteristics. Three sampling stations were established along an urban reach passing Cuiabá city, realizing four campaigns at the right and left river margins. Canonical Correspondence Analysis was conducted to study relationships of chemical and physical water characteristics with the colonization of the periphytic community of Testaceans on artificial substrata. Assemblage composition varies according to seasonal hydrological cycles and water quality, as well as spatially along the pollution gradient reflected by sampling sites along the river reach. -
Effect of Taxonomic Resolution on Ecological and Palaeoecological Inference E a Test Using Testate Amoeba Water Table Depth Transfer Functions
1 Published in Quaternary Science Reviews, Vol. 91, 2014, p. 62-69 which should be used for any reference to this work Effect of taxonomic resolution on ecological and palaeoecological inference e a test using testate amoeba water table depth transfer functions Edward A.D. Mitchell a,*, Mariusz Lamentowicz b, Richard J. Payne c, Yuri Mazei d a Laboratory of Soil Biology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland b Department of Biogeography and Palaeoecology, Faculty of Geosciences, Adam Mickiewicz University, Dzie˛gielowa 27, 61-680 Poznan, Poland c Biological and Environmental Science, University of Stirling, Stirling FK94LA, Scotland, UK d Department of Zoology and Ecology, Penza State University, Krasnaya str., 40, Penza 440026, Russia abstract Sound taxonomy is a major requirement for quantitative environmental reconstruction using biological Keywords: data. Transfer function performance should theoretically be expected to decrease with reduced taxo- Palaeoecology nomic resolution. However for many groups of organisms taxonomy is imperfect and species level Bioindication identification not always possible. Transfer function We conducted numerical experiments on five testate amoeba water table (DWT) transfer function data Taxonomy sets. We sequentially reduced the number of taxonomic groups by successively merging morphologically Testate amoebae similar species and removing inconspicuous species. We then assessed how these changes affected Quantitative ecology Peatland model performance and palaeoenvironmental reconstruction using two fossil data sets. Model performance decreased with decreasing taxonomic resolution, but this had only limited effects on patterns of inferred DWT, at least to detect major dry/wet shifts. Higher-resolution taxonomy may however still be useful to detect more subtle changes, or for reconstructed shifts to be significant. -
The Phanerozoic Diversification of Silica-Cycling Testate Amoebae and Its Possible Links to Changes in Terrestrial Ecosystems
The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems Daniel J.G. Lahr1, Tanja Bosak2, Enrique Lara3 and Edward A.D. Mitchell3,4 1 Department of Zoology, Institute of Biosciences, University of Sao˜ Paulo, Rua do Matao,˜ Sao˜ Paulo, Brazil 2 Department of Earth, Atmospheric and Planetary Sciences, Massachussetts Institute of Technology, Cambridge, MA, USA 3 Laboratory of Soil Biology, University of Neuchatel, Neuchatel, Switzerland 4 Jardin Botanique de Neuchatel,ˆ Neuchatel, Switzerland ABSTRACT The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as Submitted 29 May 2015 old as 50 million years, but older fossils are scarce and diYcult to interpret. Poor Accepted 19 August 2015 taxon sampling of euglyphids has also prevented the development of molecular Published 8 September 2015 clocks. -
Molecular Phylogeny and Taxonomy of Testate Amoebae (Protist) and Host-Symbiont Evolutionary Relationships Within Mixotrophic Taxa
Molecular Phylogeny and Taxonomy of Testate Amoebae (Protist) and Host-Symbiont Evolutionary Relationships within Mixotrophic Taxa Thesis Submitted to Faculty of Science, University of Neuchâtel in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Science By Fatma Gomaa Members of the jury: Prof. Edward Mitchell: University of Neuchâtel, Thesis director, Switzerland Dr. Enrique Lara: University of Neuchâtel, Thesis co-director, Switzerland Dr. Christophe Praz: University of Neuchâtel, Switzerland Prof. Jan Pawlowski: University of Geneva, Switzerland Dr. Alexander Kudryavtsev: University of St-Petersburg, Russia Prof. Milcho Todorov: Bulgarian Academy of Sciences, Bulgaria Accepted in 24/08/2012 University of Neuchâtel 2013 • Faculté des sciences Secrétariat-décanat de Faculté U111e Rue Emile-Argand 11 2000 Neuchatel - Suisse UNIVERSITÉ DE Tél: + 41 (0)32 718 2100 NEUCHÂTEL E-mail: [email protected] IMPRIMATUR POUR TH ESE DE DOCTORAT La Faculté des sciences de l'Université de Neuchâtel autorise l'impression de la présente thèse soutenue par Madame Fatma Fathy Sayed GOMAA Titre : Molecular Phylogeny and Taxonomy of Testate Amoebae (Protist) and Host-Symbiont Evolutionary Relationships Within Mixotrophic Taxa sur le rapport des membres du jury: • Prof. Edward Mitchell, directeur de thèse, UniNe • Dr Enrique Lara, UniNe • Dr Christophe Praz, UniNe • Prof. Jan Pawlowski, Université de Genève • Dr Alexander Kudryavtsev, St. Petersburg State University, Russie • Prof. Milcho Todorov, Académie des Sciences de Bulgarie Neuchâtel, le 30 avril'2013 Le Doyen, Prof. P. Kropf 1 Imprimatur pour thèse de doctorat www.unine.ch/sclences “Travel through the earth and find how I originated creation” (El Ainkabout, 20 Quran 610CE) Contents Abstract 8 Résumé 11 1 Introduction 14 1. -
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Brazilian Journal of Biology https://doi.org/10.1590/1519-6984.222607 ISSN 1519-6984 (Print) Original Article ISSN 1678-4375 (Online) Structure and dynamics of the protoplankton community in an environmentally protected urban stream M. A. M. Lipperta , F. M. Lansac-Tôhab , B. R. Meirab , L. F. M. Velhob,c and F. A. Lansac-Tohab* aPrograma de Pós-graduação em Biologia Comparada, Universidade Estadual de Maringá – UEM, Av. Colombo, 5790, CEP 87020-900, Maringá, PR, Brasil bNúcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura – NUPELIA, Programa de Pós-graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá – UEM, Av. Colombo, 5790, CEP 87020-900, Maringá, PR, Brasil cInstituto Cesumar de Ciência, Tecnologia e Inovação – ICETI, Centro Universitário Cesumar – Unicesumar, Av. Guedner, 1610, CEP 87050-900, Maringá, PR, Brasil *e-mail: [email protected] Received: April 12, 2019 – Accepted: July 31, 2019 – Distributed: November 30, 2020 (With 10 figures) Abstract We aimed to investigate spatial and temporal scales, abundance, and factors that structure the communities of protozoans in a tropical urban stream. Methods: Samples of water for analysis of biological communities (testate amoebae, ciliates and bacteria) and limnological variables were taken in the Mandacaru stream located in the Conservation Unit of Parque do Cinquentenário, in the city of Maringá, Paraná State, Brazil, in two hydrological periods (dry and rainy). We calculated the Water Quality Index (WQI) composed by nine parameters of water quality (dissolved oxygen, thermotolerant coliforms, pH, BOD, water temperature, total nitrogen, total phosphorous, turbidity, and total solids), Trophic State Index (TSI) for phosphorous and we used a Redundancy Analysis (RDA) to verify the influence of environmental variables in the protozoan community.