Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSU-Rdna and Actin Genes
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Protozoan Fauna of Freshwater Habitats in South Dum Dum Municipality, North 24 Parganas, West Bengal
Journal of Academia and Industrial Research (JAIR) Volume 3, Issue 3 August 2014 139 ISSN: 2278-5213 RESEARCH ARTICLE Protozoan Fauna of Freshwater Habitats in South Dum Dum Municipality, North 24 Parganas, West Bengal J. Chitra Protozoology Section, Lower Invertebrate Division, M Block, New Alipore, Kolkata-700053, India [email protected]; +91 98315 47265 ______________________________________________________________________________________________ Abstract Wetlands of South Dum Dum Municipality were focused to reveal the status of the planktonic protozoan fauna in detail. A total of 37 different sites were selected and plankton samples from these sites were collected. About 16 sp. of protozoa were identified from few localities from the present investigation. Eight species of rhizopoda belonged to 4 genera, 4 family (Pelomyxidae, Arcellidae, Centropyxidae and Difflugiidae) and 2 order (Pelobintida and Arcellinida), Four species of flagellate belongs to 2 genera, 1 family (Euglinidae) and 1 order (Euglenida), 4 species of ciliate belongs to 4 genera, 4 family (Colepidae, Vorticellidae, Euplotidae and Paramaeciidae), 2 order (Prorodontida and Peritrichida) and 2 suborder (Sporadotrichinia and Peniculina). Among 37 localities, protozoans were observed only in L2, L3, L8, L9, L12, L13, L15, L17, L18, L19, L21, L24, L26, L32, L33, L34 and L36 localities. Protozoan diversity and their abundance were noticed higher in L12, L18, L21, L26, L33 and L34 localities. Euglena viridis, E. acus, E. oxyuris and Phacus acumininata, Pelomyxa palustris, Vorticella companula were found to be higher in abundance and distribution. Keywords: South Dum Dum municipality, planktonic protozoan, Euglena viridis, abundance, distribution. Introduction Dumdum Park, Amarpalli, Telipukur, Nager Bazar, Protozoa are highly abundant in all aquatic habitats and Patipukur and Dum Dum were selected and the plankton greatly involved in food chain (Finlay, 1997). -
Novaya Zemlya Archipelago (Russian Arctic)
This is a repository copy of First records of testate amoebae from the Novaya Zemlya archipelago (Russian Arctic). White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/127196/ Version: Accepted Version Article: Mazei, Yuri, Tsyganov, Andrey N, Chernyshov, Viktor et al. (2 more authors) (2018) First records of testate amoebae from the Novaya Zemlya archipelago (Russian Arctic). Polar Biology. ISSN 0722-4060 https://doi.org/10.1007/s00300-018-2273-x Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ 1 First records of testate amoebae from the Novaya Zemlya archipelago (Russian Arctic) 2 Yuri A. Mazei1,2, Andrey N. Tsyganov1, Viktor A. Chernyshov1, Alexander A. Ivanovsky2, Richard J. 3 Payne1,3* 4 1. Penza State University, Krasnaya str., 40, Penza 440026, Russia. 5 2. Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow 119991, Russia. 6 3. University of York, Heslington, York YO10 5DD, United Kingdom. -
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PUBLIC LIBRARY of SCIENCE | plosgenetics.org | ISSN 1553-7390 | Volume 2 | Issue 12 | DECEMBER 2006 GENETICS PUBLIC LIBRARY of SCIENCE www.plosgenetics.org Volume 2 | Issue 12 | DECEMBER 2006 Interview Review Knight in Common Armor: 1949 Unraveling the Genetics 1956 An Interview with Sir John Sulston e225 of Human Obesity e188 Jane Gitschier David M. Mutch, Karine Clément Research Articles Natural Variants of AtHKT1 1964 The Complete Genome 2039 Enhance Na+ Accumulation e210 Sequence and Comparative e206 in Two Wild Populations of Genome Analysis of the High Arabidopsis Pathogenicity Yersinia Ana Rus, Ivan Baxter, enterocolitica Strain 8081 Balasubramaniam Muthukumar, Nicholas R. Thomson, Sarah Jeff Gustin, Brett Lahner, Elena Howard, Brendan W. Wren, Yakubova, David E. Salt Matthew T. G. Holden, Lisa Crossman, Gregory L. Challis, About the Cover Drosophila SPF45: A Bifunctional 1974 Carol Churcher, Karen The jigsaw image of representatives Protein with Roles in Both e178 Mungall, Karen Brooks, Tracey of various lines of eukaryote evolution Splicing and DNA Repair Chillingworth, Theresa Feltwell, refl ects the current lack of consensus as Ahmad Sami Chaouki, Helen K. Zahra Abdellah, Heidi Hauser, to how the major branches of eukaryotes Salz Kay Jagels, Mark Maddison, fi t together. The illustrations from upper Sharon Moule, Mandy Sanders, left to bottom right are as follows: a single Mammalian Small Nucleolar 1984 Sally Whitehead, Michael A. scale from the surface of Umbellosphaera; RNAs Are Mobile Genetic e205 Quail, Gordon Dougan, Julian Amoeba, the large amoeboid organism Elements Parkhill, Michael B. Prentice used as an introduction to protists for Michel J. Weber many school children; Euglena, the iconic Low Levels of Genetic 2052 fl agellate that is often used to challenge Soft Sweeps III: The Signature 1998 Divergence across e215 ideas of plants (Euglena has chloroplasts) of Positive Selection from e186 Geographically and and animals (Euglena moves); Stentor, Recurrent Mutation Linguistically Diverse one of the larger ciliates; Cacatua, the Pleuni S. -
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. -
Protistology Mitochondrial Genomes of Amoebozoa
Protistology 13 (4), 179–191 (2019) Protistology Mitochondrial genomes of Amoebozoa Natalya Bondarenko1, Alexey Smirnov1, Elena Nassonova1,2, Anna Glotova1,2 and Anna Maria Fiore-Donno3 1 Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia 2 Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, 194064 Saint Petersburg, Russia 3 University of Cologne, Institute of Zoology, Terrestrial Ecology, 50674 Cologne, Germany | Submitted November 28, 2019 | Accepted December 10, 2019 | Summary In this mini-review, we summarize the current knowledge on mitochondrial genomes of Amoebozoa. Amoebozoa is a major, early-diverging lineage of eukaryotes, containing at least 2,400 species. At present, 32 mitochondrial genomes belonging to 18 amoebozoan species are publicly available. A dearth of information is particularly obvious for two major amoebozoan clades, Variosea and Tubulinea, with just one mitochondrial genome sequenced for each. The main focus of this review is to summarize features such as mitochondrial gene content, mitochondrial genome size variation, and presence or absence of RNA editing, showing if they are unique or shared among amoebozoan lineages. In addition, we underline the potential of mitochondrial genomes for multigene phylogenetic reconstruction in Amoebozoa, where the relationships among lineages are not fully resolved yet. With the increasing application of next-generation sequencing techniques and reliable protocols, we advocate mitochondrial -
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. -
Old Woman Creek National Estuarine Research Reserve Management Plan 2011-2016
Old Woman Creek National Estuarine Research Reserve Management Plan 2011-2016 April 1981 Revised, May 1982 2nd revision, April 1983 3rd revision, December 1999 4th revision, May 2011 Prepared for U.S. Department of Commerce Ohio Department of Natural Resources National Oceanic and Atmospheric Administration Division of Wildlife Office of Ocean and Coastal Resource Management 2045 Morse Road, Bldg. G Estuarine Reserves Division Columbus, Ohio 1305 East West Highway 43229-6693 Silver Spring, MD 20910 This management plan has been developed in accordance with NOAA regulations, including all provisions for public involvement. It is consistent with the congressional intent of Section 315 of the Coastal Zone Management Act of 1972, as amended, and the provisions of the Ohio Coastal Management Program. OWC NERR Management Plan, 2011 - 2016 Acknowledgements This management plan was prepared by the staff and Advisory Council of the Old Woman Creek National Estuarine Research Reserve (OWC NERR), in collaboration with the Ohio Department of Natural Resources-Division of Wildlife. Participants in the planning process included: Manager, Frank Lopez; Research Coordinator, Dr. David Klarer; Coastal Training Program Coordinator, Heather Elmer; Education Coordinator, Ann Keefe; Education Specialist Phoebe Van Zoest; and Office Assistant, Gloria Pasterak. Other Reserve staff including Dick Boyer and Marje Bernhardt contributed their expertise to numerous planning meetings. The Reserve is grateful for the input and recommendations provided by members of the Old Woman Creek NERR Advisory Council. The Reserve is appreciative of the review, guidance, and council of Division of Wildlife Executive Administrator Dave Scott and the mapping expertise of Keith Lott and the late Steve Barry. -
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. -
Comparative Proteomic Profiling of Newly Acquired, Virulent And
www.nature.com/scientificreports OPEN Comparative proteomic profling of newly acquired, virulent and attenuated Neoparamoeba perurans proteins associated with amoebic gill disease Kerrie Ní Dhufaigh1*, Eugene Dillon2, Natasha Botwright3, Anita Talbot1, Ian O’Connor1, Eugene MacCarthy1 & Orla Slattery4 The causative agent of amoebic gill disease, Neoparamoeba perurans is reported to lose virulence during prolonged in vitro maintenance. In this study, the impact of prolonged culture on N. perurans virulence and its proteome was investigated. Two isolates, attenuated and virulent, had their virulence assessed in an experimental trial using Atlantic salmon smolts and their bacterial community composition was evaluated by 16S rRNA Illumina MiSeq sequencing. Soluble proteins were isolated from three isolates: a newly acquired, virulent and attenuated N. perurans culture. Proteins were analysed using two-dimensional electrophoresis coupled with liquid chromatography tandem mass spectrometry (LC–MS/MS). The challenge trial using naïve smolts confrmed a loss in virulence in the attenuated N. perurans culture. A greater diversity of bacterial communities was found in the microbiome of the virulent isolate in contrast to a reduction in microbial community richness in the attenuated microbiome. A collated proteome database of N. perurans, Amoebozoa and four bacterial genera resulted in 24 proteins diferentially expressed between the three cultures. The present LC–MS/ MS results indicate protein synthesis, oxidative stress and immunomodulation are upregulated in a newly acquired N. perurans culture and future studies may exploit these protein identifcations for therapeutic purposes in infected farmed fsh. Neoparamoeba perurans is an ectoparasitic protozoan responsible for the hyperplastic gill infection of marine cultured fnfsh referred to as amoebic gill disease (AGD)1. -
Testate Lobose Amoebae)
Palaeontologia Electronica palaeo-electronica.org Mediolus, a new genus of Arcellacea (Testate Lobose Amoebae) R. Timothy Patterson ABSTRACT Mediolus, a new arcellacean genus of the Difflugidae (informally known as the- camoebia, testate rhizopods, or testate lobose amoebae) differs from other genera of the family in having distinctive tooth-like inward oriented apertural crenulations and tests generally characterized by a variable number of hollow basal spines. R. Timothy Patterson. Ottawa-Carleton Geoscience Centre and Department of Earth Sciences, Carleton University, Ottawa, Ontario, K1S 5B6, Canada. [email protected] Keywords: Arcellacea; thecamoebian; testate lobose amoebae; Quaternary, new genus INTRODUCTION of the simple unilocular test (e.g., Bonnet, 1975; Medioli et al., 1987, 1990; Beyens and Meisterfeld, Arcellacea (also informally known as the- 2001), although some researchers have placed camoebians, testate amoebae, testate rhizopods, more emphasis on test composition (e.g., Ander- or testate lobose amoebae; Patterson et al., 2012) son, 1988). The proliferation of species descrip- are a diverse group of unicellular testate rhizopods tions within the Difflugia, often based on subtle test that occur in a wide array of aquatic and terrestrial differences, has resulted in considerable taxo- environments (Patterson and Kumar, 2002) from nomic confusion (Patterson and Kumar, 2002). the tropics to poles (Dalby et al., 2000). Although Researchers have often described new species most common in Quaternary sediments fossil based on regional interest, often with little consid- arcellaceans have been found preserved in sedi- eration of the previous literature or the systematic ments deposited under freshwater and brackish value of distinguishing characters (see discussions conditions spanning the Phanerozoic and into the in Medioli and Scott, 1983; Medioli et al., 1987; Neoproterozoic (Porter and Knoll, 2000; Van Ogden and Hedley, 1980; Tolonen, 1986; Bobrov Hengstum, 2007). -
Slime Moulds
Queen’s University Biological Station Species List: Slime Molds The current list has been compiled by Richard Aaron, a naturalist and educator from Toronto, who has been running the Fabulous Fall Fungi workshop at QUBS between 2009 and 2019. Dr. Ivy Schoepf, QUBS Research Coordinator, edited the list in 2020 to include full taxonomy and information regarding species’ status using resources from The Natural Heritage Information Centre (April 2018) and The IUCN Red List of Threatened Species (February 2018); iNaturalist and GBIF. Contact Ivy to report any errors, omissions and/or new sightings. Based on the aforementioned criteria we can expect to find a total of 33 species of slime molds (kingdom: Protozoa, phylum: Mycetozoa) present at QUBS. Species are Figure 1. One of the most commonly encountered reported using their full taxonomy; common slime mold at QUBS is the Dog Vomit Slime Mold (Fuligo septica). Slime molds are unique in the way name and status, based on whether the species is that they do not have cell walls. Unlike fungi, they of global or provincial concern (see Table 1 for also phagocytose their food before they digest it. details). All species are considered QUBS Photo courtesy of Mark Conboy. residents unless otherwise stated. Table 1. Status classification reported for the amphibians of QUBS. Global status based on IUCN Red List of Threatened Species rankings. Provincial status based on Ontario Natural Heritage Information Centre SRank. Global Status Provincial Status Extinct (EX) Presumed Extirpated (SX) Extinct in the -
Biodiversity of Plasmodial Slime Moulds (Myxogastria): Measurement and Interpretation
Protistology 1 (4), 161–178 (2000) Protistology August, 2000 Biodiversity of plasmodial slime moulds (Myxogastria): measurement and interpretation Yuri K. Novozhilova, Martin Schnittlerb, InnaV. Zemlianskaiac and Konstantin A. Fefelovd a V.L.Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia, b Fairmont State College, Fairmont, West Virginia, U.S.A., c Volgograd Medical Academy, Department of Pharmacology and Botany, Volgograd, Russia, d Ural State University, Department of Botany, Yekaterinburg, Russia Summary For myxomycetes the understanding of their diversity and of their ecological function remains underdeveloped. Various problems in recording myxomycetes and analysis of their diversity are discussed by the examples taken from tundra, boreal, and arid areas of Russia and Kazakhstan. Recent advances in inventory of some regions of these areas are summarised. A rapid technique of moist chamber cultures can be used to obtain quantitative estimates of myxomycete species diversity and species abundance. Substrate sampling and species isolation by the moist chamber technique are indispensable for myxomycete inventory, measurement of species richness, and species abundance. General principles for the analysis of myxomycete diversity are discussed. Key words: slime moulds, Mycetozoa, Myxomycetes, biodiversity, ecology, distribu- tion, habitats Introduction decay (Madelin, 1984). The life cycle of myxomycetes includes two trophic stages: uninucleate myxoflagellates General patterns of community structure of terrestrial or amoebae, and a multi-nucleate plasmodium (Fig. 1). macro-organisms (plants, animals, and macrofungi) are The entire plasmodium turns almost all into fruit bodies, well known. Some mathematics methods are used for their called sporocarps (sporangia, aethalia, pseudoaethalia, or studying, from which the most popular are the quantita- plasmodiocarps).