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  • 1.
    Adl, Sina M.
    et al.
    Univ Saskatchewan, Dept Soil Sci, Coll Agr & Bioresources, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
    Bass, David
    Nat Hist Museum, Dept Life Sci, Cromwell Rd, London SW7 5BD, England;CEFAS, Barrack Rd, Weymouth DT4 8UB, Dorset, England.
    Lane, Christopher E.
    Univ Rhode Isl, Dept Biol Sci, Kingston, RI 02881 USA.
    Lukes, Julius
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic;Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic.
    Schoch, Conrad L.
    Natl Inst Biotechnol Informat, Natl Lib Med, NIH, Bethesda, MD 20892 USA.
    Smirnov, Alexey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Agatha, Sabine
    Univ Salzburg, Dept Biosci, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Berney, Cedric
    CNRS, UMR 7144 AD2M, Grp Evolut Protistes & Ecosyst Pelag, Stn Biol Roscoff, Pl Georges Teissier, F-29680 Roscoff, France.
    Brown, Matthew W.
    Mississippi State Univ, Dept Biol Sci, Starkville, MS 39762 USA;Mississippi State Univ, Inst Genom Biocomp & Biotechnol, Starkville, MS 39762 USA.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Cepicka, Ivan
    Charles Univ Prague, Dept Zool, Fac Sci, Vinicna 7, CR-12844 Prague, Czech Republic.
    Chistyakova, Lyudmila
    St Petersburg State Univ, Core Facil Ctr Culture Collect Microorganisms, St Petersburg 198504, Russia.
    del Campo, Javier
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Dunthorn, Micah
    Univ Kaiserslautern, Dept Ecol, Erwin Schroedinger St, D-67663 Kaiserslautern, Germany;Univ Duisburg Essen, Dept Eukaryot Microbiol, Univ Str 5, D-45141 Essen, Germany.
    Edvardsen, Bente
    Univ Oslo, Dept Biosci, POB 1066 Blindern, N-0316 Oslo, Norway.
    Eglit, Yana
    Dalhousie Univ, Dept Biol, Halifax B3H 4R2, NS, Canada.
    Guillou, Laure
    Univ Paris 06, Sorbonne Univ, Paris 6, CNRS,UMR 7144 AD2M,Stn Biol Roscoff, Pl Georges Teissier,,CS90074, F-29688 Roscoff, France.
    Hampl, Vladimir
    Charles Univ Prague, Dept Parasitol, Fac Sci, BIOCEV, Prumyslov 595, Vestec 25242, Czech Republic.
    Heiss, Aaron A.
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Hoppenrath, Mona
    DZMB German Ctr Marine Biodivers Res, D-26382 Wilhelmshaven, Germany.
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Karnkowska, Anna
    Univ Warsaw, Dept Mol Phylogenet & Evolut, PL-02089 Warsaw, Poland.
    Karpov, Sergey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Kim, Eunsoo
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Kolisko, Martin
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic.
    Kudryavtsev, Alexander
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Lahr, Daniel J. G.
    Univ Sao Paulo, Dept Zool, Inst Biosci, Matao Travessa 14 Cidade Univ, BR-05508090 Sao Paulo, SP, Brazil.
    Lara, Enrique
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;CSIC, Real Jardim Bot,Plaza Murillo 2, E-28014 Madrid, Spain.
    Le Gall, Line
    Sorbonne Univ, Museum Natl Hist Nat, Inst Systemat Evolut Biodiversit, 57 Rue Cuvier,CP 39, F-75005 Paris, France.
    Lynn, Denis H.
    Univ Guelph, Dept Integrat Biol, Summerlee Sci Complex, Guelph, ON N1G 2W1, Canada;Univ British Columbia, Dept Zool, 4200-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.
    Mann, David G.
    Royal Bot Garden, Edinburgh EH3 5LR, Midlothian, Scotland;Inst Agrifood Res & Technol, C Poble Nou Km 5-5, E-43540 San Carlos de la Rapita, Spain.
    Massana, Ramon
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Mitchell, Edward A. D.
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;Jardin Bot Neuchatel,Chemin Perthuis du Salut 58, CH-2000 Neuchatel, Switzerland.
    Morrow, Christine
    Natl Museums Northern Ireland, Dept Nat Sci, 153 Bangor Rd, Holywood BT18 0EU, England.
    Park, Jong Soo
    Kyungpook Natl Univ, Sch Earth Syst Sci, Dept Oceanog, Daegu, South Korea;Kyungpook Natl Univ, Sch Earth Syst Sci, Kyungpook Inst Oceanog, Daegu, South Korea.
    Pawlowski, Jan W.
    Univ Geneva, Dept Genet & Evolut, CH-1211 Geneva 4, Switzerland.
    Powell, Martha J.
    Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA.
    Richter, Daniel J.
    Univ Pompeu Fabra, CSIC, Inst Biol Evolut, Passeig Maritim Barceloneta 37-49, Barcelona 08003, Spain.
    Rueckert, Sonja
    Edinburgh Napier Univ, Sch Appl Sci, Edinburgh EH11 4BN, Midlothian, Scotland.
    Shadwick, Lora
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Shimano, Satoshi
    Hosei Univ, Sci Res Ctr, Chiyoda Ku, 2-17-1 Fujimi, Tokyo, Japan.
    Spiegel, Frederick W.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Torruella, Guifre
    Univ Paris XI, Lab Evolut & Systemat, F-91405 Orsay, France.
    Youssef, Noha
    Oklahoma State Univ, Dept Microbiol & Mol Genet, Stillwater, OK 74074 USA.
    Zlatogursky, Vasily V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Zhang, Qianqian
    Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
    Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes2019In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 66, no 1, p. 4-119Article in journal (Refereed)
    Abstract [en]

    This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

  • 2. Carr, Martin
    et al.
    Leadbeater, Barry S C
    Baldauf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Conserved Meiotic Genes Point to Sex in the Choanoflagellates2010In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 57, no 1, p. 56-62Article in journal (Refereed)
    Abstract [en]

    The choanoflagellates are a widespread group of heterotrophic aquatic nanoflagellates, which have recently been confirmed as the sister-group to Metazoa. Asexual reproduction is the only mode of cell division that has been observed within the group; at present the range of reproductive modes, as well as the ploidy level, within choanoflagellates are unknown. The recent discovery of long terminal repeat retrotransposons within the genome of Monosiga brevicollis suggests that this species also has sexual stages in its life cycle because asexual organisms cannot tolerate retrotransposons due to the rapid accumulation of deleterious mutations caused by their transposition. We screened the M. brevicollis genome for known eukaryotic meiotic genes, using a recently established "meiosis detection toolkit" of 19 genes. Eighteen of these genes were identified, none of which appears to be a pseudogene. Four of the genes were also identified in expressed sequence tag data from the distantly related Monosiga ovata. The presence of these meiosis-specific genes provides evidence for meiosis, and by implication sex, within this important group of protists.

  • 3. Chang, Yue
    et al.
    Liu, Guanglong
    Guo, Lina
    Liu, Hongbo
    Yuan, Dongxia
    Xiong, Jie
    Ning, Yingzhi
    Fu, Chengjie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Miao, Wei
    Cd-Metallothioneins in Three Additional Tetrahymena Species: Intragenic Repeat Patterns and Induction by Metal Ions2014In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 61, no 4, p. 333-342Article in journal (Refereed)
    Abstract [en]

    Ciliate metallothioneins (MTs) possess many unique features compared to the "classic" MTs in other organisms, but they have only been studied in a small number of species. In this study, we investigated cDNAs encoding subfamily 7a metallothioneins (CdMTs) in three Tetrahymena species (T. hegewischi, T. malaccensis, and T. mobilis). Four CdMT genes (ThegMT1, ThegMT2, TmalMT1, and TmobMT1) were cloned and characterized. They share high sequence similarity to previously identified subfamily 7a MT members. Tetrahymena CdMTs exhibit a remarkably regular intragenic repeat homology. The CdMT sequences were divided into two main types of modules, which had been previously described, and which we name "A" and "B". ThegMT2 was identified as the first MT isoform solely composed of module "B". A phylogenetic analysis of individual modules of every characterized Tetrahymena CdMT rigorously documents the conclusion that modules are important units of CdMT evolution, which have undergone frequent and rapid gain/loss and shuffling. The transcriptional activity of the four newly identified genes was measured under different heavy metal exposure (Cd, Cu, Zn, Pb) using real-time quantitative PCR. The results showed that these genes were differentially induced after short (1 h) or long (24 h) metal exposure. The evolutionary diversity of Tetrahymena CdMTs is further discussed with regard to their induction by metal ions.

  • 4.
    Gran-Stadniczeñko, Sandra
    et al.
    Univ Oslo, Dept Biosci, POB 1066 Blindern, N-0316 Oslo, Norway.
    Supraha, Luka
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Egge, Elianne D.
    Univ Oslo, Dept Biosci, POB 1066 Blindern, N-0316 Oslo, Norway.
    Edvardsen, Bente
    Univ Oslo, Dept Biosci, POB 1066 Blindern, N-0316 Oslo, Norway.
    Haptophyte diversity and vertical distribution explored by 18S and 28S ribosomal RNA gene metabarcoding and scanning electron microscopy2017In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 64, no 4, p. 514-532Article in journal (Refereed)
    Abstract [en]

    Haptophyta encompasses more than 300 species of mostly marine pico- and nanoplanktonic flagellates. Our aims were to investigate the Oslofjorden haptophyte diversity and vertical distribution by metabarcoding, and to improve the approach to study haptophyte community composition, richness and proportional abundance by comparing two rRNA markers and scanning electron microscopy (SEM). Samples were collected in August 2013 at the Outer Oslofjorden, Norway. Total RNA/cDNA was amplified by haptophyte-specific primers targeting the V4 region of the 18S, and the D1-D2 region of the 28S rRNA. Taxonomy was assigned using curated haptophyte reference databases and phylogenetic analyses. Both marker genes showed Chrysochromulinaceae and Prymnesiaceae to be the families with highest number of Operational Taxonomic Units (OTUs), as well as proportional abundance. The 18S rRNA data setalso contained OTUs assigned to eight supported and defined clades consisting of environmental sequences only, possibly representing novel lineages from family to class. We also recorded new species for the area. Comparing coccolithophores by SEM with metabarcoding shows a good correspondence with the 18S rRNA gene proportional abundances. Our results contribute to link morphological and molecular data and 28S to 18S rRNA gene sequences of haptophytes without cultured representatives, and to improve metabarcoding methodology.

  • 5. Leblond, Jeffrey D.
    et al.
    Dahmen, Aaron S.
    Lebret, Karen
    Lund University.
    Rengefors, Karin
    Sterols of the Green-Pigmented, Freshwater Raphidophyte, Gonyostomum semen, from Scandinavian Lakes2013In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 60, no 4, p. 399-405Article in journal (Refereed)
    Abstract [en]

    Sterols are a class of membrane-reinforcing, ringed lipids which have a long history of examination in algae as a means of deriving chemotaxonomic relationships and as potential lipidic biomarkers. The Raphidophyceae represent a class of harmful, bloom-forming, marine and freshwater algae. To date, there have been four published examinations of their sterol composition, focusing primarily on brown-pigmented, marine species within the genera, Chattonella, Fibrocapsa, and Heterosigma. Lacking in these examinations has been the species Gonyostomum semen Ehrenb., which is a green-pigmented, freshwater raphidophyte with a worldwide distribution. The goal of this study was to examine the sterol composition of this nuisance alga, determine the potential of using its sterol profile as a biomarker, and finally to determine if there is any intraspecific variability between isolates. We have examined 21 isolates of G. semen from a number of Scandinavian lakes, and all were found to produce two major sterols, 24-ethylcholesta-5,22E-dien-3-ol and 24-ethylcholest-5-en-3-ol, and 24-methylcholest-5-en-3-ol as a minor sterol; the presence of 24-ethylcholesta-5,22E-dien-3-ol differentiates G. semen from brown-pigmented, marine raphidophytes which generally lack it. The results of this study indicate that isolates of G. semen from geographically separate lakes across Finland and Scandinavia have the same sterol biosynthetic pathway, and that there is no evolutionary divergence between the isolates with regard to sterol composition. The sterols of G. semen are not considered to be useful biomarkers for this particular organism because they are commonly found in other algae and plants.

  • 6.
    Radek, Renate
    et al.
    Free Univ Berlin, Inst Biol Zool, Evolutionary Biol, Konigin Luise Str 1-3, D-14195 Berlin, Germany..
    Meuser, Katja
    Max Planck Inst Terr Microbiol, Insect Gut Microbiol & Symbiosis Grp, D-35043 Marburg, Germany..
    Strassert, Jürgen F. H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Max Planck Inst Terr Microbiol, Insect Gut Microbiol & Symbiosis Grp, D-35043 Marburg, Germany.
    Arslan, Oguzhan
    Free Univ Berlin, Inst Biol Zool, Evolutionary Biol, Konigin Luise Str 1-3, D-14195 Berlin, Germany..
    Tessmer, Anika
    Free Univ Berlin, Inst Biol Zool, Evolutionary Biol, Konigin Luise Str 1-3, D-14195 Berlin, Germany..
    Sobotnik, Jan
    Czech Univ Life Sci Prague, Fac Forestry & Wood Sci, Prague 16500 6, Suchdol, Czech Republic..
    Sillam-Dusses, David
    Univ Paris 13, Sorbonne Paris Cite, Lab Expt & Comparat Ethol EA 4443, F-93430 Villetaneuse, France.;Sorbonne Univ, Inst Ecol & Environm Sci Paris, Inst Res Dev U242, F-93143 Bondy, France..
    Nink, Ricardo A.
    Max Planck Inst Terr Microbiol, Insect Gut Microbiol & Symbiosis Grp, D-35043 Marburg, Germany..
    Brune, Andreas
    Max Planck Inst Terr Microbiol, Insect Gut Microbiol & Symbiosis Grp, D-35043 Marburg, Germany..
    Exclusive Gut Flagellates of Serritermitidae Suggest a Major Transfaunation Event in Lower Termites: Description of Heliconympha glossotermitis gen. nov spec. nov.2018In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 65, no 1, p. 77-92Article in journal (Refereed)
    Abstract [en]

    The guts of lower termites are inhabited by host-specific consortia of cellulose-digesting flagellate protists. In this first investigation of the symbionts of the family Serritermitidae, we found that Glossotermes oculatus and Serritermes serrifer each harbor similar parabasalid morphotypes: large Pseudotrichonympha-like cells, medium-sized Leptospironympha-like cells with spiraled bands of flagella, and small Hexamastix-like cells; oxymonadid flagellates were absent. Despite their morphological resemblance to Pseudotrichonympha and Leptospironympha, a SSU rRNA-based phylogenetic analysis identified the two larger, trichonymphid flagellates as deep-branching sister groups of Teranymphidae, with Leptospironympha sp. (the only spirotrichosomid with sequence data) in a moderately supported basal position. Only the Hexamastix-like flagellates are closely related to trichomonadid flagellates from Rhinotermitidae. The presence of two deep-branching lineages of trichonymphid flagellates in Serritermitidae and the absence of all taxa characteristic of the ancestral rhinotermitids underscores that the flagellate assemblages in the hindguts of lower termites were shaped not only by a progressive loss of flagellates during vertical inheritance but also by occasional transfaunation events, where flagellates were transferred horizontally between members of different termite families. In addition to the molecular phylogenetic analyses, we present a detailed morphological characterization of the new spirotrichosomid genus Heliconympha using light and electron microscopy.

  • 7.
    Strassert, Jürgen F. H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ British Columbia, Dept Bot, 3529-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.
    Hehenberger, Elisabeth
    Univ British Columbia, Dept Bot, 3529-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada;Monterey Bay Aquarium Res Inst, 7700 Sandholdt Rd, Moss Landing, CA 95039 USA.
    del Campo, Javier
    Univ British Columbia, Dept Bot, 3529-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada;CSIC, Inst Ciencies Mar, Dept Biol Marina & Oceanog, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Spain.
    Okamoto, Noriko
    Univ British Columbia, Dept Bot, 3529-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.
    Kolisko, Martin
    Univ British Columbia, Dept Bot, 3529-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada;Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic.
    Richards, Thomas A.
    Univ Exeter, Biosci, Geoffrey Pope Bldg,Stocker Rd, Exeter EX 44QD, Devon, England.
    Worden, Alexandra Z.
    Monterey Bay Aquarium Res Inst, 7700 Sandholdt Rd, Moss Landing, CA 95039 USA.
    Santoro, Alyson E.
    Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
    Keeling, Patrick J.
    Univ British Columbia, Dept Bot, 3529-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.
    Phylogeny, Evidence for a Cryptic Plastid, and Distribution of Chytriodinium Parasites (Dinophyceae) Infecting Copepods2019In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 66, no 4, p. 574-581Article in journal (Refereed)
    Abstract [en]

    Spores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium, which seemed to be attached to a copepod nauplius, to analyze the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.

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