Revisiting the Phylogenetic Position of Caullerya Mesnili (Ichthyosporea), a Common
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A Unicellular Relative of Animals Generates a Layer of Polarized Cells
RESEARCH ARTICLE A unicellular relative of animals generates a layer of polarized cells by actomyosin- dependent cellularization Omaya Dudin1†*, Andrej Ondracka1†, Xavier Grau-Bove´ 1,2, Arthur AB Haraldsen3, Atsushi Toyoda4, Hiroshi Suga5, Jon Bra˚ te3, In˜ aki Ruiz-Trillo1,6,7* 1Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; 2Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom; 3Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway; 4Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan; 5Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan; 6Departament de Gene`tica, Microbiologia i Estadı´stica, Universitat de Barcelona, Barcelona, Spain; 7ICREA, Barcelona, Spain Abstract In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an *For correspondence: actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a [email protected] (OD); polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly [email protected] (IR-T) regulated transcriptional activation of genes involved in cell adhesion. -
Group of Microorganisms at the Animal-Fungal Boundary
16 Aug 2002 13:56 AR AR168-MI56-14.tex AR168-MI56-14.SGM LaTeX2e(2002/01/18) P1: GJC 10.1146/annurev.micro.56.012302.160950 Annu. Rev. Microbiol. 2002. 56:315–44 doi: 10.1146/annurev.micro.56.012302.160950 First published online as a Review in Advance on May 7, 2002 THE CLASS MESOMYCETOZOEA: A Heterogeneous Group of Microorganisms at the Animal-Fungal Boundary Leonel Mendoza,1 John W. Taylor,2 and Libero Ajello3 1Medical Technology Program, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing Michigan, 48824-1030; e-mail: [email protected] 2Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102; e-mail: [email protected] 3Centers for Disease Control and Prevention, Mycotic Diseases Branch, Atlanta Georgia 30333; e-mail: [email protected] Key Words Protista, Protozoa, Neomonada, DRIP, Ichthyosporea ■ Abstract When the enigmatic fish pathogen, the rosette agent, was first found to be closely related to the choanoflagellates, no one anticipated finding a new group of organisms. Subsequently, a new group of microorganisms at the boundary between an- imals and fungi was reported. Several microbes with similar phylogenetic backgrounds were soon added to the group. Interestingly, these microbes had been considered to be fungi or protists. This novel phylogenetic group has been referred to as the DRIP clade (an acronym of the original members: Dermocystidium, rosette agent, Ichthyophonus, and Psorospermium), as the class Ichthyosporea, and more recently as the class Mesomycetozoea. Two orders have been described in the mesomycetozoeans: the Der- mocystida and the Ichthyophonida. So far, all members in the order Dermocystida have been pathogens either of fish (Dermocystidium spp. -
Diversity and Distribution of Unicellular Opisthokonts Along the European Coast Analyzed Using High-Throughput Sequencing
Diversity and distribution of unicellular opisthokonts along the European coast analyzed using high-throughput sequencing Javier del Campo1,2,*, Diego Mallo3, Ramon Massana4, Colomban de Vargas5,6, Thomas A. Richards7,8, and Iñaki Ruiz-Trillo1,9,10 1Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain. 3Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Galicia, Spain 4Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain 5CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France 6UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France 7Geoffrey Pope Building, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK 8Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity 9Departament de Genètica, Universitat de Barcelona, Barcelona, Catalonia, Spain 10Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain Summary The opisthokonts are one of the major super-groups of eukaryotes. It comprises two major clades: 1) the Metazoa and their unicellular relatives and 2) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non-metazoan and non-fungal opisthokonts. Here we begin to address this gap by analyzing high throughput 18S rDNA and 18S rRNA sequencing data from different European coastal sites, sampled at different size fractions and depths. In particular, we analyze the diversity and abundance of choanoflagellates, filastereans, ichthyosporeans, nucleariids, corallochytreans and their related lineages. Our results show the great diversity of choanoflagellates in coastal waters as well as a relevant role of the ichthyosporeans and the uncultured marine opisthokonts (MAOP). -
A Higher-Level Phylogenetic Classification of the Fungi
mycological research 111 (2007) 509–547 available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/mycres A higher-level phylogenetic classification of the Fungi David S. HIBBETTa,*, Manfred BINDERa, Joseph F. BISCHOFFb, Meredith BLACKWELLc, Paul F. CANNONd, Ove E. ERIKSSONe, Sabine HUHNDORFf, Timothy JAMESg, Paul M. KIRKd, Robert LU¨ CKINGf, H. THORSTEN LUMBSCHf, Franc¸ois LUTZONIg, P. Brandon MATHENYa, David J. MCLAUGHLINh, Martha J. POWELLi, Scott REDHEAD j, Conrad L. SCHOCHk, Joseph W. SPATAFORAk, Joost A. STALPERSl, Rytas VILGALYSg, M. Catherine AIMEm, Andre´ APTROOTn, Robert BAUERo, Dominik BEGEROWp, Gerald L. BENNYq, Lisa A. CASTLEBURYm, Pedro W. CROUSl, Yu-Cheng DAIr, Walter GAMSl, David M. GEISERs, Gareth W. GRIFFITHt,Ce´cile GUEIDANg, David L. HAWKSWORTHu, Geir HESTMARKv, Kentaro HOSAKAw, Richard A. HUMBERx, Kevin D. HYDEy, Joseph E. IRONSIDEt, Urmas KO˜ LJALGz, Cletus P. KURTZMANaa, Karl-Henrik LARSSONab, Robert LICHTWARDTac, Joyce LONGCOREad, Jolanta MIA˛ DLIKOWSKAg, Andrew MILLERae, Jean-Marc MONCALVOaf, Sharon MOZLEY-STANDRIDGEag, Franz OBERWINKLERo, Erast PARMASTOah, Vale´rie REEBg, Jack D. ROGERSai, Claude ROUXaj, Leif RYVARDENak, Jose´ Paulo SAMPAIOal, Arthur SCHU¨ ßLERam, Junta SUGIYAMAan, R. Greg THORNao, Leif TIBELLap, Wendy A. UNTEREINERaq, Christopher WALKERar, Zheng WANGa, Alex WEIRas, Michael WEISSo, Merlin M. WHITEat, Katarina WINKAe, Yi-Jian YAOau, Ning ZHANGav aBiology Department, Clark University, Worcester, MA 01610, USA bNational Library of Medicine, National Center for Biotechnology Information, -
Survey of Mesomycetozoans in Millipedes and Terrestrial Isopods of Southeastern New
Survey of Mesomycetozoans in Millipedes and Terrestrial Isopods of Southeastern New England By: Stephanie Langlois A Study Presented to the Faculty of Wheaton College in Partial Fulfillment of the Requirements for Graduation with Departmental Honors in Biology Norton, Massachusetts 5/20/17 2 Acknowledgements Thank you, First and foremost, to Professor Dyer for your support, encouragement, and enthusiasm throughout the duration of this project. This project was a huge learning curve for the both of us, and I am happy I had the privilege to work with you. Thank you for believing I could do this. To Zephorene Stickney-Helmreich for your advice and encouragement. You helped me complete this project in an organized and timely manner. Thank you for keeping me level-headed. To Professor Cato and Professor Celada for being on my thesis committee. Your advice and edits were greatly appreciated. I hope you enjoyed learning all about trichomycetes. To Professor Post, for your friendliness and always being super quick to get things done. To Jillian Amaral for her help finding such obscure sources. To Nathan Kelly, for digging through woodpiles with me in the dead of winter and rescuing me from the spiders. Someday, I may forgive you for falling asleep several times while reading my thesis introduction. To Laura Wajda, for being my one friend with a passion for science. It means the world to me that you think this stuff is cool. You are so smart, talented, and hardworking, and you inspire me every day. To all of my friends and family, who have spent way too much time listening to me talk about obscure gut fungi and protists. -
Controlled Sampling of Ribosomally Active Protistan Diversity in Sediment-Surface Layers Identifies Putative Players in the Marine Carbon Sink
The ISME Journal (2020) 14:984–998 https://doi.org/10.1038/s41396-019-0581-y ARTICLE Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink 1,2 1 1 3 3 Raquel Rodríguez-Martínez ● Guy Leonard ● David S. Milner ● Sebastian Sudek ● Mike Conway ● 1 1 4,5 6 7 Karen Moore ● Theresa Hudson ● Frédéric Mahé ● Patrick J. Keeling ● Alyson E. Santoro ● 3,8 1,9 Alexandra Z. Worden ● Thomas A. Richards Received: 6 October 2019 / Revised: 4 December 2019 / Accepted: 17 December 2019 / Published online: 9 January 2020 © The Author(s) 2020. This article is published with open access Abstract Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the ‘ribosomally active’ eukaryotic diversity present in sediments close to the water/sediment interface. We 1234567890();,: 1234567890();,: demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms. -
Sequencing Abstracts Msa Annual Meeting Berkeley, California 7-11 August 2016
M S A 2 0 1 6 SEQUENCING ABSTRACTS MSA ANNUAL MEETING BERKELEY, CALIFORNIA 7-11 AUGUST 2016 MSA Special Addresses Presidential Address Kerry O’Donnell MSA President 2015–2016 Who do you love? Karling Lecture Arturo Casadevall Johns Hopkins Bloomberg School of Public Health Thoughts on virulence, melanin and the rise of mammals Workshops Nomenclature UNITE Student Workshop on Professional Development Abstracts for Symposia, Contributed formats for downloading and using locally or in a Talks, and Poster Sessions arranged by range of applications (e.g. QIIME, Mothur, SCATA). 4. Analysis tools - UNITE provides variety of analysis last name of primary author. Presenting tools including, for example, massBLASTer for author in *bold. blasting hundreds of sequences in one batch, ITSx for detecting and extracting ITS1 and ITS2 regions of ITS 1. UNITE - Unified system for the DNA based sequences from environmental communities, or fungal species linked to the classification ATOSH for assigning your unknown sequences to *Abarenkov, Kessy (1), Kõljalg, Urmas (1,2), SHs. 5. Custom search functions and unique views to Nilsson, R. Henrik (3), Taylor, Andy F. S. (4), fungal barcode sequences - these include extended Larsson, Karl-Hnerik (5), UNITE Community (6) search filters (e.g. source, locality, habitat, traits) for 1.Natural History Museum, University of Tartu, sequences and SHs, interactive maps and graphs, and Vanemuise 46, Tartu 51014; 2.Institute of Ecology views to the largest unidentified sequence clusters and Earth Sciences, University of Tartu, Lai 40, Tartu formed by sequences from multiple independent 51005, Estonia; 3.Department of Biological and ecological studies, and for which no metadata Environmental Sciences, University of Gothenburg, currently exists. -
Throughput Environmental Sequencing Reveals High Diversity of Litter and Moss Associated Protist Communities Along a Gradient of Drainage and Tree Productivity
Environmental Microbiology (2018) 20(3), 1185–1203 doi:10.1111/1462-2920.14061 High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity Thierry J. Heger ,1,2,3* Ian J. W. Giesbrecht,3,4 alpha diversity from the blanket bog ecosystem to Julia Gustavsen ,5 Javier del Campo,2,3 the zonal forest ecosystem. Among all investigated Colleen T. E. Kellogg,3,7 Kira M. Hoffman,3,6 environmental variables, calcium content was the Ken Lertzman,3,4 William W. Mohn3,7 and most strongly associated with the community Patrick J. Keeling2,3 composition of protists, but substrate composition, 1Soil Science Group, CHANGINS, University of Applied plant cover and other edaphic factors were also Sciences and Arts Western Switzerland, Delemont, significantly correlated with these communities. Switzerland. Furthermore, a detailed phylogenetic analysis of uni- 2Botany Department, University of British Columbia, cellular opisthokonts identified OTUs covering most Vancouver, BC, Canada. lineages, including novel OTUs branching with Disci- 3Hakai Institute, Heriot Bay, BC, Canada. cristoidea, the sister group of Fungi, and with 4School of Resource and Environmental Management, Filasterea, one of the closest unicellular relatives to Simon Fraser University, Burnaby, BC, Canada. animals. Altogether, this study provides unprece- 5Department of Earth, Ocean and Atmospheric dented insight into the community composition of Sciences, University of British Columbia, Vancouver, moss- and litter-associated protists. BC, Canada. 6School of Environmental Studies, University of Victoria, Victoria, BC, Canada. Introduction 7Department of Microbiology and Immunology, Life Mosses and litter are major sources of organic matter in Sciences Institute, University of British Columbia, peatland and forest soils. -
Capsaspora Owczarzaki
The origin of metazoan multicellularity: what comparative genomics is telling us and how we could go forward Iñaki Ruiz-Trillo, Institute of Evolutionary Biology & Universitat de Barcelona & Kitp Cooperation And The Evolution Of Multicellularity, Kitp, 21 February 2013 1 Institut de Biologia Evolutiva (UPF-CSIC) 2 3 3 3 3 last common unicellular ancestor 4 last common unicellular ancestor 4 1. A phylogenetic framework 5 who are the closest living relatives of animals? Fungi Choanoflagellata Metazoa 6 who are the closest living relatives of animals? Fungi Choanoflagellata Metazoa Capsaspora Ministeria Nuclearia Ichthyosporea ? Corallochytrium 6 A new phylogenetic framework Fungi Choanoflagellata Metazoa Holozoa Ruiz-Trillo et al. 2008 Mol Biol Evol 25:664-672. Shalchian-Tabrizi et al. 2008 PLoS ONE 3:e2098. Brown et al. 2009 Mol Biol Evol 26:2699-2709. Torruella et al. 2012 Mol Biol Evol 29, 531–544. 7 A new phylogenetic framework Fungi Choanoflagellata Metazoa Nucleariidae Fonticula alba Holozoa Ruiz-Trillo et al. 2008 Mol Biol Evol 25:664-672. Shalchian-Tabrizi et al. 2008 PLoS ONE 3:e2098. Brown et al. 2009 Mol Biol Evol 26:2699-2709. Torruella et al. 2012 Mol Biol Evol 29, 531–544. 7 A new phylogenetic framework Fungi Choanoflagellata Metazoa Nucleariidae Filasterea Capsaspora Ministeria Fonticula alba Holozoa Ruiz-Trillo et al. 2008 Mol Biol Evol 25:664-672. Shalchian-Tabrizi et al. 2008 PLoS ONE 3:e2098. Brown et al. 2009 Mol Biol Evol 26:2699-2709. Torruella et al. 2012 Mol Biol Evol 29, 531–544. 7 A new phylogenetic framework Fungi Choanoflagellata Metazoa Nucleariidae Filasterea Capsaspora Ministeria Fonticula alba Ichthyosporea Holozoa Ruiz-Trillo et al. -
David López Escardó
Unveiling new molecular Opisthokonta diversity: A perspective from evolutionary genomics David López Escardó TESI DOCTORAL UPF / ANY 2017 DIRECTOR DE LA TESI Dr. Iñaki Ruiz Trillo DEPARTAMENT DE CIÈNCIES EXPERIMENTALS I DE LA SALUT ii Acknowledgements: Aquesta tesi va començar el dia que, mirant grups on poguer fer el projecte de màster, vaig trobar la web d'un grup de recerca que treballaven amb uns microorganismes, desconeguts per mi en aquell moment, per entendre l'origen dels animals. Tres o quatre assignatures de micro a la carrera, i cap d'elles tractava a fons amb protistes i menys els parents unicel·lulars dels animals. En fi, "Bitxos" raros, origen dels animals... em va semblar interessant. Així que em vaig presentar al despatx del Iñaki vestit amb el tratge de comercial de Tecnocasa, per veure si podia fer les pràctiques del Màster amb ells. El primer que vaig volguer remarcar durant l'entrevista és que no pretenia anar amb tratge a la feina, que no es pensés que jo de normal vaig tan seriós... Sigui com sigui, després de rumiar-s'ho, em va dir que endavant i em va emplaçar a fer una posterior entrevista amb els diferents membres del lab perquè tries un projecte de màster. Per tant, aquí el meu primer agraïment i molt gran, al Iñaki, per permetre'm, no només fer el màster, sinó també permetre'm fer aquesta tesis al seu laboratori. També per la llibertat alhora de triar projectes i per donar-li al MCG un ambient cordial on hi dóna gust treballar. Gràcies, doncs, per deixar-me entrar al món científic per la porta de la protistologia, la genòmica i l'evolució, que de ben segur m'acompanyaran sempre. -
The Taxonomic Status of Lacazia Loboi and Rhinosporidium Seeberi Has Been Finally Resolved with the Use of Molecular Tools Leonel Mendoza1, Libero Ajello2 & John W
Forum micológico Rev Iberoam Micol 2001; 18: 95-98 95 The taxonomic status of Lacazia loboi and Rhinosporidium seeberi has been finally resolved with the use of molecular tools Leonel Mendoza1, Libero Ajello2 & John W. Taylor3 1Medical Technology Program, Department of Microbiology, Michigan State University, East Lansing MI, 2School of Medicine, Emory University, Atlanta GA, and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA The etiologic agents of lobomycosis and rhinospo- fungal pathogen Paracoccidioides brasiliensis. More than ridiosis, Lacazia loboi and Rhinosporidium seeberi res- 70 years later, however, his hypothesis was still awaiting pectively, have long been confined in a taxonomic limbo. verification. Although their invasive cells in the tissues of infected To resolve this taxonomic standoff, a team of humans and other animals are abundant and readily detec- scientists from Sri Lanka, where R. seeberi infections are table histologically, they have been intractable to isolation common, and Brazil, where lobomycosis is endemic, and and culture. Thus, it has not been possible to objectively the USA was assembled to study R. seeberi’s and place them in any of the kingdoms in which all living enti- L. loboi’s phylogenetic links with other eukaryotic orga- ties are classified. In addition to their uncultivatable sta- nisms. The strategy was to collect fresh tissue samples tus, L. loboi and R. seeberi shared in common from cases of lobomycosis and rhinosporidiosis, isolate morphological features that resemble those of certain pat- genomic DNAs and then amplify their 18S small subunit hogenic fungi and protozoans: viz. essentially similar (SSU) rDNA by using standard primers and PCR techno- inflammatory host reactions, unresponsiveness to antifun- logy. -
Eccrinales (Trichomycetes) Are Not Fungi, but a Clade of Protists at the Early Divergence of Animals and Fungi
Molecular Phylogenetics and Evolution 35 (2005) 21–34 www.elsevier.com/locate/ympev Eccrinales (Trichomycetes) are not fungi, but a clade of protists at the early divergence of animals and fungi Matías J. Cafaro¤ Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA Received 22 July 2003; revised 3 September 2004 Available online 25 January 2005 Abstract The morphologically diverse orders Eccrinales and Amoebidiales have been considered members of the fungal class Trichomyce- tes (Zygomycota) for the last 50 years. These organisms either inhabit the gut or are ectocommensals on the exoskeleton of a wide range of arthropods—Crustacea, Insecta, and Diplopoda—in varied habitats. The taxonomy of both orders is based on a few micro- morphological characters. One species, Amoebidium parasiticum, has been axenically cultured and this has permitted several bio- chemical and phylogenetic analyses. As a consequence, the order Amoebidiales has been removed from the Trichomycetes and placed in the class Mesomycetozoea. An aYnity between Eccrinales and Amoebidiales was Wrst suggested when the class Trichomy- cetes was erected by Duboscq et al. [Arch. Zool. Exp. Gen. 86 (1948) 29]. Subsequently, molecular markers have been developed to study the relationship of these orders to other groups. Ribosomal gene (18S and 28S) sequence analyses generated by this study do not support a close association of these orders to the Trichomycetes or to other fungi. Rather, Eccrinales share a common ancestry with the Amoebidiales and belong to the protist class Mesomycetozoea, placed at the animal–fungi boundary. 2004 Elsevier Inc. All rights reserved. Keywords: Mesomycetozoea; DRIPs; Bayesian analysis; Ichthyosporea; Trichomycetes 1.