DOCSLIB.ORG

Interactions Between Marine Picoeukaryotes and Their Viruses One Cell at a Time

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Interactions Between Marine Picoeukaryotes and Their Viruses One Cell at a Time Interactions between marine picoeukaryotes and their viruses one cell at a time Interacciones entre picoeucariotas marinos y sus virus célula a célula Yaiza M. Castillo de la Peña Aquesta tesi doctoral està subjecta a la llicència Reconeixement 4.0. Espanya de Creative Commons . Esta tesis doctoral está sujeta a la licencia Reconocimiento 4.0. España de Creative Commons . This doctoral thesis is licensed under the Creative Commons Attribution 4.0. Spain License . Interactions between marine picoeukaryotes and their viruses one cell at a time (Interacciones entre picoeucariotas marinos y sus virus célula a célula) Yaiza M. Castillo de la Peña Tesis doctoral presentada por Dª Yaiza M. Castillo de la Peña para obtener el grado de Doctora por la Universitat de Barcelona y el Institut de Ciències del Mar, programa de doctorado en Biotecnología, Facultat de Farmàcia i Ciències de l’Alimentació . Directoras: Dra. Mª Dolors Vaqué Vidal y Dra. Marta Sebastián Caumel Tutora: Dra. Josefa Badía Palacín Universitat de Barcelona (UB) Institut de Ciències del Mar (ICM-CSIC) La doctoranda La directora La co -directora La tutora Yaiza M. Castillo Dolors Vaqué Marta Sebastián Josefa Badía En Barcelona, a 25 de noviembre de 2019 Cover design and images: © Yaiza M. Castillo. TEM images from Derelle et al ., 2008 This thesis has been funded by the Spanish Ministry of Economy and competitivity (MINECO) through a PhD fellowship to Yaiza M. Castillo de la Peña (BES-2014- 067849), under the program “Formación de Personal Investigador (FPI)”, and adscribed to the project: “Impact of viruses on marine microbial communities using virus-host models and metagenomic analyzes.” MEFISTO (Ref. CTM2013‐43767‐P, P.I.Dr. Dolors Vaqué). Other projects that contributed partially to the completion of this thesis were: ALLFLAGS (CTM2016‐75083‐R, MINECO, P.I. Dr. Ramon Massana), INTERACTOMICS (CTM2015‐69936‐P, MINECO, Dr. Ramiro Logares), the EU project SINGEK (H2020‐ MSCAITN‐2015‐675752, P.I. Dr. Ramon Massana) and Tara Oceans Expedition (http://www.embl.de/tara-ocean s/). A mis padres y a mis abuelos ACKNOWLEDGEMENTS Primero de todo quiero agradecer a mis directoras de tesis Dolors Vaqué y Marta Sebastián por apoyarme y guiarme a lo largo de estos años de doctorado. Por su paciencia, motivación y conocimientos. Sin ellas esta tesis no habría sido posible. Tampoco habría sido posible sin la inmensa ayuda de Irene Forn y Jeff Mangot, los cuales han trabajado conmigo codo con codo para poder sacar adelante este trabajo. A todas mis compañeras del ICM que me han acompañado durante estos años y han hecho que la experiencia de la tesis tuviera un toque de luz especial. Gracias a Mariri Vicioso, Marta Masdeu, Idaira Santos, Carolina Marín, Elisabet Sà, Isabel Sanz, Anna Arias, Sergio González, Caterina Rodríguez, Dorleta Orue-Echevarría, Mireia Mestre, Ramiro Logares, Xavi Leal, Estela Romero, Isabel Marín, Néstor Arandia, Sheree Yau, Fran Aparicio y Sdena Nunes. Espero no haberme dejado a nadie, si es así, espero que me disculpéis. Por último, gracias a mi familia por su apoyo incondicional. A mis padres, por todo el amor que me han dado y todo lo que han hecho por mí. A mis abuelos, por haber creído siempre en mí y haber estado tan orgullosos de su nieta, siempre estaréis en mi memoria. Os quiero. CONTENTS Abstract/Resumen/Resum ................................................................ 11 General introduction and aim of the thesis ........................................ 17 General Introduction ............................................................................... 19 Aim of the thesis ..................................................................................... 33 Chapter 1 ................................ ................................ .......................... 39 Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using VirusFISH. Abstract ................................................................................................... 41 1.1. Introduction ..................................................................................... 42 1.2. Materials and methods .................................................................... 43 1.3. Results .............................................................................................. 48 1.4. Discussion ......................................................................................... 55 References ............................................................................................... 62 Supplementary information .................................................................... 65 Chapter 2 ................................ ................................ .......................... 73 Seasonal dynamics of Ostreococcus spp. viral infection at the single cell level using VirusFISH Abstract ................................................................................................... 75 2.1. Introduction ..................................................................................... 76 2.2. Materials and methods .................................................................... 79 2.3. Results .............................................................................................. 83 2.4. Discussion ......................................................................................... 92 References ............................................................................................... 96 Supplementary information ................................................................... 100 9 Chapter 3 ................................ ................................ ........................ 109 Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics Abstract ................................................................................................. 111 3.1. Introduction ................................................................................... 112 3.2. Materials and methods .................................................................. 115 3.3. Results ............................................................................................ 120 3.4. Discussion ....................................................................................... 136 References ............................................................................................. 142 Supplementary information ................................................................... 150 Comments and future perspectives ................................ ................. 191 General conclusions ................................ ................................ ........ 199 10 Abstract/Resumen/Resum ABSTRACT Marine viruses are key components of marine microbial communities, as they influence the cellular abundances and the community structure of microbes, participate in their genetic exchange, and intervene in the ocean biogeochemical cycles. Most studies dealing with the role of viruses in the marine environment have been done from a bulk community point of view, but going from the bu lk community perspective to specific virus ─host relationships is essential in order to understand the role of viruses in shaping a determined host community, in modifying host genomes, and ultimately in the release of organic compounds from the lysed cells. For this reason, in this thesis we implemented and applied different methodologies that are able to detect, visualize and quantify virus ─host interactions in marine eukaryotes at the single cell level. We focused on picoeukaryotes (cells <3 µm) because they play crucial roles in marine food webs and biogeochemical cycles, and virus ─host interactions in natural populations of these minute eukaryotes are largely unknown. In the first chapter we combined previously developed techniques, used to assess prokaryotic host ─phage interactions, to implement VirusFISH for detecting specific virus ─host dynamics, using as a model system the photosynthetic picoeukaryote Ostreoccocus tauri and its virus OtV5. With the VirusFISH technique, we could also monitor the infection, as well as quantify the free viruses produced during the lysis of the host in a non-axenic culture, which allowed the calculation of the burst size. This study set the ground for the application of the VirusFISH technique to natural samples. In the second chapter of this thesis, we applied VirusFISH to seawater samples from the Bay of Biscay (Cantabrian Sea) to study the dynamics of viral infection in natural populations of Ostreococcus along a seasonal cycle. We were able to quantify the percentage of cells infected over time, and compared these results with the transcriptional viral and host activities derived from metatranscriptomic 11 Abstract/Resumen/Resum data. This constitutes the first study where a specific viral ─host interaction has been visualized and monitored over time in a natural system. Picoeukaryotes in the ocean are prevalently uncultured, and thus, in the third chapter of this thesis we went an step further to unveil novel viral ─host relationships in eukaryotic uncultured hosts. For this purpose, we mined single amplified genomes (SAGs) of picoeukaryotes obtained during the Tara Oceans expedition for viral signatures. We found that almost 60% of the cells analyzed presented an associated virus with narrow host specificity. Some of the viral sequences were widely distributed and some geographically constrained, and they were preferentially
Load more

Recommended publications
  • A New Family of Hybrid Virophages from an Animal Gut Metagenome Natalya Yutin, Vladimir V Kapitonov and Eugene V Koonin*
    Yutin et al. Biology Direct (2015) 10:19 DOI 10.1186/s13062-015-0054-9 DISCOVERY NOTES Open Access A new family of hybrid virophages from an animal gut metagenome Natalya Yutin, Vladimir V Kapitonov and Eugene V Koonin* Abstract Search of metagenomics sequence databases for homologs of virophage capsid proteins resulted in the discovery of a new family of virophages in the sheep rumen metagenome. The genomes of the rumen virophages (RVP) encode a typical virophage major capsid protein, ATPase and protease combined with a Polinton-type, protein primed family B DNA polymerase. The RVP genomes appear to be linear molecules, with terminal inverted repeats. Thus, the RVP seem to represent virophage-Polinton hybrids that are likely capable of formation of infectious virions. Virion proteins of mimiviruses were detected in the same metagenomes as the RVP suggesting that the virophages of the new family parasitize on giant viruses that infect protist inhabitants of the rumen. This article was reviewed by Mart Krupovic and Kenneth Stedman; for complete reviews, see the Reviewers’ Reports section. Findings been isolated as infectious particles and shown to be associ- With the rapid increase of the quantity and quality of ated with different members of the family Mimiviridae available metagenomics sequences, metagenomes have [11-13], and 9 additional virophage genomes have been as- become a rich source for the discovery of novel viruses sembled from aquatic metagenomes [14-16]. The first vir- [1-3]. A prominent case in point is the recent discovery ophage, named Sputnik, was discovered as a parasite of of a novel, abundant and diversified group of viruses that Acanthamoeba castellani mimivirus [11], and reproduction are chimeras of genes from single-stranded DNA and of the related Zamilon virophage is supported by several positive-strand RNA viruses [4-7].
    [Show full text]
  • Complete Sections As Applicable
    This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2015.001a-kF officers) Short title: A new family and two new genera for classification of virophages two new species (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 10 are required) 6 7 8 9 10 Author(s): Matthias Fischer – Max Planck Institute for Medical Research, Germany Mart Krupovic – Institut Pasteur, France Jens H. Kuhn – NIH/NIAID/IRF-Frederick, Maryland, USA Bernard La Scola – Aix Marseille Université, France Didier Raoult – Aix Marseille Université, France Corresponding author with e-mail address: Matthias Fischer, [email protected] Mart Krupovic, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . If in doubt, contact the appropriate subcommittee chair (fungal, invertebrate, plant, prokaryote or vertebrate viruses) ICTV Study Group comments (if any) and response of the proposer: Date first submitted to ICTV: June 11, 2015 Date of this revision (if different to above): ICTV-EC comments and response of the proposer: Fungal and Protist Viruses Subcommittee Chair: Proposal approved for submission.
    [Show full text]
  • Coming-Of-Age Characterization of Soil Viruses: a User's Guide To
    Review Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics Gareth Trubl 1,* , Paul Hyman 2 , Simon Roux 3 and Stephen T. Abedon 4,* 1 Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA 2 Department of Biology/Toxicology, Ashland University, Ashland, OH 44805, USA; [email protected] 3 DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; [email protected] 4 Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA * Correspondence: [email protected] (G.T.); [email protected] (S.T.A.) Received: 25 February 2020; Accepted: 17 April 2020; Published: 21 April 2020 Abstract: The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses.
    [Show full text]
  • A Field Guide to Eukaryotic Transposable Elements
    GE54CH23_Feschotte ARjats.cls September 12, 2020 7:34 Annual Review of Genetics A Field Guide to Eukaryotic Transposable Elements Jonathan N. Wells and Cédric Feschotte Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; email: [email protected], [email protected] Annu. Rev. Genet. 2020. 54:23.1–23.23 Keywords The Annual Review of Genetics is online at transposons, retrotransposons, transposition mechanisms, transposable genet.annualreviews.org element origins, genome evolution https://doi.org/10.1146/annurev-genet-040620- 022145 Abstract Annu. Rev. Genet. 2020.54. Downloaded from www.annualreviews.org Access provided by Cornell University on 09/26/20. For personal use only. Copyright © 2020 by Annual Reviews. Transposable elements (TEs) are mobile DNA sequences that propagate All rights reserved within genomes. Through diverse invasion strategies, TEs have come to oc- cupy a substantial fraction of nearly all eukaryotic genomes, and they rep- resent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic be- havior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species. 23.1 Review in Advance first posted on , September 21, 2020.
    [Show full text]
  • Marine Microplankton Ecology Reading
    Marine Microplankton Ecology Reading Microbes dominate our planet, especially the Earth’s oceans. The distinguishing feature of microorganisms is their small size, usually defined as less than 200 micrometers (µm); they are all invisible to the naked eye. As a group, sea microbes are extremely diverse, and extremely versatile with respect to their abilities to make and eat food. All marine microbes are too small to swim against the current and are therefore classified as plankton. First we will discuss several ways to classify marine microbes. 1. Size Planktonic marine organisms can be divided into the following size categories: Category Size femtoplankton <0.2 µm picoplankton 0.2-2 µm nanoplankton 2-20 µm microplankton 20-200 µm mesoplankton 200-2000 µm In this laboratory we are concerned with the microscopic portion of the plankton, less than 200 µm. These organisms are not visible to the naked eye (Figure 1). Figure 1. Size classes of marine plankton 2. Type A. Viruses Viruses are the smallest and simplest microplankton. They range from 0.01 to 0.3 um in diameter. Externally, viruses have a capsid, or protein coat. Viruses can also have simple or complex external morphologies with tail fibers and structures that are used to inject DNA or RNA into their host. Viruses have little internal morphology. They do not have a nucleus or organelles. They do not have chlorophyll. Inside a virus there is only nucleic acid, either DNA or RNA. Viruses do not grow and have no metabolism. Marine viruses are highly abundant. There are up to 10 billion in one liter of seawater! B.
    [Show full text]
  • Marine Microbiology at Scripps
    81832_Ocean 8/28/03 7:18 PM Page 67 Special Issue—Scripps Centennial Marine Microbiology at Scripps A. Aristides Yayanos Scripps Institution of Oceanography, University of California, • San Diego, California USA Marine microbiology is the study of the smallest isolated marine bioluminescent bacteria, isolated and organisms found in the oceans—bacteria and archaea, characterized sulfate-reducing bacteria, and showed many eukaryotes (among the protozoa, fungi, and denitrifying bacteria could both produce and consume plants), and viruses. Most microorganisms can be seen nitrous oxide, now known to be an important green- only with a microscope. Microbes pervade the oceans, house gas. Beijerinck also founded the field of virology its sediments, and some hydrothermal fluids and through his work on plant viruses (van Iterson et al., exhibit solitary life styles as well as complex relation- 1983). Mills (1989) describes the significance of the ships with animals, other microorganisms, and each work of Beijerink and Winogradsky to plankton other. The skeletal remains of microorganisms form the research and marine chemistry. largest component of sedimentary fossils whose study Around 1903, bacteriology in California was reveals Earth’s history. The enormous morphological, emerging in the areas of medicine and public health physiological, and taxonomic diversity of marine and accordingly was developing into an academic dis- microorganisms remains far from adequately cipline in medical schools (McClung and Meyer, 1974). described and studied. Because the sea receives terres- Whereas the branch of microbiology dealing with bac- trial microorganisms from rivers, sewage outfalls, and teria and viruses was just beginning, the branch con- other sources, marine microbiology also includes the cerning protozoa and algae was a relatively more estab- study of alien microorganisms.
    [Show full text]
  • A Distinct Lineage of Giant Viruses Brings a Rhodopsin Photosystem to Unicellular Marine Predators
    A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators David M. Needhama,1, Susumu Yoshizawab,1, Toshiaki Hosakac,1, Camille Poiriera,d, Chang Jae Choia,d, Elisabeth Hehenbergera,d, Nicholas A. T. Irwine, Susanne Wilkena,2, Cheuk-Man Yunga,d, Charles Bachya,3, Rika Kuriharaf, Yu Nakajimab, Keiichi Kojimaf, Tomomi Kimura-Someyac, Guy Leonardg, Rex R. Malmstromh, Daniel R. Mendei, Daniel K. Olsoni, Yuki Sudof, Sebastian Sudeka, Thomas A. Richardsg, Edward F. DeLongi, Patrick J. Keelinge, Alyson E. Santoroj, Mikako Shirouzuc, Wataru Iwasakib,k,4, and Alexandra Z. Wordena,d,4 aMonterey Bay Aquarium Research Institute, Moss Landing, CA 95039; bAtmosphere & Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan; cLaboratory for Protein Functional & Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; dOcean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, 24105 Kiel, Germany; eDepartment of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; fGraduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan; gLiving Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4SB, United Kingdom; hDepartment of Energy Joint Genome Institute, Walnut Creek, CA 94598; iDaniel K. Inouye Center for Microbial Oceanography, University of Hawaii, Manoa, Honolulu, HI 96822; jDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106; and kDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0032, Japan Edited by W. Ford Doolittle, Dalhousie University, Halifax, Canada, and approved August 8, 2019 (received for review May 27, 2019) Giant viruses are remarkable for their large genomes, often rivaling genomes that range up to 2.4 Mb (Fig.
    [Show full text]
  • Aquatic Microbial Ecology 79:1
    Vol. 79: 1–12, 2017 AQUATIC MICROBIAL ECOLOGY Published online March 28 https://doi.org/10.3354/ame01811 Aquat Microb Ecol Contribution to AME Special 6 ‘SAME 14: progress and perspectives in aquatic microbial ecology’ OPENPEN ACCESSCCESS REVIEW Exploring the oceanic microeukaryotic interactome with metaomics approaches Anders K. Krabberød1, Marit F. M. Bjorbækmo1, Kamran Shalchian-Tabrizi1, Ramiro Logares2,1,* 1University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, 0316 Oslo, Norway 2Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain ABSTRACT: Biological communities are systems composed of many interacting parts (species, populations or single cells) that in combination constitute the functional basis of the biosphere. Animal and plant ecologists have advanced substantially our understanding of ecological inter- actions. In contrast, our knowledge of ecological interaction in microbes is still rudimentary. This represents a major knowledge gap, as microbes are key players in almost all ecosystems, particu- larly in the oceans. Several studies still pool together widely different marine microbes into broad functional categories (e.g. grazers) and therefore overlook fine-grained species/population-spe- cific interactions. Increasing our understanding of ecological interactions is particularly needed for oceanic microeukaryotes, which include a large diversity of poorly understood symbiotic rela- tionships that range from mutualistic to parasitic. The reason for the current state of affairs is that determining ecological interactions between microbes has proven to be highly challenging. How- ever, recent technological developments in genomics and transcriptomics (metaomics for short), coupled with microfluidics and high-performance computing are making it increasingly feasible to determine ecological interactions at the microscale.
    [Show full text]
  • The Origins of Giant Viruses, Virophages and Their Relatives in Host Genomes Aris Katzourakis* and Amr Aswad
    Katzourakis A and Aswad A BMC Biology 2014, 12:51 http://www.biomedcentral.com/1741-7007/12/51 COMMENTARY The origins of giant viruses, virophages and their relatives in host genomes Aris Katzourakis* and Amr Aswad Abstract including the discovery last month of Samba virus, a wild mimivirus from the Amazonian Rio Negro [4]. Al- Giant viruses have revealed a number of surprises that though slightly larger, Samba virus shares identity across challenge conventions on what constitutes a virus. the majority of its genome to the original Bradford The Samba virus newly isolated in Brazil expands the mimivirus, further expanding the widespread distribu- known distribution of giant mimiviruses to a near- tion of these giant viruses. The defining feature of giant global scale. These viruses, together with the viruses is that they are an extreme outlier in terms of transposon-related virophages that infect them, pose a genome size: Acanthamoeba polyphaga mimivirus has a number of questions about their evolutionary origins 1.2 Mb genome [1], which was double the size of the lar- that need to be considered in the light of the gest virus known at the time, and pandoravirus genomes complex entanglement between host, virus and reach up to 2.5 Mb [2]. Giant viruses are also extreme virophage genomes. outliers in terms of their physical size, being too large to pass through porcelain filters, a criterion historically See research article: used to define a virus. As a further challenge to the trad- http://www.virologyj.com/content/11/1/95. itional definition of viruses, giant viruses have several es- sential protein synthesis genes that have thus far been The discovery of giant viruses thought to be exclusive to cellular life [1].
    [Show full text]
  • Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems
    fmars-08-698853 August 11, 2021 Time: 11:16 # 1 REVIEW published: 16 August 2021 doi: 10.3389/fmars.2021.698853 Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems Chloé Stévenne*†, Maud Micha*†, Jean-Christophe Plumier and Stéphane Roberty InBioS – Animal Physiology and Ecophysiology, Department of Biology, Ecology & Evolution, University of Liège, Liège, Belgium In the past 20 years, a new concept has slowly emerged and expanded to various domains of marine biology research: the holobiont. A holobiont describes the consortium formed by a eukaryotic host and its associated microorganisms including Edited by: bacteria, archaea, protists, microalgae, fungi, and viruses. From coral reefs to the Viola Liebich, deep-sea, symbiotic relationships and host–microbiome interactions are omnipresent Bremen Society for Natural Sciences, and central to the health of marine ecosystems. Studying marine organisms under Germany the light of the holobiont is a new paradigm that impacts many aspects of marine Reviewed by: Carlotta Nonnis Marzano, sciences. This approach is an innovative way of understanding the complex functioning University of Bari Aldo Moro, Italy of marine organisms, their evolution, their ecological roles within their ecosystems, and Maria Pia Miglietta, Texas A&M University at Galveston, their adaptation to face environmental changes. This review offers a broad insight into United States key concepts of holobiont studies and into the current knowledge of marine model *Correspondence: holobionts. Firstly, the history of the holobiont concept and the expansion of its use Chloé Stévenne from evolutionary sciences to other fields of marine biology will be discussed.
    [Show full text]
  • Virophages Question the Existence of Satellites
    CORRESPONDENCE LINK TO ORIGINAL ARTICLE LINK TO AUTHOR’S REPLY located in front of 12 out of 21 Sputnik coding sequences and all 20 Cafeteria roenbergensis Virophages question the virus coding sequences (both promoters being associated with the late expression of genes) existence of satellites imply that virophage gene expression is gov- erned by the transcription machinery of the Christelle Desnues and Didier Raoult host virus during the late stages of infection. Another point concerns the effect of the virophage on the host virus. It has been argued In a recent Comment (Virophages or satel- genome sequences of other known viruses that the effect of Sputnik or Mavirus on the lite viruses? Nature Rev. Microbiol. 9, 762– indicates that the virophages probably belong host is similar to that observed for STNV and 763 (2011))1, Mart Krupovic and Virginija to a new viral family. This is further supported its helper virus1. However, in some cases the Cvirkaite-Krupovic argued that the recently by structural analysis of Sputnik, which infectivity of TNV is greater when inoculated described virophages, Sputnik and Mavirus, showed that MCP probably adopts a double- along with STNV (or its nucleic acid) than should be classified as satellite viruses. In a jelly-roll fold, although there is no sequence when inoculated alone, suggesting that STNV response2, to which Krupovic and Cvirkaite- similarity between the virophage MCPs and makes cells more susceptible to TNV11. Such Krupovic replied3, Matthias Fisher presented those of other members of the bacteriophage an effect has never been observed for Sputnik two points supporting the concept of the PRD1–adenovirus lineage9.
    [Show full text]
  • Exploration of the Propagation of Transpovirons Within Mimiviridae Reveals a Unique Example of Commensalism in the Viral World
    The ISME Journal (2020) 14:727–739 https://doi.org/10.1038/s41396-019-0565-y ARTICLE Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world 1 1 1 1 1 Sandra Jeudy ● Lionel Bertaux ● Jean-Marie Alempic ● Audrey Lartigue ● Matthieu Legendre ● 2 1 1 2 3 4 Lucid Belmudes ● Sébastien Santini ● Nadège Philippe ● Laure Beucher ● Emanuele G. Biondi ● Sissel Juul ● 4 2 1 1 Daniel J. Turner ● Yohann Couté ● Jean-Michel Claverie ● Chantal Abergel Received: 9 September 2019 / Revised: 27 November 2019 / Accepted: 28 November 2019 / Published online: 10 December 2019 © The Author(s) 2019. This article is published with open access Abstract Acanthamoeba-infecting Mimiviridae are giant viruses with dsDNA genome up to 1.5 Mb. They build viral factories in the host cytoplasm in which the nuclear-like virus-encoded functions take place. They are themselves the target of infections by 20-kb-dsDNA virophages, replicating in the giant virus factories and can also be found associated with 7-kb-DNA episomes, dubbed transpovirons. Here we isolated a virophage (Zamilon vitis) and two transpovirons respectively associated to B- and C-clade mimiviruses. We found that the virophage could transfer each transpoviron provided the host viruses were devoid of 1234567890();,: 1234567890();,: a resident transpoviron (permissive effect). If not, only the resident transpoviron originally isolated from the corresponding virus was replicated and propagated within the virophage progeny (dominance effect). Although B- and C-clade viruses devoid of transpoviron could replicate each transpoviron, they did it with a lower efficiency across clades, suggesting an ongoing process of adaptive co-evolution.
    [Show full text]