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Chase EE, Pitot T, Bouchard S, Triplet S, Przybyla C, Gobet A, Desnues C, Blanc G. Viral dynamics in a high-rate algal pond reveals a burst of Phycodnaviridae diversity correlated with episodic algal mortality. mBio 2024; 15:e0280324. [PMID: 39530688 PMCID: PMC11633385 DOI: 10.1128/mbio.02803-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Accepted: 10/15/2024] [Indexed: 11/16/2024] Open
Abstract
This study explores virus-host dynamics in a unique environment: an industrial high-rate algal pond (HRAP). A wealth of novel DNA algal viruses are revealed, including members of Nucleocytoviricota "giant viruses" and the enigmatic Preplasmiviricota (e.g., virophages and polinton-like viruses). Several species of single-celled eukaryotic photosynthetic algae are identified (Chlorophyta) as putative hosts, with alternating dominant populations during the year of study. We specifically observe a surprising diversity of giant viruses from the family Phycodnaviridae (Nucleocytoviricota), including phylogenetically related but highly diversified genotypes appearing in the HRAP that we suggest are implicated in bloom collapse. We hypothesize that these related Phycodnaviridae lineages infect the same algal species of the genus Picochlorum that has been identified in the HRAP. This study establishes a baseline for comprehending the role viruses play in algal farming and emphasizes the necessity of controlling the viral load in future culture system development to optimize algal growth. IMPORTANCE The virosphere is ubiquitous, but we have yet to characterize many environments where viruses exist. In an industrial polyculture of microalgae, a wealth of viruses persist, their diversity and dynamics changing over time and consequently give evidence of their evolution and ecological strategies. Several notable infectious agents of the culture's algae appear, including giant viruses, polinton-like viruses, and a virophage. As our reliance and interest in algal compound-based cosmetics, pharmaceuticals, and bio-plastics increases, so must our understanding of these systems, including the unique viruses that appear there.
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Affiliation(s)
- E. E. Chase
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d'Océanologie, Campus de Luminy, Marseille, France
- Institut hospitalo-universitaire (IHU) Méditerranée infection, Marseille, France
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | - T. Pitot
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Québec, Canada
| | - S. Bouchard
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d'Océanologie, Campus de Luminy, Marseille, France
| | - S. Triplet
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - C. Przybyla
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - A. Gobet
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - C. Desnues
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d'Océanologie, Campus de Luminy, Marseille, France
- Institut hospitalo-universitaire (IHU) Méditerranée infection, Marseille, France
| | - G. Blanc
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d'Océanologie, Campus de Luminy, Marseille, France
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2
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Piedade GJ, Schön ME, Lood C, Fofanov MV, Wesdorp EM, Biggs TEG, Wu L, Bolhuis H, Fischer MG, Yutin N, Dutilh BE, Brussaard CPD. Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape. Nat Commun 2024; 15:9192. [PMID: 39448562 PMCID: PMC11502894 DOI: 10.1038/s41467-024-53317-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 10/04/2024] [Indexed: 10/26/2024] Open
Abstract
The Southern Ocean microbial ecosystem, with its pronounced seasonal shifts, is vulnerable to the impacts of climate change. Since viruses are key modulators of microbial abundance, diversity, and evolution, we need a better understanding of the effects of seasonality on the viruses in this region. Our comprehensive exploration of DNA viral diversity in the Southern Ocean reveals a unique and largely uncharted viral landscape, of which 75% was previously unidentified in other oceanic areas. We uncover novel viral taxa at high taxonomic ranks, expanding our understanding of crassphage, polinton-like virus, and virophage diversity. Nucleocytoviricota viruses represent an abundant and diverse group of Antarctic viruses, highlighting their potential as important regulators of phytoplankton population dynamics. Our temporal analysis reveals complex seasonal patterns in marine viral communities (bacteriophages, eukaryotic viruses) which underscores the apparent interactions with their microbial hosts, whilst deepening our understanding of their roles in the world's most sensitive and rapidly changing ecosystem.
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Affiliation(s)
- Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands.
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands.
| | - Max E Schön
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120, Heidelberg, Germany
| | - Cédric Lood
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743, Jena, Germany
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Mikhail V Fofanov
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743, Jena, Germany
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Ella M Wesdorp
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Tristan E G Biggs
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Lingyi Wu
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Matthias G Fischer
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120, Heidelberg, Germany
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743, Jena, Germany
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands.
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands.
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3
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Banerji A, Brinkman NE, Davis B, Franklin A, Jahne M, Keely SP. Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms. Microorganisms 2024; 12:2121. [PMID: 39597512 PMCID: PMC11596618 DOI: 10.3390/microorganisms12112121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 10/16/2024] [Accepted: 10/17/2024] [Indexed: 11/29/2024] Open
Abstract
Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.
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Affiliation(s)
- Aabir Banerji
- US Environmental Protection Agency, Office of Research and Development, Duluth, MN 55804, USA
| | - Nichole E. Brinkman
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA; (N.E.B.); (B.D.); (M.J.)
| | - Benjamin Davis
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA; (N.E.B.); (B.D.); (M.J.)
| | - Alison Franklin
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA; (N.E.B.); (B.D.); (M.J.)
| | - Michael Jahne
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA; (N.E.B.); (B.D.); (M.J.)
| | - Scott P. Keely
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA; (N.E.B.); (B.D.); (M.J.)
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4
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Koonin EV, Fischer MG, Kuhn JH, Krupovic M. The polinton-like supergroup of viruses: evolution, molecular biology, and taxonomy. Microbiol Mol Biol Rev 2024; 88:e0008623. [PMID: 39023254 PMCID: PMC11426020 DOI: 10.1128/mmbr.00086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Abstract
SUMMARYPolintons are 15-20 kb-long self-synthesizing transposons that are widespread in eukaryotic, and in particular protist, genomes. Apart from a transposase and a protein-primed DNA polymerase, polintons encode homologs of major and minor jelly-roll capsid proteins, DNA-packaging ATPases, and proteases involved in capsid maturation of diverse eukaryotic viruses of kingdom Bamfordvirae. Given the conservation of these structural and morphogenetic proteins among polintons, these elements are predicted to alternate between transposon and viral lifestyles and, although virions have thus far not been detected, are classified as viruses (class Polintoviricetes) in the phylum Preplasmiviricota. Related to polintoviricetes are vertebrate adenovirids; unclassified polinton-like viruses (PLVs) identified in various environments or integrated into diverse protist genomes; virophages (Maveriviricetes), which are part of tripartite hyperparasitic systems including protist hosts and giant viruses; and capsid-less derivatives, such as cytoplasmic linear DNA plasmids of fungi and transpovirons. Phylogenomic analysis indicates that the polinton-like supergroup of viruses bridges bacterial tectivirids (preplasmiviricot class Tectiliviricetes) to the phylum Nucleocytoviricota that includes large and giant eukaryotic DNA viruses. Comparative structural analysis of proteins encoded by polinton-like viruses led to the discovery of previously undetected functional domains, such as terminal proteins and distinct proteases implicated in DNA polymerase processing, and clarified the evolutionary relationships within Polintoviricetes. Here, we leverage these insights into the evolution of the polinton-like supergroup to develop an amended megataxonomy that groups Polintoviricetes, PLVs (new class 'Aquintoviricetes'), and virophages (renamed class 'Virophaviricetes') together with Adenoviridae (new class 'Pharingeaviricetes') in a preplasmiviricot subphylum 'Polisuviricotina' sister to a subphylum including Tectiliviricetes ('Prepoliviricotina').
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthias G Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
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5
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Rahimian M, Panahi B. Metagenome sequence data mining for viral interaction studies: Review on progress and prospects. Virus Res 2024; 349:199450. [PMID: 39151562 PMCID: PMC11388672 DOI: 10.1016/j.virusres.2024.199450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 08/11/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research.
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Affiliation(s)
- Mohammadreza Rahimian
- Department of Biology, Faculty of Basic Sciences, University of Maragheh, Maragheh, Iran
| | - Bahman Panahi
- Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.
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6
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Barth ZK, Hicklin I, Thézé J, Takatsuka J, Nakai M, Herniou EA, Brown AM, Aylward FO. Genomic analysis of hyperparasitic viruses associated with entomopoxviruses. Virus Evol 2024; 10:veae051. [PMID: 39100687 PMCID: PMC11296320 DOI: 10.1093/ve/veae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/17/2024] [Accepted: 07/11/2024] [Indexed: 08/06/2024] Open
Abstract
Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread. Here, we analyze the genomes of novel PLVs associated with the occlusion bodies of entomopoxvirus (EPV) infections of two separate lepidopteran hosts. The presence of these elements within EPV occlusion bodies suggests that they are the first known hyperparasites of poxviruses. We find that these PLVs belong to two distinct lineages that are highly diverged from known PLVs. These PLVs possess mosaic genomes, and some essential genes share homology with mobile genes within EPVs. Based on this homology and observed PLV mosaicism, we propose a mechanism to explain the turnover of PLV replication and integration genes.
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Affiliation(s)
- Zachary K Barth
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
| | - Ian Hicklin
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Julien Thézé
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Jun Takatsuka
- Forestry and Forest Products Research Institute, Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Madoka Nakai
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183-8509, Japan
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Anne M Brown
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, 1981 Kraft Dr, Blacksburg, VA 24061, USA
- Research and Informatics, University Libraries, Virginia Tech, Blacksburg, VA 24061, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, 1981 Kraft Dr, Blacksburg, VA 24061, USA
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7
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Tokarz-Deptuła B, Chrzanowska S, Baraniecki Ł, Gurgacz N, Stosik M, Sobolewski J, Deptuła W. Virophages, Satellite Viruses, Virophage Replication and Its Effects and Virophage Defence Mechanisms for Giant Virus Hosts and Giant Virus Defence Systems against Virophages. Int J Mol Sci 2024; 25:5878. [PMID: 38892066 PMCID: PMC11172284 DOI: 10.3390/ijms25115878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
In this paper, the characteristics of 40 so far described virophages-parasites of giant viruses-are given, and the similarities and differences between virophages and satellite viruses, which also, like virophages, require helper viruses for replication, are described. The replication of virophages taking place at a specific site-the viral particle factory of giant viruses-and its consequences are presented, and the defence mechanisms of virophages for giant virus hosts, as a protective action for giant virus hosts-protozoa and algae-are approximated. The defence systems of giant viruses against virophages were also presented, which are similar to the CRISPR/Cas defence system found in bacteria and in Archea. These facts, and related to the very specific biological features of virophages (specific site of replication, specific mechanisms of their defensive effects for giant virus hosts, defence systems in giant viruses against virophages), indicate that virophages, and their host giant viruses, are biological objects, forming a 'novelty' in biology.
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Affiliation(s)
| | - Sara Chrzanowska
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland (Ł.B.)
| | - Łukasz Baraniecki
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland (Ł.B.)
| | - Natalia Gurgacz
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland (Ł.B.)
| | - Michał Stosik
- Institute of Biological Science, Faculty of Biological Sciences, University of Zielona Góra, 65-516 Zielona Góra, Poland;
| | - Jarosław Sobolewski
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland;
| | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland;
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8
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Felipe Benites L, Stephens TG, Van Etten J, James T, Christian WC, Barry K, Grigoriev IV, McDermott TR, Bhattacharya D. Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts. Commun Biol 2024; 7:312. [PMID: 38594478 PMCID: PMC11003980 DOI: 10.1038/s42003-024-05931-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 04/11/2024] Open
Abstract
Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Julia Van Etten
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Timeeka James
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - William C Christian
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Timothy R McDermott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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9
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Koslová A, Hackl T, Bade F, Sanchez Kasikovic A, Barenhoff K, Schimm F, Mersdorf U, Fischer MG. Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae. Proc Natl Acad Sci U S A 2024; 121:e2314606121. [PMID: 38446847 PMCID: PMC10945749 DOI: 10.1073/pnas.2314606121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/14/2024] [Indexed: 03/08/2024] Open
Abstract
Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.
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Affiliation(s)
- Anna Koslová
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Thomas Hackl
- Faculty of Science and Engineering, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen9747 AG, The Netherlands
| | - Felix Bade
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | | | - Karina Barenhoff
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Fiona Schimm
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Ulrike Mersdorf
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Matthias G. Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
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10
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del Arco A, Fischer MG, Becks L. Evolution of exploitation and replication of giant viruses and virophages. Virus Evol 2024; 10:veae021. [PMID: 38562952 PMCID: PMC10984621 DOI: 10.1093/ve/veae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/05/2024] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
Tripartite biotic interactions are inherently complex, and the strong interdependence of species and often one-sided exploitation can make these systems vulnerable to extinction. The persistence of species depends then on the balance between exploitation and avoidance of exploitation beyond the point where sustainable resource use is no longer possible. We used this general prediction to test the potential role of trait evolution for persistence in a tripartite microbial system consisting of a marine heterotrophic flagellate preyed upon by a giant virus, which in turn is parasitized by a virophage. Host and virophage may benefit from this interaction because the virophage reduces the harmful effects of the giant virus on the host population and the virophage can persist integrated into the host genome when giant viruses are scarce. We grew hosts and virus in the presence and absence of the virophage over ∼280 host generations and tested whether levels of exploitation and replication in the giant virus and/or virophage population evolved over the course of the experiment, and whether the changes were such that they could avoid overexploitation and extinction. We found that the giant virus evolved toward lower levels of replication and the virophage evolved toward increased replication but decreased exploitation of the giant virus. These changes reduced overall host exploitation by the virus and virus exploitation by the virophage and are predicted to facilitate persistence.
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Affiliation(s)
- Ana del Arco
- Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Mainaustraße 252, Konstanz/Egg 78464, Germany
| | - Matthias G Fischer
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Lutz Becks
- Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Mainaustraße 252, Konstanz/Egg 78464, Germany
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11
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Ni Y, Chu T, Yan S, Wang Y. Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae. J Gen Virol 2024; 105. [PMID: 38446011 DOI: 10.1099/jgv.0.001967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Twenty complete genomes (29-63 kb) and 29 genomes with an estimated completeness of over 90 % (30-90 kb) were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered viruses contribute to the expansion of viral taxonomy by introducing 46 potential new families. Except for one virus, all others belong to the class Caudoviricetes. The exception is a novel member of the recently characterized viral group known as Gossevirus. Fifteen viruses were predicted to be temperate. The predicted hosts for the viruses appear to be involved in various aspects of the nitrogen cycle, including nitrogen fixation, oxidation and denitrification. Two viruses were identified to have a host of Flavobacterium and Tepidimonas fonticaldi, respectively, by matching CRISPR spacers with viral protospacers. Our findings provide an overview for characterizing and identifying specific viruses from Yangshan Harbor. The Gossevirus-like virus uncovered emphasizes the need for further comprehensive isolation and investigation of polinton-like viruses.
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Affiliation(s)
- Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Ting Chu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Shuling Yan
- Entwicklungsgenetik und Zellbiologie der Tiere, Philipps-Universität Marburg, Marburg, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, PR China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, PR China
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12
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Potapov SA, Belykh OI. Virophages Found in Viromes from Lake Baikal. Biomolecules 2023; 13:1773. [PMID: 38136644 PMCID: PMC10741620 DOI: 10.3390/biom13121773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, a previously little-studied group of viruses-virophages-was searched for and identified in the viromes of the ancient oligotrophic Lake Baikal. Virophages are small dsDNA viruses that parasitize giant viruses (e.g., Mimiviridae), which in turn affect unicellular eukaryotes. We analyzed eight viromes obtained from the deep-water areas of three basins of Lake Baikal and the shallow-water strait Maloye More in different seasons. The sequences of virophages were revealed in all viromes and were dominant after bacteriophages and algal viruses. Sixteen putative complete genomes of virophages were assembled, all of which contained four conserved genes encoding major capsid protein (MCP), minor capsid protein (mCP), maturation cysteine protease (PRO), and FtsK-HerA family DNA-packaging ATPase (ATPase). The MCP-based cluster analysis showed a sequence separation according to seasons, and a dependence on the geographical localization was not detected.
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Affiliation(s)
- Sergey Anatoljevich Potapov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, Irkutsk 664033, Russia;
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13
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Jeong DE, Sundrani S, Hall RN, Krupovic M, Koonin EV, Fire AZ. DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution. Mol Biol Evol 2023; 40:msad274. [PMID: 38069639 DOI: 10.1093/molbev/msad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/01/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
Polintons are double-stranded DNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family but encode a distinct protein-primed DNA polymerase B (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda. Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting interphylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of an HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.
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Affiliation(s)
- Dae-Eun Jeong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sameer Sundrani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Present address: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Eugene V Koonin
- National National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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14
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Jeong DE, Sundrani S, Hall RN, Krupovic M, Koonin EV, Fire AZ. DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554363. [PMID: 37662302 PMCID: PMC10473752 DOI: 10.1101/2023.08.22.554363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda . Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.
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15
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Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA, Johnson JC, Borges S, Weber PK, Pett-Ridge J, Boston PJ. Astrovirology: how viruses enhance our understanding of life in the Universe. INTERNATIONAL JOURNAL OF ASTROBIOLOGY 2023; 22:247-271. [PMID: 38046673 PMCID: PMC10691837 DOI: 10.1017/s1473550423000058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus-host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth M. Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, OR, USA
| | | | | | | | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Nancy Merino
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter Anto Johnson
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
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16
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Wu Z, Chu T, Sheng Y, Yu Y, Wang Y. Diversity, Relationship, and Distribution of Virophages and Large Algal Viruses in Global Ocean Viromes. Viruses 2023; 15:1582. [PMID: 37515268 PMCID: PMC10385804 DOI: 10.3390/v15071582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Virophages are a group of small double-stranded DNA viruses that replicate and proliferate with the help of the viral factory of large host viruses. They are widely distributed in aquatic environments but are more abundant in freshwater ecosystems. Here, we mined the Global Ocean Viromes 2.0 (GOV 2.0) dataset for the diversity, distribution, and association of virophages and their potential host large viruses in marine environments. We identified 94 virophage sequences (>5 kbp in length), of which eight were complete genomes. The MCP phylogenetic tree showed that the GOV virophages were widely distributed on the global virophage tree but relatively clustered on three major branches. The gene-sharing network divided GOV virophages into 21 outliers, 2 overlaps, and 14 viral clusters, of which 4 consisted of only the GOV virophages. We also identified 45 large virus sequences, 8 of which were >100 kbp in length and possibly involved in cell-virus-virophage (C-V-v) trisome relationships. The potential eukaryotic hosts of these eight large viruses and the eight virophages with their complete genomes identified are likely to be algae, based on comparative genomic analysis. Both homologous gene and codon usage analyses support a possible interaction between a virophage (GOVv18) and a large algal virus (GOVLV1). These results indicate that diverse and novel virophages and large viruses are widespread in global marine environments, suggesting their important roles and the presence of complicated unknown C-V-v relationships in marine ecosystems.
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Affiliation(s)
- Zhenqi Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
| | - Ting Chu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
| | - Yijian Sheng
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201304, China
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201304, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
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Tokarz-Deptuła B, Chrzanowska S, Gurgacz N, Stosik M, Deptuła W. Virophages-Known and Unknown Facts. Viruses 2023; 15:1321. [PMID: 37376621 PMCID: PMC10301787 DOI: 10.3390/v15061321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The paper presents virophages, which, like their host, giant viruses, are "new" infectious agents whose role in nature, including mammalian health, is important. Virophages, along with their protozoan and algal hosts, are found in fresh inland waters and oceanic and marine waters, including thermal waters and deep-sea vents, as well as in soil, plants, and in humans and animals (ruminants). Representing "superparasitism", almost all of the 39 described virophages (except Zamilon) interact negatively with giant viruses by affecting their replication and morphogenesis and their "adaptive immunity". This causes them to become regulators and, at the same time, defenders of the host of giant viruses protozoa and algae, which are organisms that determine the homeostasis of the aquatic environment. They are classified in the family Lavidaviridae with two genus (Sputnikovirus, Mavirus). However, in 2023, a proposal was presented that they should form the class Maveriviricetes, with four orders and seven families. Their specific structure, including their microsatellite (SSR-Simple Sequence Repeats) and the CVV (cell-virus-virophage, or transpovirion) system described with them, as well as their function, makes them, together with the biological features of giant viruses, form the basis for discussing the existence of a fourth domain in addition to Bacteria, Archaea, and Eukaryota. The paper also presents the hypothetical possibility of using them as a vector for vaccine antigens.
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Affiliation(s)
| | - Sara Chrzanowska
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
| | - Natalia Gurgacz
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
| | - Michał Stosik
- Institute of Biological Science, Faculty of Biological Sciences, University of Zielona Góra, 65-417 Zielona Góra, Poland
| | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University of Toruń, 87-100 Toruń, Poland
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18
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Bellas C, Hackl T, Plakolb MS, Koslová A, Fischer MG, Sommaruga R. Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses. Proc Natl Acad Sci U S A 2023; 120:e2300465120. [PMID: 37036967 PMCID: PMC10120064 DOI: 10.1073/pnas.2300465120] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/20/2023] [Indexed: 04/12/2023] Open
Abstract
Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be "genomic fossils." Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses. These EVEs, composed of virophages, Polinton-like viruses, and related entities, have remained hitherto hidden owing to poor sequence conservation between virus groups and their repetitive nature that precluded accurate short-read assembly. We show that long-read sequencing technology is ideal for resolving virus insertions. Many protist EVEs appear intact, and most encode integrases, which suggests that they have actively colonized hosts across the tree of eukaryotes. We also found evidence for gene expression in host transcriptomes and that closely related virophage and Polinton-like virus genomes are abundant in viral metagenomes, indicating that many EVEs are probably functional viruses.
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Affiliation(s)
| | - Thomas Hackl
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747AGGroningen, The Netherlands
| | | | - Anna Koslová
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120Heidelberg, Germany
| | - Matthias G. Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120Heidelberg, Germany
| | - Ruben Sommaruga
- Department of Ecology, Universität Innsbruck, 6020Innsbruck, Austria
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