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Metz S, Itoïz S, Obiol A, Derelle E, Massana R, Berney C, de Vargas C, Soudant P, Monier A, Chambouvet A. Global perspective of environmental distribution and diversity of Perkinsea (Alveolata) explored by a meta-analysis of eDNA surveys. Sci Rep 2023; 13:20111. [PMID: 37978260 PMCID: PMC10656510 DOI: 10.1038/s41598-023-47378-0] [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: 01/09/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023] Open
Abstract
Perkinsea constitutes a lineage within the Alveolata eukaryotic superphylum, mainly composed of parasitic organisms. Some described species represent significant ecological and economic threats due to their invasive ability and pathogenicity, which can lead to mortality events. However, the genetic diversity of these described species is just the tip of the iceberg. Environmental surveys targeting this lineage are still scarce and mainly limited to the Northern Hemisphere. Here, we aim to conduct an in depth exploration of the Perkinsea group, uncovering the diversity across a variety of environments, including those beyond freshwater and marine ecosystems. We seek to identify and describe putative novel organisms based on their genetic signatures. In this study, we conducted an extensive analysis of a metabarcoding dataset, focusing on the V4 region of the 18S rRNA gene (the EukBank dataset), to investigate the diversity, distribution and environmental preferences of the Perkinsea. Our results reveal a remarkable diversity within the Perkinsea, with 1568 Amplicon Sequence Variants (ASVs) identified across thousands of environmental samples. Surprisingly, we showed a substantial diversity of Perkinsea within soil samples (269 ASVs), challenging the previous assumption that this group is confined to marine and freshwater environments. In addition, we revealed that a notable proportion of Perkinsea ASVs (428 ASVs) could correspond to putative new organisms, encompassing the well-established taxonomic group Perkinsidae. Finally, our study shed light on previously unveiled taxonomic groups, including the Xcellidae, and revealed their environmental distribution. These findings demonstrate that Perkinsea exhibits far greater diversity than previously detected and surprisingly extends beyond marine and freshwater environments. The meta-analysis conducted in this study has unveiled the existence of previously unknown clusters within the Perkinsea lineage, solely identified based on their genetic signatures. Considering the ecological and economic importance of described Perkinsea species, these results suggest that Perkinsea may play a significant, yet previously unrecognized, role across a wide range of environments, spanning from soil environments to the abyssal zone of the open ocean with important implications for ecosystem functioning.
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Affiliation(s)
- Sebastian Metz
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Sorbonne Universités, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France.
- Department of Archaeology, University of York, York, UK.
| | - Sarah Itoïz
- CNRS, IRD, Ifremer, LEMAR, Univ Brest, Plouzané, France
- Rivages Pro Tech, 2, Allée Théodore Monod, 64210, Bidart, France
| | - Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | | | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Cédric Berney
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Sorbonne Universités, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Sorbonne Universités, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | | | - Adam Monier
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
| | - Aurélie Chambouvet
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Sorbonne Universités, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France.
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2
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Ruiz VL, Robert J. The amphibian immune system. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220123. [PMID: 37305914 PMCID: PMC10258673 DOI: 10.1098/rstb.2022.0123] [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: 02/05/2023] [Accepted: 04/16/2023] [Indexed: 06/13/2023] Open
Abstract
Amphibians are at the forefront of bridging the evolutionary gap between mammals and more ancient, jawed vertebrates. Currently, several diseases have targeted amphibians and understanding their immune system has importance beyond their use as a research model. The immune system of the African clawed frog, Xenopus laevis, and that of mammals is well conserved. We know that several features of the adaptive and innate immune system are very similar for both, including the existence of B cells, T cells and innate-like T cells. In particular, the study of the immune system at early stages of development is benefitted by studying X. laevis tadpoles. The tadpoles mainly rely on innate immune mechanisms including pre-set or innate-like T cells until after metamorphosis. In this review we lay out what is known about the innate and adaptive immune system of X. laevis including the lymphoid organs as well as how other amphibian immune systems are similar or different. Furthermore, we will describe how the amphibian immune system responds to some viral, bacterial and fungal insults. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Vania Lopez Ruiz
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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Amphibian Perkinsea. Curr Biol 2023; 33:R8-R10. [PMID: 36626865 DOI: 10.1016/j.cub.2022.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Vanessa Smilansky and Thomas A. Richards introduce Perkinsea - a lineage of freshwater parasitic protists that infect certain amphibians and cause of severe Perkinsea infection.
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Sutherland WJ, Bennett C, Brotherton PNM, Butterworth HM, Clout MN, Côté IM, Dinsdale J, Esmail N, Fleishman E, Gaston KJ, Herbert-Read JE, Hughes A, Kaartokallio H, Le Roux X, Lickorish FA, Matcham W, Noor N, Palardy JE, Pearce-Higgins JW, Peck LS, Pettorelli N, Pretty J, Scobey R, Spalding MD, Tonneijck FH, Tubbs N, Watson JEM, Wentworth JE, Wilson JD, Thornton A. A global biological conservation horizon scan of issues for 2023. Trends Ecol Evol 2023; 38:96-107. [PMID: 36460563 DOI: 10.1016/j.tree.2022.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2022]
Abstract
We present the results of our 14th horizon scan of issues we expect to influence biological conservation in the future. From an initial set of 102 topics, our global panel of 30 scientists and practitioners identified 15 issues we consider most urgent for societies worldwide to address. Issues are novel within biological conservation or represent a substantial positive or negative step change at global or regional scales. Issues such as submerged artificial light fisheries and accelerating upper ocean currents could have profound negative impacts on marine or coastal ecosystems. We also identified potentially positive technological advances, including energy production and storage, improved fertilisation methods, and expansion of biodegradable materials. If effectively managed, these technologies could realise future benefits for biological diversity.
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Affiliation(s)
- William J Sutherland
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; Biosecurity Research Initiative at St Catharine's (BioRISC), St Catharine's College, University of Cambridge, Cambridge, UK.
| | - Craig Bennett
- Royal Society of Wildlife Trusts, The Kiln, Waterside, Mather Road, Newark, Nottinghamshire NG24 1WT, UK
| | - Peter N M Brotherton
- Natural England, 4th Floor Foss House, Kings Pool, 1-2 Peasholme Green, York YO1 7PX, UK
| | - Holly M Butterworth
- Natural Resources Wales, Cambria House, 29 Newport Road, Cardiff CF24 0TP, UK
| | - Mick N Clout
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, PB 92019, Auckland, New Zealand
| | - Isabelle M Côté
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jason Dinsdale
- Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Nafeesa Esmail
- Wilder Institute/Calgary Zoo, 1300 Zoo Road NE, Calgary, AB T2E 7V6, Canada
| | - Erica Fleishman
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Kevin J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | | | - Alice Hughes
- School of Biological Sciences, University of Hong Kong, Pok Fu Lam, Hong Kong
| | | | - Xavier Le Roux
- University of Lyon, Microbial Ecology Centre, INRAE (UMR1418), CNRS (UMR5557), University Lyon 1, 69622 Villeurbanne, France
| | - Fiona A Lickorish
- UK Research and Consultancy Services (RCS) Ltd, Valletts Cottage, Westhope, Hereford HR4 8BU, UK
| | - Wendy Matcham
- Natural Environment Research Council, UK Research and Innovation, Polaris House, North Star Avenue, Swindon SN2 1FL, UK
| | - Noor Noor
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, Cambridge CB3 0DL, UK
| | - James E Palardy
- The Pew Charitable Trusts, 901 E St. NW, Washington, DC 20004, USA
| | - James W Pearce-Higgins
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; British Trust for Ornithology, The Nunnery, Thetford, Norfolk IP24 2PU, UK
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Nathalie Pettorelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Jules Pretty
- Centre for Public and Policy Engagement and School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Richard Scobey
- TRAFFIC, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK
| | - Mark D Spalding
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; The Nature Conservancy, Strade delle Tolfe, 14, Siena 53100, Italy
| | | | - Nicolas Tubbs
- WWF-Belgium, BD Emile Jacqumainlaan 90, 1000 Brussels, Belgium
| | - James E M Watson
- School of Earth and Environmental Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Jonathan E Wentworth
- Parliamentary Office of Science and Technology, 14 Tothill Street, Westminster, London SW1H 9NB, UK
| | - Jeremy D Wilson
- RSPB Centre for Conservation Science, 2 Lochside View, Edinburgh EH12 9DH, UK
| | - Ann Thornton
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK
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Alacid E, Irwin NAT, Smilansky V, Milner DS, Kilias ES, Leonard G, Richards TA. A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa. Open Biol 2022; 12:220126. [PMID: 36000319 PMCID: PMC9399869 DOI: 10.1098/rsob.220126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Spliced-leader trans-splicing (SLTS) has been described in distantly related eukaryotes and acts to mark mRNAs with a short 5′ exon, giving different mRNAs identical 5′ sequence-signatures. The function of these systems is obscure. Perkinsozoa encompasses a diversity of parasitic protists that infect bivalves, toxic-tide dinoflagellates, fish and frog tadpoles. Here, we report considerable sequence variation in the SLTS-system across the Perkinsozoa and find that multiple variant SLTS-systems are encoded in parallel in the ecologically important Perkinsozoa parasite Parvilucifera sinerae. These results demonstrate that the transcriptome of P. sinerae is segregated based on the addition of different spliced-leader (SL) exons. This segregation marks different gene categories, suggesting that SL-segregation relates to functional differentiation of the transcriptome. By contrast, both sets of gene categories are present in the single SL-transcript type sampled from Maranthos, implying that the SL-segregation of the Parvilucifera transcriptome is a recent evolutionary innovation. Furthermore, we show that the SLTS-system marks a subsection of the transcriptome with increased mRNA abundance and includes genes that encode the spliceosome system necessary for SLTS-function. Collectively, these data provide a picture of how the SLTS-systems can vary within a major evolutionary group and identify how additional transcriptional-complexity can be achieved through SL-segregation.
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Affiliation(s)
- Elisabet Alacid
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Nicholas A T Irwin
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK.,Merton College, University of Oxford, Oxford, Oxfordshire OX1 4JD, UK
| | - Vanessa Smilansky
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - David S Milner
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Estelle S Kilias
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Guy Leonard
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Thomas A Richards
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
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Urgiles VL, Ramírez ER, Villalta CI, Siddons DC, Savage AE. Three Pathogens Impact Terrestrial Frogs from a High-Elevation Tropical Hotspot. ECOHEALTH 2021; 18:451-464. [PMID: 34894333 DOI: 10.1007/s10393-021-01570-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Three infectious pathogens Batrachochytrium dendrobatidis (Bd), Ranavirus (Rv) and Perkinsea (Pr) are associated with widespread and ongoing amphibian population declines. Although their geographic and host ranges vary widely, recent studies have suggested that the occurrence of these pathogens could be more common than previously thought, even in direct-developing terrestrial species traditionally considered less likely to harbor these largely aquatic pathogens. Here, we characterize Bd, Rv, and Pr infections in direct-developing terrestrial amphibians of the Pristimantis genus from the highland Ecuadorean Andes. We confirm the first detection of Pr in terrestrial-breeding amphibians and in the Andean region, present the first report of Rv in Ecuador, and we add to the handful of studies finding Bd infecting Pristimantis. Infection prevalence did not differ significantly among pathogens, but infection intensity was significantly higher for Bd compared to Pr. Neither prevalence nor intensity differed significantly across locality and elevation for Bd and Rv, although low prevalence in our dataset and lack of seasonal sampling could have prevented important epidemiological patterns from emerging. Our study highlights the importance of incorporating pathogen surveillance in biodiversity monitoring in the Andean region and serves as starting point to understand pathogen dynamics, transmission, and impacts in terrestrial-breeding frogs.
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Affiliation(s)
- Veronica L Urgiles
- Department of Biology, University of Central Florida, 4110 Libra Dr, Orlando, FL, 32816, USA.
- Instituto Nacional de Biodiversidad del Ecuador, Pasaje Rumipamba 341 y Avenida de los Shirys, Quito, Ecuador.
| | - Ervin R Ramírez
- Escuela de Biología, Ecología y Gestión, Universidad del Azuay, Ave 24 de Mayo 7-77, Cuenca, Ecuador
| | - Cristian I Villalta
- Escuela de Biología, Ecología y Gestión, Universidad del Azuay, Ave 24 de Mayo 7-77, Cuenca, Ecuador
| | - David C Siddons
- Escuela de Biología, Ecología y Gestión, Universidad del Azuay, Ave 24 de Mayo 7-77, Cuenca, Ecuador
| | - Anna E Savage
- Department of Biology, University of Central Florida, 4110 Libra Dr, Orlando, FL, 32816, USA
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7
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Metz S, Huber P, Accattatis V, Lopes Dos Santos A, Bigeard E, Unrein F, Chambouvet A, Not F, Lara E, Devercelli M. Freshwater protists: unveiling the unexplored in a large floodplain system. Environ Microbiol 2021; 24:1731-1745. [PMID: 34783136 DOI: 10.1111/1462-2920.15838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/23/2021] [Accepted: 10/31/2021] [Indexed: 12/25/2022]
Abstract
Protists play a fundamental role in all ecosystems, but we are still far from estimating the total diversity of many lineages, in particular in highly diverse environments, such as freshwater. Here, we survey the protist diversity of the Paraná River using metabarcoding, and we applied an approach that includes sequence similarity and phylogeny to evaluate the degree of genetic novelty of the protists' communities against the sequences described in the reference database PR2 . We observed that ~28% of the amplicon sequence variants were classified as novel according to their similarity with sequences from the reference database; most of them were related to heterotrophic groups traditionally overlooked in freshwater systems. This lack of knowledge extended to those groups within the green algae (Archaeplastida) that are well documented such as Mamiellophyceae, and also to the less studied Pedinophyceae, for which we found sequences representing novel deep-branching clusters. Among the groups with potential novel protists, Bicosoecida (Stramenopiles) were the best represented, followed by Codosiga (Opisthokonta), and the Perkinsea (Alveolata). This illustrates the lack of knowledge on freshwater planktonic protists and also the need for isolation and/or cultivation of new organisms to better understand their role in ecosystem functioning.
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Affiliation(s)
- Sebastian Metz
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, F-29280, France.,Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Buenos Aires, Argentina
| | - Paula Huber
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil.,Instituto Nacional de Limnología (INALI), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Ciudad Universitaria, Santa Fe, Argentina
| | - Victoria Accattatis
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil
| | | | - Estelle Bigeard
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Buenos Aires, Argentina
| | | | - Fabrice Not
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Enrique Lara
- Real Jardín Botánico de Madrid, CSIC, Madrid, 28014, Spain
| | - Melina Devercelli
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil
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