1
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Partemi R, Debortoli N, Martínez A, Kamburska L, Souffreau C, Matheve H, Vantieghem P, De Meester L, Van Doninck K, Merckx T, Fontaneto D. Weak effect of urbanization on bdelloid rotifers living in lichens. R Soc Open Sci 2024; 11:231978. [PMID: 38633346 PMCID: PMC11021934 DOI: 10.1098/rsos.231978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 04/19/2024]
Abstract
Human activities have an overwhelming impact on the natural environment, leading to a deep biodiversity crisis whose effects range from genes to ecosystems. Here, we analysed the effect of such anthropogenic impacts on bdelloid rotifers (Rotifera Bdelloidea), for whom these effects are poorly understood. We targeted bdelloid rotifers living in lichen patches across urbanization gradients in Flanders and Brussels (Belgium). Urbanization was measured as the percentage of built-up area (BU) across different spatial scales, at circles from 50 to 3200 m of radius around the lichen. Urbanization effects on biodiversity were assessed on abundance, species richness and community-weighted mean body size of bdelloid rotifers, as well as on genetic diversity of a mitochondrial marker (cytochrome c oxidase subunit I) of one of the most common and widespread bdelloid species, Adineta vaga. Overall, no negative effect of urbanization was found at any diversity level and any spatial scale. Counterintuitively, the BU area quantified at the largest spatial scale had a positive effect on abundance. These results leave open the question of whether negative effects of urbanization are present for bdelloid rotifers, if they are mediated by other unexplored drivers, or if such effects are only visible at even larger spatial scales.
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Affiliation(s)
- Rebecca Partemi
- Department of Chemical and Geological Sciences, Modena and
Reggio-Emilia University, Modena41125, Italy
- National Research Council of Italy (CNR), Water Research
Institute (IRSA), Verbania Pallanza, 28922,
Italy
| | | | - Alejandro Martínez
- National Research Council of Italy (CNR), Water Research
Institute (IRSA), Verbania Pallanza, 28922,
Italy
| | - Lyudmila Kamburska
- National Research Council of Italy (CNR), Water Research
Institute (IRSA), Verbania Pallanza, 28922,
Italy
- National Biodiversity Future Center (NBFC), Palermo90133, Italy
| | - Caroline Souffreau
- Laboratory of Freshwater Ecology, Evolution & Conservation,
KU Leuven, Charles Deberiotstraat 32, Leuven3000, Belgium
| | - Hans Matheve
- Terrestrial Ecology Unit, Department of Biology, Ghent
University, Gent9000, Belgium
| | - Pieter Vantieghem
- Terrestrial Ecology Unit, Department of Biology, Ghent
University, Gent9000, Belgium
| | - Luc De Meester
- Laboratory of Freshwater Ecology, Evolution & Conservation,
KU Leuven, Charles Deberiotstraat 32, Leuven3000, Belgium
- Leibniz Institut für Gewässerökologie und Binnenfischerei
(IGB), Berlin12587, Germany
- Institute of Biology, Freie Universität Berlin, Berlin14195, Germany
| | - Karine Van Doninck
- Research Unit in Molecular Biology and Evolution, DBO,
Université libre de Bruxelles (ULB), Brussels1050, Belgium
| | - Thomas Merckx
- WILD, Biology Department, Vrije Universiteit Brussel
(VUB), Brussels1050, Belgium
| | - Diego Fontaneto
- National Research Council of Italy (CNR), Water Research
Institute (IRSA), Verbania Pallanza, 28922,
Italy
- National Biodiversity Future Center (NBFC), Palermo90133, Italy
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2
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Moris VC, Bruneau L, Berthe J, Heuskin AC, Penninckx S, Ritter S, Weber U, Durante M, Danchin EGJ, Hespeels B, Doninck KV. Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biol 2024; 22:11. [PMID: 38273318 PMCID: PMC10809525 DOI: 10.1186/s12915-023-01807-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species. RESULTS In this study, we analyzed the transcriptomic response of the bdelloid rotifer Adineta vaga to desiccation and to low- (X-rays) and high- (Fe) LET radiation to highlight the molecular and genetic mechanisms triggered by both stresses. We identified numerous genes encoding antioxidants, but also chaperones, that are constitutively highly expressed, which may contribute to the protection of proteins against oxidative stress during desiccation and ionizing radiation. We also detected a transcriptomic response common to desiccation and ionizing radiation with the over-expression of genes mainly involved in DNA repair and protein modifications but also genes with unknown functions that were bdelloid-specific. A distinct transcriptomic response specific to rehydration was also found, with the over-expression of genes mainly encoding Late Embryogenesis Abundant proteins, specific heat shock proteins, and glucose repressive proteins. CONCLUSIONS These results suggest that the extreme resistance of bdelloid rotifers to radiation might indeed be a consequence of their capacity to resist complete desiccation. This study paves the way to functional genetic experiments on A. vaga targeting promising candidate proteins playing central roles in radiation and desiccation resistance.
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Affiliation(s)
- Victoria C Moris
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium.
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium.
| | - Lucie Bruneau
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Jérémy Berthe
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Anne-Catherine Heuskin
- Namur Research Institute for Life Sciences (NARILIS), Laboratory of Analysis By Nuclear Reactions (LARN), University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet - Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070, Brussels, Belgium
| | - Sylvia Ritter
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Uli Weber
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Marco Durante
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 06903, Sophia Antipolis, France
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium
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3
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Nicolas E, Simion P, Guérineau M, Terwagne M, Colinet M, Virgo J, Lingurski M, Boutsen A, Dieu M, Hallet B, Van Doninck K. Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes. Nat Commun 2023; 14:7638. [PMID: 37993452 PMCID: PMC10665377 DOI: 10.1038/s41467-023-43075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga is used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis shows that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis reveals its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improves their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.
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Affiliation(s)
- Emilien Nicolas
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
| | - Paul Simion
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
- Université de Rennes, Ecosystèmes, biodiversité, évolution (ECOBIO UMR 6553), CNRS, Rennes, France
| | - Marc Guérineau
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Matthieu Terwagne
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Mathilde Colinet
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Julie Virgo
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Maxime Lingurski
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Anaïs Boutsen
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Marc Dieu
- Université de Namur, MaSUN-mass spectrometry facility, Namur, 5000, Belgium
| | - Bernard Hallet
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve, 1348, Belgium.
| | - Karine Van Doninck
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium.
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4
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Hespeels B, Fontaneto D, Cornet V, Penninckx S, Berthe J, Bruneau L, Larrick JW, Rapport E, Bailly J, Debortoli N, Iakovenko N, Janko K, Heuskin AC, Lucas S, Hallet B, Van Doninck K. Back to the roots, desiccation and radiation resistances are ancestral characters in bdelloid rotifers. BMC Biol 2023; 21:72. [PMID: 37024917 PMCID: PMC10080820 DOI: 10.1186/s12915-023-01554-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Bdelloid rotifers are micro-invertebrates distributed worldwide, from temperate latitudes to the most extreme areas of the planet like Antarctica or the Atacama Desert. They have colonized any habitat where liquid water is temporarily available, including terrestrial environments such as soils, mosses, and lichens, tolerating desiccation and other types of stress such as high doses of ionizing radiation (IR). It was hypothesized that bdelloid desiccation and radiation resistance may be attributed to their potential ability to repair DNA double-strand breaks (DSBs). Here, these properties are investigated and compared among nine bdelloid species collected from both mild and harsh habitats, addressing the correlation between the ability of bdelloid rotifers to survive desiccation and their capacity to repair massive DNA breakage in a phylogenetically explicit context. Our research includes both specimens isolated from habitats that experience frequent desiccation (at least 1 time per generation), and individuals sampled from habitats that rarely or never experienced desiccation. RESULTS Our analysis reveals that DNA repair prevails in somatic cells of both desiccation-tolerant and desiccation-sensitive bdelloid species after exposure to X-ray radiation. Species belonging to both categories are able to withstand high doses of ionizing radiation, up to 1000 Gy, without experiencing any negative effects on their survival. However, the fertility of two desiccation-sensitive species, Rotaria macrura and Rotaria rotatoria, was more severely impacted by low doses of radiation than that of desiccation-resistant species. Surprisingly, the radioresistance of desiccation-resistant species is not related to features of their original habitat. Indeed, bdelloids isolated from Atacama Desert or Antarctica were not characterized by a higher radioresistance than species found in more temperate environments. CONCLUSIONS Tolerance to desiccation and radiation are supported as ancestral features of bdelloid rotifers, with a group of species of the genus Rotaria having lost this trait after colonizing permanent water habitats. Together, our results provide a comprehensive overview of the evolution of desiccation and radiation resistance among bdelloid rotifers.
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Affiliation(s)
- Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium.
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania Pallanza, Italy
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Valérie Cornet
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Jérémy Berthe
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
- Research Unit in Molecular Biology and Evolution, DBO, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Lucie Bruneau
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - James W Larrick
- Panorama Research Institute, Sunnyvale, CA, USA
- SETI Institute, Mountain View, CA, USA
| | - Eloïse Rapport
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Jérémie Bailly
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Nicolas Debortoli
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Nataliia Iakovenko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, CZ - 165 21 Praha 6, Suchdol, Czech Republic
- Faculty of Science, University of Ostrava, Chittussiho 10, 71000, Ostrava, Czech Republic
| | - Karel Janko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
- Faculty of Science, University of Ostrava, Chittussiho 10, 71000, Ostrava, Czech Republic
| | - Anne-Catherine Heuskin
- Laboratory of Analysis by Nuclear Reactions (LARN), Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Stéphane Lucas
- Laboratory of Analysis by Nuclear Reactions (LARN), Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Bernard Hallet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium.
- Research Unit in Molecular Biology and Evolution, DBO, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium.
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5
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Zeng C, Tang Y, Vastrade M, Coughlan NE, Zhang T, Cai Y, Van Doninck K, Li D. Salinity appears to be the main factor shaping spatial
COI
diversity of Corbicula lineages within the Chinese Yangtze River Basin. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Cong Zeng
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology Hunan Agricultural University Changsha China
- School of Oceanography Shanghai Jiao Tong University Shanghai China
| | - Yangxin Tang
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology Hunan Agricultural University Changsha China
| | - Martin Vastrade
- Laboratory of Evolutionary Genetics and Ecology; Research Unit in Environmental and Evolutionary Biology; Institute of Life, Earth and Environment (ILEE) University of Namur Namur Belgium
| | - Neil E. Coughlan
- School of Biological, Earth and Environmental Sciences University College Cork Cork Ireland
| | - Ting Zhang
- College of Chemistry and Chemical Engineering Central South University Changsha China
| | - Yongjiu Cai
- Nanjing Institute of Geography and Limnology Chinese Academy of Sciences Nanjing China
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology; Research Unit in Environmental and Evolutionary Biology; Institute of Life, Earth and Environment (ILEE) University of Namur Namur Belgium
- Molecular Biology & Evolution Université Libre de Bruxelles Brussels Belgium
| | - Deliang Li
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology Hunan Agricultural University Changsha China
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6
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Terwagne M, Nicolas E, Hespeels B, Herter L, Virgo J, Demazy C, Heuskin AC, Hallet B, Van Doninck K. DNA repair during nonreductional meiosis in the asexual rotifer Adineta vaga. Sci Adv 2022; 8:eadc8829. [PMID: 36449626 PMCID: PMC9710870 DOI: 10.1126/sciadv.adc8829] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Rotifers of the class Bdelloidea are microscopic animals notorious for their long-term persistence in the apparent absence of sexual reproduction and meiotic recombination. This evolutionary paradox is often counterbalanced by invoking their ability to repair environmentally induced genome breakage. By studying the dynamics of DNA damage response in the bdelloid species Adineta vaga, we found that it occurs rapidly in the soma, producing a partially reassembled genome. By contrast, germline DNA repair is delayed to a specific time window of oogenesis during which homologous chromosomes adopt a meiotic-like juxtaposed configuration, resulting in accurate reconstitution of the genome in the offspring. Our finding that a noncanonical meiosis is the mechanism of germline DNA repair in bdelloid rotifers gives previously unidentified insights on their enigmatic long-term evolution.
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Affiliation(s)
- Matthieu Terwagne
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
| | - Emilien Nicolas
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
- Research Unit of Molecular Biology and Evolution (MBE), Université Libre de Bruxelles (ULB), Brussels, 1050, Belgium
| | - Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment (ILEE), University of Namur (UNamur), Namur 5000, Belgium
| | - Ludovic Herter
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Julie Virgo
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Catherine Demazy
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Cellular Biology Research Unit (URBC), University of Namur (UNamur), Namur 5000, Belgium
| | - Anne-Catherine Heuskin
- Laboratory of Analysis by Nuclear Reaction (LARN), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Bernard Hallet
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Research Unit of Molecular Biology and Evolution (MBE), Université Libre de Bruxelles (ULB), Brussels, 1050, Belgium
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment (ILEE), University of Namur (UNamur), Namur 5000, Belgium
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7
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Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot JF, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Sci Adv 2021; 7:eabg4216. [PMID: 34613768 PMCID: PMC8494291 DOI: 10.1126/sciadv.abg4216] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g., chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success.
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Affiliation(s)
- Paul Simion
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Jitendra Narayan
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Antoine Houtain
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Alessandro Derzelle
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Emilien Nicolas
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Rohan Arora
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Marie Cariou
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | | | - Clément Gilbert
- Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, CNRS, IRD, UMR, 91198 Gif-sur-Yvette, France
| | - Nadège Guiglielmoni
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Djampa K. L. Kozlowski
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Antoine Limasset
- Université de Lille, CNRS, UMR 9189 - CRIStAL, 59655 Villeneuve-d’Ascq, France
| | - Marc Llirós
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Institut d’Investigació Biomédica de Girona, Malalties Digestives i Microbiota, 17190 Salt, Spain
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Matthieu Terwagne
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Julie Virgo
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Richard Cordaux
- Ecologie et Biologie des interactions, Université de Poitiers, UMR CNRS 7267, 5 rue Albert Turpain, 86073 Poitiers, France
| | - Etienne G. J. Danchin
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Bernard Hallet
- LIBST, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, Louvain-la-Neuve 1348, Belgium
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Thomas Lenormand
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Jean-Francois Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
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8
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Coughlan NE, Cunningham EM, Cuthbert RN, Joyce PWS, Anastácio P, Banha F, Bonel N, Bradbeer SJ, Briski E, Butitta VL, Čadková Z, Dick JTA, Douda K, Eagling LE, Ferreira‐Rodríguez N, Hünicken LA, Johansson ML, Kregting L, Labecka AM, Li D, Liquin F, Marescaux J, Morris TJ, Nowakowska P, Ożgo M, Paolucci EM, Peribáñez MA, Riccardi N, Smith ERC, Spear MJ, Steffen GT, Tiemann JS, Urbańska M, Van Doninck K, Vastrade M, Vong GYW, Wawrzyniak‐Wydrowska B, Xia Z, Zeng C, Zhan A, Sylvester F. Biometric conversion factors as a unifying platform for comparative assessment of invasive freshwater bivalves. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Guiglielmoni N, Houtain A, Derzelle A, Van Doninck K, Flot JF. Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms. BMC Bioinformatics 2021; 22:303. [PMID: 34090340 PMCID: PMC8178825 DOI: 10.1186/s12859-021-04118-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/02/2021] [Indexed: 12/21/2022] Open
Abstract
Background Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are usually error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Failure to properly collapse haplotypes results in fragmented and structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, yet this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking. Results We tested different assembly strategies on the genome of the rotifer Adineta vaga, a non-model organism for which high coverages of both PacBio and Nanopore reads were available. The assemblers we tested (Canu, Flye, NextDenovo, Ra, Raven, Shasta and wtdbg2) exhibited strikingly different behaviors when dealing with highly heterozygous regions, resulting in variable amounts of uncollapsed haplotypes. Filtering reads generally improved haploid assemblies, and we also benchmarked three post-processing tools aimed at detecting and purging uncollapsed haplotypes in long-read assemblies: HaploMerger2, purge_haplotigs and purge_dups. Conclusions We provide a thorough evaluation of popular assemblers on a non-model eukaryote genome with variable levels of heterozygosity. Our study highlights several strategies using pre and post-processing approaches to generate haploid assemblies with high continuity and completeness. This benchmark will help users to improve haploid assemblies of non-model organisms, and evaluate the quality of their own assemblies. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04118-3.
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Affiliation(s)
- Nadège Guiglielmoni
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Antoine Houtain
- Laboratoire d'Ecologie et Génétique Evolutive, Université de Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Alessandro Derzelle
- Laboratoire d'Ecologie et Génétique Evolutive, Université de Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Karine Van Doninck
- Laboratoire d'Ecologie et Génétique Evolutive, Université de Namur, Rue de Bruxelles 61, 5000, Namur, Belgium.,Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
| | - Jean-François Flot
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)², Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
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10
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Hespeels B, Penninckx S, Cornet V, Bruneau L, Bopp C, Baumlé V, Redivo B, Heuskin AC, Moeller R, Fujimori A, Lucas S, Van Doninck K. Iron Ladies - How Desiccated Asexual Rotifer Adineta vaga Deal With X-Rays and Heavy Ions? Front Microbiol 2020; 11:1792. [PMID: 32849408 PMCID: PMC7412981 DOI: 10.3389/fmicb.2020.01792] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/09/2020] [Indexed: 11/29/2022] Open
Abstract
Space exposure experiments from the last 15 years have unexpectedly shown that several terrestrial organisms, including some multi-cellular species, are able to survive in open space without protection. The robustness of bdelloid rotifers suggests that these tiny creatures can possibly be added to the still restricted list of animals that can deal with the exposure to harsh condition of space. Bdelloids are one of the smallest animals on Earth. Living all over the world, mostly in semi-terrestrial environments, they appear to be extremely stress tolerant. Their desiccation tolerance at any stage of their life cycle is known to confer tolerance to a variety of stresses including high doses of radiation and freezing. In addition, they constitute a major scandal in evolutionary biology due to the putative absence of sexual reproduction for at least 60 million years. Adineta vaga, with its unique characteristics and a draft genome available, was selected by ESA (European Space Agency) as a model system to study extreme resistance of organisms exposed to space environment. In this manuscript, we documented the resistance of desiccated A. vaga individuals exposed to increasing doses of X-ray, protons and Fe ions. Consequences of exposure to different sources of radiation were investigated in regard to the cellular type including somatic (survival assay) and germinal cells (fertility assay). Then, the capacity of A. vaga individuals to repair DNA DSB induced by different source of radiation was investigated. Bdelloid rotifers represent a promising model in order to investigate damage induced by high or low LET radiation. The possibility of exposure both on hydrated or desiccated specimens may help to decipher contribution of direct and indirect radiation damage on biological processes. Results achieved through this study consolidate our knowledge about the radioresistance of A. vaga and improve our capacity to compare extreme resistance against radiation among living organisms including metazoan.
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Affiliation(s)
- Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.,Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium
| | - Sébastien Penninckx
- Laboratory of Analysis by Nuclear Reaction (LARN), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Valérie Cornet
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium
| | - Lucie Bruneau
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Cécile Bopp
- Laboratory of Analysis by Nuclear Reaction (LARN), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Véronique Baumlé
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.,Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium
| | - Baptiste Redivo
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium
| | - Anne-Catherine Heuskin
- Laboratory of Analysis by Nuclear Reaction (LARN), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Ralf Moeller
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany.,Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg (BRSU), Rheinbach, Germany
| | - Akira Fujimori
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences (NIRS), Chiba, Japan
| | - Stephane Lucas
- Laboratory of Analysis by Nuclear Reaction (LARN), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.,Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium
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11
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Quinet T, Samba-Louaka A, Héchard Y, Van Doninck K, Van der Henst C. Delayed cytokinesis generates multinuclearity and potential advantages in the amoeba Acanthamoeba castellanii Neff strain. Sci Rep 2020; 10:12109. [PMID: 32694508 PMCID: PMC7374626 DOI: 10.1038/s41598-020-68694-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/26/2020] [Indexed: 12/29/2022] Open
Abstract
Multinuclearity is a widespread phenomenon across the living world, yet how it is achieved, and the potential related advantages, are not systematically understood. In this study, we investigate multinuclearity in amoebae. We observe that non-adherent amoebae are giant multinucleate cells compared to adherent ones. The cells solve their multinuclearity by a stretchy cytokinesis process with cytosolic bridge formation when adherence resumes. After initial adhesion to a new substrate, the progeny of the multinucleate cells is more numerous than the sibling cells generated from uninucleate amoebae. Hence, multinucleate amoebae show an advantage for population growth when the number of cells is quantified over time. Multiple nuclei per cell are observed in different amoeba species, and the lack of adhesion induces multinuclearity in diverse protists such as Acanthamoeba castellanii, Vermamoeba vermiformis, Naegleria gruberi and Hartmannella rhysodes. In this study, we observe that agitation induces a cytokinesis delay, which promotes multinuclearity. Hence, we propose the hypothesis that multinuclearity represents a physiological adaptation under non-adherent conditions that can lead to biologically relevant advantages.
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Affiliation(s)
- Théo Quinet
- Laboratory of Evolutionary Genetics and Ecology, URBE, University of Namur, Namur, Belgium
| | - Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions, Equipe Microbiologie de L'Eau, Université de Poitiers, UMR CNRS 7267, 86073, Poitiers, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions, Equipe Microbiologie de L'Eau, Université de Poitiers, UMR CNRS 7267, 86073, Poitiers, France
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, URBE, University of Namur, Namur, Belgium
| | - Charles Van der Henst
- Laboratory of Evolutionary Genetics and Ecology, URBE, University of Namur, Namur, Belgium. .,Research Unit in the Biology of Microorganisms (URBM), NARILIS, University of Namur (UNamur), Namur, Belgium. .,Microbial Resistance and Drug Discovery, Center for Structural Biology (CSB), Flanders Institute for Biotechnology (VIB), Vrije Universiteit Brussel (VUB), Pleinlaan 2, Building E-3, 1050, Brussels, Belgium. .,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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12
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Piano E, Souffreau C, Merckx T, Baardsen LF, Backeljau T, Bonte D, Brans KI, Cours M, Dahirel M, Debortoli N, Decaestecker E, De Wolf K, Engelen JMT, Fontaneto D, Gianuca AT, Govaert L, Hanashiro FTT, Higuti J, Lens L, Martens K, Matheve H, Matthysen E, Pinseel E, Sablon R, Schön I, Stoks R, Van Doninck K, Van Dyck H, Vanormelingen P, Van Wichelen J, Vyverman W, De Meester L, Hendrickx F. Urbanization drives cross-taxon declines in abundance and diversity at multiple spatial scales. Glob Chang Biol 2020; 26:1196-1211. [PMID: 31755626 DOI: 10.1111/gcb.14934] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/01/2019] [Indexed: 05/12/2023]
Abstract
The increasing urbanization process is hypothesized to drastically alter (semi-)natural environments with a concomitant major decline in species abundance and diversity. Yet, studies on this effect of urbanization, and the spatial scale at which it acts, are at present inconclusive due to the large heterogeneity in taxonomic groups and spatial scales at which this relationship has been investigated among studies. Comprehensive studies analysing this relationship across multiple animal groups and at multiple spatial scales are rare, hampering the assessment of how biodiversity generally responds to urbanization. We studied aquatic (cladocerans), limno-terrestrial (bdelloid rotifers) and terrestrial (butterflies, ground beetles, ground- and web spiders, macro-moths, orthopterans and snails) invertebrate groups using a hierarchical spatial design, wherein three local-scale (200 m × 200 m) urbanization levels were repeatedly sampled across three landscape-scale (3 km × 3 km) urbanization levels. We tested for local and landscape urbanization effects on abundance and species richness of each group, whereby total richness was partitioned into the average richness of local communities and the richness due to variation among local communities. Abundances of the terrestrial active dispersers declined in response to local urbanization, with reductions up to 85% for butterflies, while passive dispersers did not show any clear trend. Species richness also declined with increasing levels of urbanization, but responses were highly heterogeneous among the different groups with respect to the richness component and the spatial scale at which urbanization impacts richness. Depending on the group, species richness declined due to biotic homogenization and/or local species loss. This resulted in an overall decrease in total richness across groups in urban areas. These results provide strong support to the general negative impact of urbanization on abundance and species richness within habitat patches and highlight the importance of considering multiple spatial scales and taxa to assess the impacts of urbanization on biodiversity.
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Affiliation(s)
- Elena Piano
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Thomas Merckx
- Behavioural Ecology and Conservation Group, Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Lisa F Baardsen
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Kristien I Brans
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Marie Cours
- Royal Belgian Institute of Natural Sciences, OD Natural Environment, Brussels, Belgium
| | - Maxime Dahirel
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
- Ecosystems, Biodiversity and Evolution Unit, Université de Rennes 1 (CNRS), Rennes, France
| | - Nicolas Debortoli
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Namur, Belgium
| | | | - Katrien De Wolf
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Jessie M T Engelen
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Diego Fontaneto
- CNR-IRSA, National Research Council, Water Research Institute, Verbania-Pallanza, Italy
| | - Andros T Gianuca
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
- Department of Ecology, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Lynn Govaert
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Fabio T T Hanashiro
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Janet Higuti
- Centre of Research in Limnology, Ichthyology and Aquaculture/PEA, State University of Maringá, Maringá, Paraná, Brazil
| | - Luc Lens
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Natural Environment, Brussels, Belgium
- Laboratory of Limnology, Biology Department, Ghent University, Ghent, Belgium
| | - Hans Matheve
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Erik Matthysen
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Eveline Pinseel
- Laboratory of Protistology & Aquatic Ecology, Biology Department, Ghent University, Ghent, Belgium
- Research Department, Meise Botanic Garden, Meise, Belgium
| | - Rose Sablon
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
| | - Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Natural Environment, Brussels, Belgium
- Zoology Research Group, University of Hasselt, Hasselt, Belgium
| | - Robby Stoks
- Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, Leuven, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Namur, Belgium
| | - Hans Van Dyck
- Behavioural Ecology and Conservation Group, Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Pieter Vanormelingen
- Laboratory of Protistology & Aquatic Ecology, Biology Department, Ghent University, Ghent, Belgium
| | - Jeroen Van Wichelen
- Laboratory of Protistology & Aquatic Ecology, Biology Department, Ghent University, Ghent, Belgium
- Aquatic Management, Research Institute for Nature and Forest (INBO), Brussels, Belgium
| | - Wim Vyverman
- Laboratory of Protistology & Aquatic Ecology, Biology Department, Ghent University, Ghent, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
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13
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Merckx T, Souffreau C, Kaiser A, Baardsen LF, Backeljau T, Bonte D, Brans KI, Cours M, Dahirel M, Debortoli N, De Wolf K, Engelen JMT, Fontaneto D, Gianuca AT, Govaert L, Hendrickx F, Higuti J, Lens L, Martens K, Matheve H, Matthysen E, Piano E, Sablon R, Schön I, Van Doninck K, De Meester L, Van Dyck H. Body-size shifts in aquatic and terrestrial urban communities. Nature 2018; 558:113-116. [PMID: 29795350 DOI: 10.1038/s41586-018-0140-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 04/11/2018] [Indexed: 01/09/2023]
Abstract
Body size is intrinsically linked to metabolic rate and life-history traits, and is a crucial determinant of food webs and community dynamics1,2. The increased temperatures associated with the urban-heat-island effect result in increased metabolic costs and are expected to drive shifts to smaller body sizes 3 . Urban environments are, however, also characterized by substantial habitat fragmentation 4 , which favours mobile species. Here, using a replicated, spatially nested sampling design across ten animal taxonomic groups, we show that urban communities generally consist of smaller species. In addition, although we show urban warming for three habitat types and associated reduced community-weighted mean body sizes for four taxa, three taxa display a shift to larger species along the urbanization gradients. Our results show that the general trend towards smaller-sized species is overruled by filtering for larger species when there is positive covariation between size and dispersal, a process that can mitigate the low connectivity of ecological resources in urban settings 5 . We thus demonstrate that the urban-heat-island effect and urban habitat fragmentation are associated with contrasting community-level shifts in body size that critically depend on the association between body size and dispersal. Because body size determines the structure and dynamics of ecological networks 1 , such shifts may affect urban ecosystem function.
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Affiliation(s)
- Thomas Merckx
- Behavioural Ecology and Conservation Group, Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Aurélien Kaiser
- Behavioural Ecology and Conservation Group, Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Lisa F Baardsen
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Thierry Backeljau
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium.,Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Kristien I Brans
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Marie Cours
- Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Maxime Dahirel
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium.,ECOBIO (Ecosystèmes, biodiversité, évolution), CNRS, Université de Rennes, Rennes, France
| | - Nicolas Debortoli
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Namur, Belgium
| | - Katrien De Wolf
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Jessie M T Engelen
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Diego Fontaneto
- National Research Council, Institute of Ecosystem Study, Verbania-Pallanza, Italy
| | - Andros T Gianuca
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany.,Helmholtz Centre for Environmental Research (UFZ), Department of Community Ecology, Halle, Germany
| | - Lynn Govaert
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Frederik Hendrickx
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Janet Higuti
- Centre of Research in Limnology, Ichthyology and Aquaculture/PEA, State University of Maringá, Maringá, Brazil
| | - Luc Lens
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Koen Martens
- Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Limnology Research Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Hans Matheve
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Erik Matthysen
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Elena Piano
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Rose Sablon
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Isa Schön
- Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Zoology Research Group, University of Hasselt, Hasselt, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Namur, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Hans Van Dyck
- Behavioural Ecology and Conservation Group, Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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14
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15
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Debortoli N, Li X, Eyres I, Fontaneto D, Hespeels B, Tang CQ, Flot JF, Van Doninck K. Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex. Curr Biol 2016; 26:723-32. [PMID: 26948882 DOI: 10.1016/j.cub.2016.01.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/27/2015] [Accepted: 01/13/2016] [Indexed: 10/22/2022]
Abstract
Although strict asexuality is supposed to be an evolutionary dead end, morphological, cytogenetic, and genomic data suggest that bdelloid rotifers, a clade of microscopic animals, have persisted and diversified for more than 60 Myr in an ameiotic fashion. Moreover, the genome of bdelloids of the genus Adineta comprises 8%-10% of genes of putative non-metazoan origin, indicating that horizontal gene transfers are frequent within this group and suggesting that this mechanism may also promote genetic exchanges among bdelloids as well. To test this hypothesis, we used five independent sequence markers to study the genetic diversity of 576 Adineta vaga individuals from a park in Belgium. Haplowebs and GMYC analyses revealed the existence of six species among our sampled A. vaga individuals, with strong evidence of both intra- and interspecific recombination. Comparison of genomic regions of three allele-sharing individuals further revealed signatures of genetic exchanges scattered among regions evolving asexually. Our findings suggest that bdelloids evolve asexually but exchange DNA horizontally both within and between species.
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Affiliation(s)
- Nicolas Debortoli
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Xiang Li
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Isobel Eyres
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Diego Fontaneto
- Institute of Ecosystem Study, National Research Council, Largo Tonolli 50, 28922 Verbania Pallanza, Italy
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Cuong Q Tang
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jean-François Flot
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050 Bruxelles, Belgium.
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium.
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Marescaux J, von Oheimb KCM, Etoundi E, von Oheimb PV, Albrecht C, Wilke T, Van Doninck K. Unravelling the invasion pathways of the quagga mussel (Dreissena rostriformis) into Western Europe. Biol Invasions 2015. [DOI: 10.1007/s10530-015-1005-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pigneur LM, Etoundi E, Aldridge DC, Marescaux J, Yasuda N, Van Doninck K. Genetic uniformity and long-distance clonal dispersal in the invasive androgenetic Corbicula clams. Mol Ecol 2014; 23:5102-16. [PMID: 25208249 DOI: 10.1111/mec.12912] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/26/2014] [Accepted: 08/27/2014] [Indexed: 11/28/2022]
Abstract
The clam genus Corbicula is an interesting model system to study the evolution of reproductive modes as it includes both sexual and asexual (androgenetic) lineages. While the sexual populations are restricted to the native Asian areas, the androgenetic lineages are widely distributed being also found in America and Europe where they form a major aquatic invasive pest. We investigated the genetic diversity of native and invasive Corbicula populations through a worldwide sampling. The use of mitochondrial and nuclear (microsatellite) markers revealed an extremely low diversity in the invasive populations with only four, undiversified, genetic lineages distributed across Europe and America. On the contrary, in the native populations, both sexual and androgenetic lineages exhibited much higher genetic diversity. Remarkably, the most abundant and widely distributed invasive forms, the so-called form A and form R found in America and Europe respectively, are fixed for the same single COI (cytochrome c oxydase subunit I) haplotype and same multilocus genotype. This suggests that form R, observed in Europe since the 1980s, derived directly from form A found in America since the 1920s. In addition, this form shares alleles with some Japanese populations, indicating a Japanese origin for this invasive lineage. Finally, our study suggests that few androgenetic Corbicula individuals successfully invaded the non-native range and then dispersed clonally. This is one striking case of genetic paradox raising the issue of invasive and evolutionary success of genetically undiversified populations.
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Affiliation(s)
- Lise-Marie Pigneur
- Laboratory of Evolutionary Genetics and Ecology, Research Unit in Environmental and Evolutionary Biology, University of Namur, 5000, Namur, Belgium
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Abstract
The zebra mussel (Dreissena polymorpha) and the quagga mussel (Dreissena rostriformis bugensis) are considered as the most competitive invaders in freshwaters of Europe and North America. Although shell characteristics exist to differentiate both species, phenotypic plasticity in the genus Dreissena does not always allow a clear identification. Therefore, the need to find an accurate identification method is essential. DNA barcoding has been proven to be an adequate procedure to discriminate species. The cytochrome c oxidase subunit I mitochondrial gene (COI) is considered as the standard barcode for animals. We tested the use of this gene as an efficient DNA barcode and found that it allow rapid and accurate identification of adult Dreissena individuals.
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Affiliation(s)
- Jonathan Marescaux
- Laboratory of Evolutionary Genetics and Ecology, Research Unit in Environmental and Evolutionary Biology, Department of Biology, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, Research Unit in Environmental and Evolutionary Biology, Department of Biology, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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Pigneur LM, Marescaux J, Roland K, Etoundi E, Descy JP, Van Doninck K. Phylogeny and androgenesis in the invasive Corbicula clams (Bivalvia, Corbiculidae) in Western Europe. BMC Evol Biol 2011; 11:147. [PMID: 21619630 PMCID: PMC3126740 DOI: 10.1186/1471-2148-11-147] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 05/27/2011] [Indexed: 11/15/2022] Open
Abstract
Background The genus Corbicula is one of the most invasive groups of molluscs. It includes both sexual and androgenetic lineages. The present study re-assessed the different morphotypes and haplotypes of West European Corbicula in order to clarify their taxonomic identification and phylogenetic relationships with American and Asian Corbicula clams. We studied several populations from West European river basins (Meuse, Seine, Rhine and Rhône) through an "integrative taxonomy" approach. We combined morphology, partial mitochondrial COI and cyt b sequences and eleven microsatellite loci. Furthermore, we looked for discrepancies between mtDNA and nrDNA/morphology, indicative of androgenesis between lineages. Results There are three Corbicula morphotypes in Western Europe associated to three mitochondrial lineages and three genotypes. Form R shares the same COI haplotype as the American form A and the Japanese C. leana. Form S and the American form C have the same haplotype, although their morphologies seem divergent. The European form Rlc belongs to the same mitochondrial lineage as both the American form B and the Asian C. fluminea. Interestingly, within each haplotype/genotype or lineage, no genetic diversity was found although their invasive success is high. Moreover, we detected rare mismatches between mtDNA and nrDNA/morphology, indicative of androgenesis and mitochondrial capture between form R and form S and therefore challenging the phylogenetic relatedness and the species status within this genus. The global phylogenetic analysis revealed that the sexual Corbicula lineages seem restricted to the native areas while their androgenetic relatives are widespread and highly invasive. Conclusions We clarified the discrepancies and incongruent results found in the literature about the European morphotypes of Corbicula and associated mitochondrial lineages. The three West European morphotypes belong to three distinct nuclear and mitochondrial lineages. However mitochondrial capture occurs in sympatric populations of forms R and S. The species status of the morphotypes therefore remains doubtful. Moreover the androgenetic lineages seem widely distributed compared to their sexual relatives, suggesting that androgenesis and invasive success may be linked in the genus Corbicula.
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Affiliation(s)
- Lise-Marie Pigneur
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Belgium.
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Abstract
Rotifers of Class Bdelloidea are abundant freshwater invertebrates known for their remarkable ability to survive desiccation and their lack of males and meiosis. Sequencing and annotation of approximately 50-kb regions containing the four hsp82 heat shock genes of the bdelloid Philodina roseola, each located on a separate chromosome, have suggested that its genome is that of a degenerate tetraploid. In order to determine whether a similar structure exists in a bdelloid distantly related to P. roseola and if degenerate tetraploidy was established before the two species separated, we sequenced regions containing the hsp82 genes of a bdelloid belonging to a different family, Adineta vaga, and the histone gene clusters of P. roseola and A. vaga. Our findings are entirely consistent with degenerate tetraploidy and show that it was established before the two bdelloid families diverged and therefore probably before the bdelloid radiation.
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Affiliation(s)
- Jae H Hur
- Department of Molecular and Cellular Biology, Harvard University, USA
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Abstract
Reproduction is a vital characteristic of life, and sex is the most common reproductive mode in the eukaryotic world. Sex and reproduction are not necessarily linked mechanisms: Sexuality without reproduction exists, while several forms of asexual reproduction are known. The occurrence of sexuality itself is paradoxical, as it is very costly in evolutionary terms. Most of the hypotheses (more than 20) attempting to explain the prevalence of sex fall into two categories: Sex either creates good gene combinations for adaptation to environments or eliminates bad gene combinations counteracting the accumulation of mutations. In spite of this apparent wealth of beneficial effects of sex, asexuality is not rare. Most eukaryotic, asexual lineages are short-lived and can only persist through the presence of sexual roots, but at least two animal groups, bdelloid rotifers and darwinulid ostracods, seem to claim the status of ancient asexuals. Research on (a)sexuality is relevant to astrobiology in a number of ways. First, strong relationships between the origin and persistence of life in extreme environments and reproductive mode are known. Second, the "habitability" of nonterrestrial environments to life greatly depends on reproductive mode. Whereas asexuals can do equally well or better in harsh environments, they fail to adapt fast enough to changing abiotic and biotic environments. Third, it has been shown that plants reproduce mainly asexually in space, and sperm production and motility in some vertebrates are hampered. Both findings indicate that extraterrestrial life under conditions different from Earth might be dominated by asexual reproduction. Finally, for exchange of biological material between planets, the choice of reproductive mode will be important.
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Affiliation(s)
- Karine Van Doninck
- Freshwater Biology Section, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.
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Gandolfi A, Todeschi EBA, Van Doninck K, Rossi V, Menozzi P. Salinity tolerance ofDarwinula stevensoni(Crustacea, Ostracoda). ACTA ACUST UNITED AC 2001. [DOI: 10.1080/11250000109356384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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