1
|
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] [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.
Collapse
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
| |
Collapse
|
2
|
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] [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.
Collapse
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.
| |
Collapse
|
3
|
Fleming JF. The wealth of shared resources: Improving molecular taxonomy using eDNA and public databases. ZOOL SCR 2023. [DOI: 10.1111/zsc.12591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
|
4
|
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] [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.
Collapse
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
| |
Collapse
|
5
|
Simultaneous Metabarcoding of Eukaryotes and Prokaryotes to Elucidate the Community Structures within Tardigrade Microhabitats. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12030110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tardigrades are microscopic invertebrates that can withstand complete desiccation, but their interspecies interactions with prokaryotes and eukaryotes within their microhabitat remain relatively unexplored. Here, I utilized combined metabarcoding of eukaryotes and prokaryotes to simultaneously identify entire community structures within xeric and mesic mosses that harbor tardigrades. The populations of organisms within the microecosystems were successfully determined in 45 xeric moss samples and 47 mesic moss samples. Organismal composition was largely consistent regardless of the moss/lichen substrate, but significantly varied in the two tested locations, possibly because of the differences in environmental humidity. Xeric mosses containing xerophilic tardigrades and other anhydrobiotic invertebrates tended to have significantly limited biological diversity and prokaryotic population dominated by cyanobacteria, suggesting a selection due to extreme desiccation. A combined metabarcoding approach to identify both eukaryotes and prokaryotes can successfully elucidate community structures within microscopic ecosystems, and this can be a potential approach to study the microecology of meiofauna, including tardigrades.
Collapse
|
6
|
Olah Z, Bush AI, Aleksza D, Galik B, Ivitz E, Macsai L, Janka Z, Karman Z, Kalman J, Datki Z. Novel in vivo experimental viability assays with high sensitivity and throughput capacity using a bdelloid rotifer. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 144:115-122. [PMID: 28605645 DOI: 10.1016/j.ecoenv.2017.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/29/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Rotifers have been used in biological research as well-characterized models of aging. Their multi-organ characters and their sensitivity for chemicals and environmental changes make them useful as in vivo toxicological and lifespan models. Our aim was to create a bdelloid rotifer model to use in high-throughput viability and non-invasive assays. In order to identify our species Philodina acuticornis odiosa (PA), 18S rDNA-based phylogenetic analysis was carried out and their species-specific morphological markers identified. To execute the rotifer-based experiments, we developed an oil-covered water-drop methodology adapted from human in vitro fertilization techniques. This enables toxicological observations of individual one-housed rotifers in a closed and controllable micro-environment for up to several weeks. Hydrogen peroxide (H2O2) and sodium azide (NaN3) exposures were used as well-understood toxins. The toxicity and survival lifespan (TSL), the bright light disturbance (BLD) the mastax contraction frequency (MCF) and the cellular reduction capacity (CRC), indices were recorded. These newly developed assays were used to test the effects of lethal and sublethal doses of the toxins. The results showed the expected dose-dependent decrease in indices. These four different assays can either be used independently or as an integrated system for studying rotifers. These new indices render the PA invertebrate rotifer model a quantitative system for measuring viability, toxicity and lifespan (with TSL), systemic reaction capacity (with BLD), organic functionality (with MCF) and reductive capability of rotifers (with CRC), in vivo. This novel multi-level system is a reliable, sensitive and replicable screening tool with potential application in pharmaceutical science.
Collapse
Affiliation(s)
- Zita Olah
- Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Ashley I Bush
- Oxidation Biology Unit, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - David Aleksza
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Bence Galik
- Bioinformatics & Scientific Computing, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Eszter Ivitz
- Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Lilla Macsai
- Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Zoltan Janka
- Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Zoltan Karman
- Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Janos Kalman
- Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Zsolt Datki
- Department of Psychiatry, University of Szeged, Szeged, Hungary.
| |
Collapse
|
7
|
Freeze-thaw revival of rotifers and algae in a desiccated, high-elevation (5500 meters) microbial mat, high Andes, Perú. Extremophiles 2017; 21:573-580. [PMID: 28321614 DOI: 10.1007/s00792-017-0926-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/06/2017] [Indexed: 12/24/2022]
Abstract
This is the first study of the highest elevation cyanobacteria-dominated microbial mat yet described. The desiccated mat was sampled in 2010 from an ephemeral rock pool at 5500 m above sea level in the Cordillera Vilcanota of southern Perú. After being frozen for 6 years at -20 °C in the lab, pieces of the mat were sequenced to fully characterize both the 16 and 18S microbial communities and experiments were conducted to determine if organisms in the mat could revive and become active under the extreme freeze-thaw conditions that these mats experience in the field. Sequencing revealed an unexpectedly diverse, multi-trophic microbial community with 16S OTU richness comparable to similar, seasonally desiccated mats from the Dry Valleys of Antarctica and low elevation sites in the Atacama Desert region. The bacterial community of the mat was dominated by phototrophs in the Cyanobacteria (Nostoc) and the Rhodospirillales, whereas the eukaryotic community was dominated by predators such as bdelloid rotifers (Philodinidae). Microcosm experiments showed that bdelloid rotifers in the mat were able to come out of dormancy and actively forage even under realistic field conditions (diurnal temperature fluctuations of -12 °C at night to + 27 °C during the day), and after being frozen for 6 years. Our results broaden our understanding of the diversity of life in periodically desiccated, high-elevation habitats and demonstrate that extreme freeze-thaw cycles per se are not a major factor limiting the development of at least some members of these unique microbial mat systems.
Collapse
|
8
|
Velasco-Castrillón A, McInnes SJ, Schultz MB, Arróniz-Crespo M, D'Haese CA, Gibson JAE, Adams BJ, Page TJ, Austin AD, Cooper SJB, Stevens MI. Mitochondrial DNA analyses reveal widespread tardigrade diversity in Antarctica. INVERTEBR SYST 2015. [DOI: 10.1071/is14019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Antarctica contains some of the most challenging environmental conditions on the planet due to freezing temperatures, prolonged winters and lack of liquid water. Whereas 99.7% of Antarctica is permanently covered by ice and snow, some coastal areas and mountain ridges have remained ice-free and are able to sustain populations of microinvertebrates. Tardigrades are one of the more dominant groups of microfauna in soil and limno-terrestrial habitats, but little is known of their diversity and distribution across Antarctica. Here, we examine tardigrades sampled from across an extensive region of continental Antarctica, and analyse and compare their partial mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences with those from the Antarctic Peninsula, maritime and sub-Antarctica, Tierra del Fuego and other worldwide locations in order to recognise operational taxonomic units (OTUs). From 439 new tardigrade COI sequences, we identified 98 unique haplotypes (85 from Antarctica) belonging to Acutuncus, Diphascon, Echiniscus, Macrobiotus, Milnesium and unidentified Parachela. Operational taxonomic units were delimited by Poisson tree processes and general mixed Yule coalescent methods, resulting in 58 and 55 putative species, respectively. Most tardigrades appear to be locally endemic (i.e. restricted to a single geographic region), but some (e.g. Acutuncus antarcticus (Richters, 1904)) are widespread across continental Antarctica. Our molecular results reveal: (i) greater diversity than has previously been appreciated with distinct OTUs that potentially represent undescribed species, and (ii) a lack of connectivity between most OTUs from continental Antarctica and those from other Antarctic geographical zones.
Collapse
|
9
|
Adhikari M, Kim S, Yadav DR, Babu AG, Kim C, Lee HB, Lee YS. A New Report on Oidiodendron flavum Isolated from Field Soil in Korea. 한국균학회지 2014. [DOI: 10.4489/kjm.2014.42.3.235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
10
|
|
11
|
Velasco-Castrillón A, Page TJ, Gibson JAE, Stevens MI. Surprisingly high levels of biodiversity and endemism amongst Antarctic rotifers uncovered with mitochondrial DNA. ACTA ACUST UNITED AC 2014. [DOI: 10.1080/14888386.2014.930717] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
12
|
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proc Natl Acad Sci U S A 2012; 109:16208-12. [PMID: 22988084 DOI: 10.1073/pnas.1209160109] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.
Collapse
|
13
|
Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites. PLoS One 2012; 7:e43865. [PMID: 22952792 PMCID: PMC3429485 DOI: 10.1371/journal.pone.0043865] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 07/27/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The molecular operational taxonomic unit (MOTU) has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of "reverse taxonomy" has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of "reverse taxonomy" has not been sufficiently evaluated. Therefore, the practical applicability of "reverse taxonomy" is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts. METHODOLOGY Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types ( = MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified. CONCLUSIONS That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.
Collapse
|
14
|
|
15
|
Guil N, Giribet G. A comprehensive molecular phylogeny of tardigrades-adding genes and taxa to a poorly resolved phylum-level phylogeny. Cladistics 2011; 28:21-49. [DOI: 10.1111/j.1096-0031.2011.00364.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
16
|
Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally. Proc Natl Acad Sci U S A 2011; 108:4406-10. [PMID: 21368117 DOI: 10.1073/pnas.1012678108] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bdelloid rotifers are important contributors to biogeochemical cycling and trophic dynamics of both aquatic and terrestrial ecosystems, but little is known about their biogeographic distribution and community structure in terrestrial environments. This lack of knowledge stems from a lack of phylogenetic information and assumptions that microbial eukaryotes are globally distributed and have very limited diversity across vast geographic distances. However, these assumptions have been based more on assessments of their morphology than any measure of their true genetic diversity and biogeographic distribution. We developed specific primers for the cytochrome c oxidase subunit 1 (cox1) gene of bdelloid rotifers and amplified and cloned sequences using a nested sampling scheme that represented local (0-10 m) to global (up to 10,000 km) scales. Using phylogenetic community analyses (UniFrac) and geospatial statistics (semivariograms, mantel tests), we were able to reject the hypothesis that communities of rotifers are the same across even fairly small geographic distances. Bdelloid communities showed highly significant spatial structuring with spatial autocorrelation ranges of 54-133 m, but beyond that distance communities were extremely dissimilar. Furthermore, we show that these spatial patterns are driven not only by changes in relative abundance of phylotypes but also by absolute changes in phylotype occurrence (richness). There is almost no overlap in phylotype [or operational taxonomic unit (OTU)] occurrence between communities at distances beyond the autocorrelation range (~133 m). Such small species ranges, combined with their ubiquity in soils, make it increasingly clear that the biodiversity of bdelloid rotifers (and other less easily dispersed microbes) is much higher than previously thought.
Collapse
|