1
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Muelbaier H, Arthen F, Collins G, Hickler T, Hohberg K, Lehmitz R, Pauchet Y, Pfenninger M, Potapov A, Romahn J, Schaefer I, Scheu S, Schneider C, Ebersberger I, Bálint M. Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates. Mol Ecol 2024:e17351. [PMID: 38712904 DOI: 10.1111/mec.17351] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 05/08/2024]
Abstract
Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.
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Affiliation(s)
- Hannah Muelbaier
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Freya Arthen
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Gemma Collins
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Thomas Hickler
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Department of Physical Geography, Goethe University, Frankfurt/Main, Germany
| | - Karin Hohberg
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Ricarda Lehmitz
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Yannick Pauchet
- Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Anton Potapov
- Senckenberg Museum for Natural History Görlitz, Görlitz, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- International Institute Zittau, TUD Dresden University of Technology, Zittau, Germany
| | - Juliane Romahn
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus-Liebig University, Giessen, Germany
| | - Ina Schaefer
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Animal Ecology, University of Goettingen, Goettingen, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany
| | - Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus-Liebig University, Giessen, Germany
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2
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Collins G, Schneider C, Boštjančić LL, Burkhardt U, Christian A, Decker P, Ebersberger I, Hohberg K, Lecompte O, Merges D, Muelbaier H, Romahn J, Römbke J, Rutz C, Schmelz R, Schmidt A, Theissinger K, Veres R, Lehmitz R, Pfenninger M, Bálint M. The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution. Commun Biol 2023; 6:1241. [PMID: 38066075 PMCID: PMC10709333 DOI: 10.1038/s42003-023-05621-4] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.
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Affiliation(s)
- Gemma Collins
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ljudevit Luka Boštjančić
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | | | - Axel Christian
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Peter Decker
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ingo Ebersberger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Karin Hohberg
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | - Dominik Merges
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hannah Muelbaier
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Juliane Romahn
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbH, Flörsheim, Germany
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | | | - Alexandra Schmidt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Kathrin Theissinger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | - Robert Veres
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Ricarda Lehmitz
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Johannes Gutenberg University, Mainz, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.
- Department of Insect Biotechnology, Justus-Liebig University, Gießen, Germany.
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3
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Merges D, Schmidt A, Schmitt I, Neuschulz EL, Dal Grande F, Bálint M. Metatranscriptomics reveals contrasting effects of elevation on the activity of bacteria and bacterial viruses in soil. Mol Ecol 2023; 32:6552-6563. [PMID: 36321191 DOI: 10.1111/mec.16756] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 11/21/2022]
Abstract
Soil microbial diversity affects ecosystem functioning and global biogeochemical cycles. Soil bacterial communities catalyse a diversity of biogeochemical reactions and have thus sparked considerable scientific interest. One driver of bacterial community dynamics in natural ecosystems has so far been largely neglected: the predator-prey interactions between bacterial viruses (bacteriophages) and bacteria. To generate ground level knowledge on environmental drivers of these particular predator-prey dynamics, we propose an activity-based ecological framework to simultaneous capture community dynamics of bacteria and bacteriophages in soils. An ecological framework and specifically the analyses of community dynamics across latitudinal and elevational gradients have been widely used in ecology to understand community-wide responses of innumerable taxa to environmental change, in particular to climate. Here, we tested the hypothesis that the activity of bacteria and bacteriophages codeclines across an elevational gradient. We used metatranscriptomics to investigate bacterial and bacteriophage activity patterns at five sites across 400 elevational metres in the Swiss Alps in 2015 and 2017. We found that metabolic activity (transcription levels) of bacteria declined significantly with increasing elevation, but activity of bacteriophages did not. We showed that bacteriophages are consistently active in soil along the entire gradient, making bacteriophage activity patterns divergent from that of their putative bacterial prey. Future efforts will be necessary to link the environment-activity relationship to predator-prey dynamics, and to understand the magnitude of viral contributions to carbon, nitrogen and phosphorus cycling when infection causes bacterial cell death, a process that may represent an overlooked component of soil biogeochemical cycles.
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Affiliation(s)
- Dominik Merges
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Alexandra Schmidt
- Department of Biology, Limnological Institute, University Konstanz, Konstanz, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Department of Biology, University of Padova, Padua, Italy
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus Liebig University Gießen, Gießen, Germany
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4
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Sylvester F, Weichert FG, Lozano VL, Groh KJ, Bálint M, Baumann L, Bässler C, Brack W, Brandl B, Curtius J, Dierkes P, Döll P, Ebersberger I, Fragkostefanakis S, Helfrich EJN, Hickler T, Johann S, Jourdan J, Klimpel S, Kminek H, Liquin F, Möllendorf D, Mueller T, Oehlmann J, Ottermanns R, Pauls SU, Piepenbring M, Pfefferle J, Schenk GJ, Scheepens JF, Scheringer M, Schiwy S, Schlottmann A, Schneider F, Schulte LM, Schulze-Sylvester M, Stelzer E, Strobl F, Sundermann A, Tockner K, Tröger T, Vilcinskas A, Völker C, Winkelmann R, Hollert H. Better integration of chemical pollution research will further our understanding of biodiversity loss. Nat Ecol Evol 2023; 7:1552-1555. [PMID: 37386085 DOI: 10.1038/s41559-023-02117-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Affiliation(s)
- Francisco Sylvester
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CCT CONICET Salta-Jujuy, Salta, Argentina
| | - Fabian G Weichert
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Verónica L Lozano
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CCT CONICET Salta-Jujuy, Salta, Argentina
| | - Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus Liebig University Gießen, Gießen, Germany
| | - Lisa Baumann
- Amsterdam Institute for Life and Environment (A-LIFE), Section Environmental Health & Toxicology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Claus Bässler
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Bavarian Forest National Park, Grafenau, Germany
| | - Werner Brack
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Barbara Brandl
- Faculty of Social Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Joachim Curtius
- Institute for Atmospheric and Environmental Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Paul Dierkes
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Petra Döll
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Institute of Physical Geography, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | | | - Eric J N Helfrich
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Thomas Hickler
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Institute of Physical Geography, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sarah Johann
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jonas Jourdan
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sven Klimpel
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Branch Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Gießen, Germany
| | - Helge Kminek
- Faculty of Educational Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Florencia Liquin
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Darrel Möllendorf
- Faculty of Social Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Thomas Mueller
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Richard Ottermanns
- Institute for Environmental Research (IER), RWTH Aachen University, Aachen, Germany
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus Liebig University Gießen, Gießen, Germany
- Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Meike Piepenbring
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jakob Pfefferle
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gerrit Jasper Schenk
- Institute of History, History of the Middle Ages, Technical University of Darmstadt, Darmstadt, Germany
| | - J F Scheepens
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Martin Scheringer
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
- RECETOX, Masaryk University, Brno, Czech Republic
| | - Sabrina Schiwy
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Antje Schlottmann
- Department of Human Geography, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Flurina Schneider
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Institute for Social-Ecological Research (ISOE), Frankfurt am Main, Germany
| | - Lisa M Schulte
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Schulze-Sylvester
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
- Geisenheim University, Department of Crop Protection, Geisenheim, Germany
- Instituto de Bio y Geociencias del Noroeste Argentino (IBIGEO-CONICET), Salta, Argentina
| | - Ernst Stelzer
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frederic Strobl
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andrea Sundermann
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Klement Tockner
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Tobias Tröger
- Department of Law, Goethe University Frankfurt, Frankfurt am Main, Germany
- Leibniz Institute for Financial Research Sustainable Architecture for Finance in Europe, Frankfurt am Main, Germany
| | - Andreas Vilcinskas
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus Liebig University Gießen, Gießen, Germany
- Branch Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Gießen, Germany
| | - Carolin Völker
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Social-Ecological Research (ISOE), Frankfurt am Main, Germany
| | - Ricarda Winkelmann
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, Germany
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | - Henner Hollert
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.
- Department of Environmental Media-related Ecotoxicology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany.
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5
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Simon MP, Schatz M, Böhm L, Papp I, Grossart HP, Andersen TJ, Bálint M, Düring RA. Dissent in the sediment? Lake sediments as archives of short- and long-range impact of anthropogenic activities in northeastern Germany. Environ Sci Pollut Res Int 2023; 30:85867-85888. [PMID: 37395875 PMCID: PMC10404210 DOI: 10.1007/s11356-023-28210-8] [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] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023]
Abstract
The suitability of lake sediment cores to reconstruct past inputs, regional pollution, and usage patterns of pesticides has been shown previously. Until now, no such data exist for lakes in eastern Germany. Therefore, 10 sediment cores (length 1 m) of 10 lakes in eastern Germany, the territory of the former German Democratic Republic (GDR), were collected and cut into 5-10-mm layers. In each layer, concentrations of trace elements (TEs) As, Cd, Cr, Cu, Ni, Pb, S, and Zn, as well as of organochlorine pesticides (OCPs), i.e., dichlorodiphenyltrichloroethane (DDT) and hexachlorocyclohexane (HCH), were analyzed. A miniaturized solid-liquid extraction technique in conjunction with headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) was used for the latter. The progression of TE concentrations over time is uniform. It follows a trans-regional pattern and is indicative of activity and policy making in West Germany before 1990 instead of those in the GDR. Of OCPs, only transformation products of DDT were found. Congener ratios indicate a mainly aerial input. In the lakes' profiles, several regional features and responses to national policies and measures are visible. Dichlorodiphenyldichloroethane (DDD) concentrations reflect the history of DDT use in the GDR. Lake sediments proved to be suitable to archive short- and long-range impacts of anthropogenic activity. Our data can be used to complement and validate other forms of environmental pollution long-term monitoring and to check for the efficiency of pollution countermeasures in the past.
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Affiliation(s)
- Marcel Pierre Simon
- Institute of Soil Science and Soil Conservation, Research Centre for BioSystems, Land Use and Nutrition (iFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Marlene Schatz
- Institute of Soil Science and Soil Conservation, Research Centre for BioSystems, Land Use and Nutrition (iFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Leonard Böhm
- Institute of Soil Science and Soil Conservation, Research Centre for BioSystems, Land Use and Nutrition (iFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - István Papp
- Doctoral School of Chemistry, University of Debrecen, Egyetem Tér 1, Debrecen, 4032, Hungary
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Dept. Plankton and Microbial Ecology, Zur alten Fischerhütte 2, OT Neuglobsow, 16775, Stechlin, Germany
- Institute for Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469, Potsdam, Germany
| | - Thorbjørn Joest Andersen
- Section for Geography, Department of Geosciences and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, 1350, Copenhagen K, Denmark
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rolf-Alexander Düring
- Institute of Soil Science and Soil Conservation, Research Centre for BioSystems, Land Use and Nutrition (iFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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6
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Müller R, Bálint M, Hardes K, Hollert H, Klimpel S, Knorr E, Kochmann J, Lee KZ, Mehring M, Pauls SU, Smets G, Steinbrink A, Vilcinskas A. RNA interference to combat the Asian tiger mosquito in Europe: A pathway from design of an innovative vector control tool to its application. Biotechnol Adv 2023; 66:108167. [PMID: 37164239 DOI: 10.1016/j.biotechadv.2023.108167] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/06/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
The Asian tiger mosquito Aedes albopictus is currently spreading across Europe, facilitated by climate change and global transportation. It is a vector of arboviruses causing human diseases such as chikungunya, dengue hemorrhagic fever and Zika fever. For the majority of these diseases, no vaccines or therapeutics are available. Options for the control of Ae. albopictus are limited by European regulations introduced to protect biodiversity by restricting or phasing out the use of pesticides, genetically modified organisms (GMOs) or products of genome editing. Alternative solutions are thus urgently needed to avoid a future scenario in which Europe faces a choice between prioritizing human health or biodiversity when it comes to Aedes-vectored pathogens. To ensure regulatory compliance and public acceptance, these solutions should preferably not be based on chemicals or GMOs and must be cost-efficient and specific. The present review aims to synthesize available evidence on RNAi-based mosquito vector control and its potential for application in the European Union. The recent literature has identified some potential target sites in Ae. albopictus and formulations for delivery. However, we found little information concerning non-target effects on the environment or human health, on social aspects, regulatory frameworks, or on management perspectives. We propose optimal designs for RNAi-based vector control tools against Ae. albopictus (target product profiles), discuss their efficacy and reflect on potential risks to environmental health and the importance of societal aspects. The roadmap from design to application will provide readers with a comprehensive perspective on the application of emerging RNAi-based vector control tools for the suppression of Ae. albopictus populations with special focus on Europe.
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Affiliation(s)
- Ruth Müller
- Unit Entomology, Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerp, Belgium; Institute of Occupational, Social and Environmental Medicine, Goethe University, Theodor-Stern-Kai 9, 60590 Frankfurt am Main, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Kornelia Hardes
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch of Bioresources, Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Infection Research "ASCRIBE", Germany
| | - Henner Hollert
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Department Media-related Toxicity, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany; Evolutionary Ecology and Environmental Toxicology, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Sven Klimpel
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Integrative Parasitology and Zoophysiology, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Eileen Knorr
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch of Bioresources, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Judith Kochmann
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany
| | - Kwang-Zin Lee
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch of Bioresources, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Marion Mehring
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; ISOE - Institute for Social-Ecological Research, Hamburger Allee 45, 60486 Frankfurt am Main, Germany
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Greet Smets
- Perseus BV, Kortrijksesteenweg 127 B1, B-9830 Sint-Martens-Latem, Belgium
| | - Antje Steinbrink
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch of Bioresources, Ohlebergsweg 12, 35392 Giessen, Germany.
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7
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [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: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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8
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Boštjančić LL, Francesconi C, Rutz C, Hoffbeck L, Poidevin L, Kress A, Jussila J, Makkonen J, Feldmeyer B, Bálint M, Schwenk K, Lecompte O, Theissinger K. Host-pathogen coevolution drives innate immune response to Aphanomyces astaci infection in freshwater crayfish: transcriptomic evidence. BMC Genomics 2022; 23:600. [PMID: 35989333 PMCID: PMC9394032 DOI: 10.1186/s12864-022-08571-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/20/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND For over a century, scientists have studied host-pathogen interactions between the crayfish plague disease agent Aphanomyces astaci and freshwater crayfish. It has been hypothesised that North American crayfish hosts are disease-resistant due to the long-lasting coevolution with the pathogen. Similarly, the increasing number of latent infections reported in the historically sensitive European crayfish hosts seems to indicate that similar coevolutionary processes are occurring between European crayfish and A. astaci. Our current understanding of these host-pathogen interactions is largely focused on the innate immunity processes in the crayfish haemolymph and cuticle, but the molecular basis of the observed disease-resistance and susceptibility remain unclear. To understand how coevolution is shaping the host's molecular response to the pathogen, susceptible native European noble crayfish and invasive disease-resistant marbled crayfish were challenged with two A. astaci strains of different origin: a haplogroup A strain (introduced to Europe at least 50 years ago, low virulence) and a haplogroup B strain (signal crayfish in lake Tahoe, USA, high virulence). Here, we compare the gene expression profiles of the hepatopancreas, an integrated organ of crayfish immunity and metabolism. RESULTS We characterised several novel innate immune-related gene groups in both crayfish species. Across all challenge groups, we detected 412 differentially expressed genes (DEGs) in the noble crayfish, and 257 DEGs in the marbled crayfish. In the noble crayfish, a clear immune response was detected to the haplogroup B strain, but not to the haplogroup A strain. In contrast, in the marbled crayfish we detected an immune response to the haplogroup A strain, but not to the haplogroup B strain. CONCLUSIONS We highlight the hepatopancreas as an important hub for the synthesis of immune molecules in the response to A. astaci. A clear distinction between the innate immune response in the marbled crayfish and the noble crayfish is the capability of the marbled crayfish to mobilise a higher variety of innate immune response effectors. With this study we outline that the type and strength of the host immune response to the pathogen is strongly influenced by the coevolutionary history of the crayfish with specific A. astaci strains.
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Affiliation(s)
- Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Caterina Francesconi
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany.
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Lucien Hoffbeck
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Laetitia Poidevin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Japo Jussila
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
| | - Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
- Present address: BioSafe - Biological Safety Solutions, Microkatu 1, 70210, Kuopio, Finland
| | - Barbara Feldmeyer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
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9
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Boštjančić LL, Francesconi C, Rutz C, Hoffbeck L, Poidevin L, Kress A, Jussila J, Makkonen J, Feldmeyer B, Bálint M, Schwenk K, Lecompte O, Theissinger K. Dataset of the de novo assembly and annotation of the marbled crayfish and the noble crayfish hepatopancreas transcriptomes. BMC Res Notes 2022; 15:281. [PMID: 35989321 PMCID: PMC9394041 DOI: 10.1186/s13104-022-06137-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVES Crayfish plague disease, caused by the oomycete pathogen Aphanomyces astaci represents one of the greatest risks for the biodiversity of the freshwater crayfish. This data article covers the de novo transcriptome assembly and annotation data of the noble crayfish and the marbled crayfish challenged with Ap. astaci. Following the controlled infection experiment (Francesconi et al. in Front Ecol Evol, 2021, https://doi.org/10.3389/fevo.2021.647037 ), we conducted a differential gene expression analysis described in (Boštjančić et al. in BMC Genom, 2022, https://doi.org/10.1186/s12864-022-08571-z ) DATA DESCRIPTION: In total, 25 noble crayfish and 30 marbled crayfish were selected. Hepatopancreas tissue was isolated, followed by RNA sequencing using the Illumina NovaSeq 6000 platform. Raw data was checked for quality with FastQC, adapter and quality trimming were conducted using Trimmomatic followed by de novo assembly with Trinity. Assembly quality was assessed with BUSCO, at 93.30% and 93.98% completeness for the noble crayfish and the marbled crayfish, respectively. Transcripts were annotated using the Dammit! pipeline and assigned to KEGG pathways. Respective transcriptome and raw datasets may be reused as the reference transcriptome assemblies for future expression studies.
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Affiliation(s)
- Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Caterina Francesconi
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany.
| | - Christelle Rutz
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Lucien Hoffbeck
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Laetitia Poidevin
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Arnaud Kress
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Japo Jussila
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
| | - Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
- BioSafe - Biological Safety Solutions, Microkatu 1, 70210, Kuopio, Finland
| | - Barbara Feldmeyer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
| | - Odile Lecompte
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
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10
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Schmidt A, Schneider C, Decker P, Hohberg K, Römbke J, Lehmitz R, Bálint M. Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties. Ecol Evol 2022; 12:e8991. [PMID: 35784064 PMCID: PMC9170594 DOI: 10.1002/ece3.8991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
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Affiliation(s)
- Alexandra Schmidt
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Biology DepartmentJ.W. Goethe UniversityFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Limnological Institute (Environmental Genomics)University of KonstanzKonstanzGermany
| | - Clément Schneider
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Peter Decker
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Blumenstr. 5GörlitzGermany
| | - Karin Hohberg
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbHFlörsheim am MainGermany
| | - Ricarda Lehmitz
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Miklós Bálint
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Insect BiotechnologyJustus Liebig UniversityGießenGermany
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11
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Pfenninger M, Bálint M. On the use of population genomic time series for environmental monitoring. Am J Bot 2022; 109:497-499. [PMID: 35253207 DOI: 10.1002/ajb2.1836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Agricultural Sciences, Nutritional Sciences, and Environmental Management, Universität Giessen, Giessen, Germany
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12
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Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M. The era of reference genomes in conservation genomics. Trends Ecol Evol 2022; 37:197-202. [PMID: 35086739 DOI: 10.1016/j.tree.2021.11.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [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: 04/25/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 02/08/2023]
Abstract
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
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Affiliation(s)
- Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; University of Koblenz-Landau, Institute for Environmental Sciences, Fortstrasse 7, 76829 Landau, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Iliana Bista
- University of Cambridge, Department of Genetics, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, CB10 1SA, Hinxton, UK
| | | | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino (FI) 50019, Italy
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - José A Godoy
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain
| | - Jacob Höglund
- Dept. of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Sweden
| | | | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Belgium
| | - Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences University of Groningen Nijenborgh, 9747, AG, Groningen, the Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5, 220 Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Belgium
| | | | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Dept. of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Germany
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark, Build 3, Universitetsparken 15, Copenhagen 2100, Denmark; China National Genebank, BGI-Shenzhen, Jinsha Road, Dapeng District, Shenzhen 518083, China
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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13
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Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O'Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. The Earth BioGenome Project 2020: Starting the clock. Proc Natl Acad Sci U S A 2022; 119:e2115635118. [PMID: 35042800 PMCID: PMC8795548 DOI: 10.1073/pnas.2115635118] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616;
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
| | - Stephen Richards
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Erez Lieberman Aiden
- DNA Zoo and The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030
| | - Miguel L Allende
- Center for Genome Regulation, Universidad de Chile 3425 Santiago, Chile
- Facultad de Ciencias, Universidad de Chile 3425 Santiago, Chile
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Miklós Bálint
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus-Liebig University 35392 Giessen, Germany
| | - Katharine B Barker
- Global Genome Biodiversity Network Secretariat, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | | | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara 44121 Ferrara, Italy
| | - Mark L Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Nicolette D Caperello
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Keith Carlson
- The Novim Group, University of California, Santa Barbara, CA 93106
| | | | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica 11529 Taipei, Taiwan
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Dalia A Conde
- Conservation Science, Species360 Conservation Science Alliance, Bloomington, MN 55425
- Department of Biology, University of Southern Denmark 5230 Odense M, Denmark
| | - Montserrat Corominas
- Department of Genetics, Microbiology, and Statistics, Universitat de Barcelona 08028 Barcelona, Spain
- Catalan Society for Biology, Institute for Catalan Studies 08001 Barcelona, Spain
| | - Keith A Crandall
- Department of Biostatistics & Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC 20052
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia
| | | | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - ThankGod E Ebenezer
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Olivier Fedrigo
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Paul Flicek
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen 1350 Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology 7491 Trondheim, Norway
| | - Melissa M Goldstein
- Department of Health Policy and Management, George Washington University, Washington, DC 20052
| | - Jennifer Marshall Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Henry T Greely
- Stanford Law School, Stanford University, Stanford, CA 94305
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Kevin J Hackett
- Office of National Programs, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - David Haussler
- Genome Institute, University of California, Santa Cruz, CA 95060
- HHMI, Chevy Chase, MD 20815
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2000, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | | | - Axel Janke
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- HHMI, Chevy Chase, MD 20815
| | - Warren E Johnson
- Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, MD 20746
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute 21990 Incheon, South Korea
| | - W John Kress
- Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics 411-8540 Shizuoka, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research 650-0047 Hyogo, Japan
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | | | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 752 36 Uppsala, Sweden
| | - Xin Liu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Pompeu Fabra University, Consejo Superior de Investigaciones Cientificas, Parc de Recerca Biomedica de Barcelona 08003 Barcelona, Spain
- Catalan Institute of Research and Advanced Studies 08010 Barcelona, Spain
- Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain
| | - Sophie Mazard
- Bioplatforms Australia, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonna A K Mazet
- One Health Institute, University of California Davis, CA 95616
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research 14195 Berlin, Germany
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research 10315 Berlin, Germany
| | - Eugene W Myers
- Max Planck Institute for Molecular Cell Biology and Genetics 01307 Dresden, Germany
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Sadye Paez
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Hyun Park
- Division of Biotechnology, Korea University 02841 Seoul, Korea
| | - Gene E Robinson
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants Associated Unit to Consejo Superior de Investigaciones Cientificas, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Spain
- Laboratoire d'Ecologie Alpine, University Grenoble Alpes, University Savoie Mont Blanc, CNRS 38000 Grenoble, France
| | - Oliver A Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Division of Biology, Department of Evolution, Behavior, and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University 21589 Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University 21589 Jeddah, Saudi Arabia
| | - H Bradley Shaffer
- La Kretz Center for California Conservation Science, Institute of Environment and Sustainability, University of California, Los Angeles, CA 90024
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Timothy M Shank
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Jacob S Sherkow
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- College of Law, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University 224002 Yancheng, China
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu 50411 Tartu, Estonia
- College of Science, King Saud University 11451 Riyadh, Saudi Arabia
| | | | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Xiaofeng Wei
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007
- Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Julia L Wilson
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Xun Xu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Huanming Yang
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 2100 Copenhagen, Denmark
- China National Genebank, Beijing Genomics Institute 51803 Shenzhen, China
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14
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Tedersoo L, Mikryukov V, Anslan S, Bahram M, Khalid AN, Corrales A, Agan A, Vasco-Palacios AM, Saitta A, Antonelli A, Rinaldi AC, Verbeken A, Sulistyo BP, Tamgnoue B, Furneaux B, Ritter CD, Nyamukondiwa C, Sharp C, Marín C, Dai DQ, Gohar D, Sharmah D, Biersma EM, Cameron EK, De Crop E, Otsing E, Davydov EA, Albornoz FE, Brearley FQ, Buegger F, Gates G, Zahn G, Bonito G, Hiiesalu I, Hiiesalu I, Zettur I, Barrio IC, Pärn J, Heilmann-Clausen J, Ankuda J, Kupagme JY, Sarapuu J, Maciá-Vicente JG, Fovo JD, Geml J, Alatalo JM, Alvarez-Manjarrez J, Monkai J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan KI, Armolaitis K, Hyde KD, Newsham KK, Panksep K, Adebola LA, Lamit LJ, Saba M, da Silva Cáceres ME, Tuomi M, Gryzenhout M, Bauters M, Bálint M, Wijayawardene N, Hagh-Doust N, Yorou NS, Kurina O, Mortimer PE, Meidl P, Nilsson RH, Puusepp R, Casique-Valdés R, Drenkhan R, Garibay-Orijel R, Godoy R, Alfarraj S, Rahimlou S, Põlme S, Dudov SV, Mundra S, Ahmed T, Netherway T, Henkel TW, Roslin T, Fedosov VE, Onipchenko VG, Yasanthika WAE, Lim YW, Piepenbring M, Klavina D, Kõljalg U, Abarenkov K. The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00493-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Pfenninger M, Reuss F, Kiebler A, Schönnenbeck P, Caliendo C, Gerber S, Cocchiararo B, Reuter S, Blüthgen N, Mody K, Mishra B, Bálint M, Thines M, Feldmeyer B. Genomic basis for drought resistance in European beech forests threatened by climate change. eLife 2021; 10:65532. [PMID: 34132196 PMCID: PMC8266386 DOI: 10.7554/elife.65532] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 12/07/2020] [Accepted: 06/07/2021] [Indexed: 12/30/2022] Open
Abstract
In the course of global climate change, Central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought-damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated single-nucleotide polymorphisms (SNPs) throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. An SNP assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding. Climate change is having a serious impact on many ecosystems. In the summer of 2018 and 2019, around two thirds of European beech trees were damaged or killed by extreme drought. It is critical to keep these beech woods healthy, as they are central to the survival of over 6,000 other species of animals and plants. The level of damage caused by the drought varied between forests. However, not all the trees in each forest responded in the same way, with severely damaged trees often sitting next to fully healthy ones. This suggests that the genetic make-up of each tree determines how well it can adapt to drought rather than its local environment. To investigate this further, Pfenninger et al. studied the genome of over 400 European beech trees from the Hesse region in Germany. The samples came from pairs of neighbouring trees that had responded differently to the droughts. The analysis found more than 80 parts of the genome that differed between healthy and damaged trees. Pfenninger et al. then used this information to create a genetic test which can quickly and inexpensively predict how well an individual beech tree might survive in a drought. Applying this test to another 92 trees revealed that it can reliably detect which ones were healthy and which ones were damaged. Beech forests are typically managed by private owners, agencies or breeders that could use this genetic test to select and reproduce trees that are better adapted to drought. The goal now is to develop the test so that it can be used more widely to manage European beech trees and potentially other species.
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Affiliation(s)
- Markus Pfenninger
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Friederike Reuss
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Angelika Kiebler
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Philipp Schönnenbeck
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Cosima Caliendo
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Berardino Cocchiararo
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Sabrina Reuter
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Nico Blüthgen
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Karsten Mody
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Department of Applied Ecology, Hochschule Geisenheim University, Geisenheim, Germany
| | - Bagdevi Mishra
- Biological Archives, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Functional Environmental Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Agricultural Sciences, Nutritional Sciences, and Environmental Management, Universität Giessen, Giessen, Germany
| | - Marco Thines
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Biological Archives, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Barbara Feldmeyer
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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16
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Schneider C, Woehle C, Greve C, D'Haese CA, Wolf M, Hiller M, Janke A, Bálint M, Huettel B. Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola). Gigascience 2021; 10:giab035. [PMID: 34018554 PMCID: PMC8138834 DOI: 10.1093/gigascience/giab035] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/05/2021] [Accepted: 04/27/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non-genetic model species. However, long-read sequencing today relies on sizable quantities of high-quality, high molecular weight DNA, which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present de novo genomes of 2 species of submillimeter Collembola. For each, we prepared the sequencing library from high molecular weight DNA extracted from a single specimen and using a novel ultra-low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole-genome amplification step. RESULTS The 2 assembled genomes have N50 values >5.5 and 8.5 Mb, respectively, and both contain ∼96% of BUSCO genes. Thus, they are highly contiguous and complete. The genomes are supported by an integrative taxonomy approach including placement in a genome-based phylogeny of Collembola and designation of a neotype for 1 of the species. Higher heterozygosity values are recorded in the more mobile species. Both species are devoid of the biosynthetic pathway for β-lactam antibiotics known in several Collembola, confirming the tight correlation of antibiotic synthesis with the species way of life. CONCLUSIONS It is now possible to generate high-quality genomes from single specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1 Mb) required by the Earth BioGenome Project.
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Affiliation(s)
- Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Abteilung Bodenzoologie, Am Museum 1, 02826 Görlitz, Germany
| | - Christian Woehle
- Max Planck Institute for Plant Breeding Research, Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Cyrille A D'Haese
- Unité Mécanismes adaptatifs & Evolution (MECADEV), CNRS, Muséum national d'Histoire naturelle, 45 rue Buffon 75005 Paris, France
| | - Magnus Wolf
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Axel Janke
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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Knisz J, Shetty P, Wirth R, Maróti G, Karches T, Dalkó I, Bálint M, Vadkerti E, Bíró T. Genome-level insights into the operation of an on-site biological wastewater treatment unit reveal the importance of storage time. Sci Total Environ 2021; 766:144425. [PMID: 33418265 DOI: 10.1016/j.scitotenv.2020.144425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
On-site wastewater treatment systems are gaining popularity in areas where centralized wastewater treatment is not available. In the current case study a domestic activated sludge system was investigated, where treated effluent was stored in a short-term (1 week turn-over time) and a long-term (over 2-3 months) storage tank and was then used for irrigation. This design provided a unique opportunity to assess the chemical and microbial changes of the effluent upon storage. Long-term storage greatly improved both the chemical quality and the degradation efficiency of most organic micropollutants examined, including petroleum hydrocarbons and the pesticide diethyltoluamide. Taxonomic profile of the core microbiome of the effluent was also influenced upon storage. Relative abundance values of the members of Azoarcus and Thauera genera, which are important in degrading polycyclic aromatic hydrocarbons compounds, clearly indicated the biodegrading activity of these microbes across samples. The abundance of xenobiotics degradation functions correlated with the observed organic micropollutant degradation values indicating efficient microbial decomposition of these contaminants. Functions related to infectious diseases also had the highest abundance in the short-term storage tank corresponding well with the relative abundance of indicator organisms and implying to the significance of storage time in the elimination of pathogens. Based on these results, small, on-site wastewater treatment systems could benefit from long-term storage of wastewater effluent.
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Affiliation(s)
- J Knisz
- Faculty of Water Sciences, National University of Public Service, Bajcsy-Zsilinszky u. 12-14., 6500 Baja, Hungary
| | - P Shetty
- Institute of Plant Biology, Biological Research Center, Temesvári krt. 62, 6726 Szeged, Hungary
| | - R Wirth
- Institute of Plant Biology, Biological Research Center, Temesvári krt. 62, 6726 Szeged, Hungary
| | - G Maróti
- Faculty of Water Sciences, National University of Public Service, Bajcsy-Zsilinszky u. 12-14., 6500 Baja, Hungary; Institute of Plant Biology, Biological Research Center, Temesvári krt. 62, 6726 Szeged, Hungary
| | - T Karches
- Faculty of Water Sciences, National University of Public Service, Bajcsy-Zsilinszky u. 12-14., 6500 Baja, Hungary
| | - I Dalkó
- Faculty of Water Sciences, National University of Public Service, Bajcsy-Zsilinszky u. 12-14., 6500 Baja, Hungary
| | - M Bálint
- Bálint Analitika Ltd, Fehérvári út 144, 1116 Budapest, Hungary
| | - E Vadkerti
- Faculty of Water Sciences, National University of Public Service, Bajcsy-Zsilinszky u. 12-14., 6500 Baja, Hungary
| | - T Bíró
- Faculty of Water Sciences, National University of Public Service, Bajcsy-Zsilinszky u. 12-14., 6500 Baja, Hungary.
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Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE, De Barba M, Dickie IA, Dumbrell AJ, Ficetola GF, Fierer N, Fumagalli L, Gilbert MTP, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L, Thomsen PF, Willerslev E, Taberlet P. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions. Mol Ecol 2019; 28:1857-1862. [DOI: 10.1111/mec.15060] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de biologie Ecole normale supérieure, CNRS, INSERM, Université PSL Paris France
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
| | - Inger G. Alsos
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG) Frankfurt Germany
| | - Holly Bik
- Department of Nematology University of California Riverside California
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
| | - Anthony A. Chariton
- Department of Biological Sciences Macquarie University Sydney New South Wales Australia
| | - Simon Creer
- School of Natural Sciences Bangor University Gwynedd UK
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
| | | | - Marta De Barba
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
| | - Ian A. Dickie
- School of Biological Sciences, BioProtection Research Centre University of Canterbury Christchurch New Zealand
| | | | - Gentile Francesco Ficetola
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
- Department of Environmental Science and Policy Università degli Studi di Milano Milano Italy
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado
- Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Colorado
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, Biological Institute University of Copenhagen Copenhagen Denmark
- Norwegian University of Science and Technology, University Museum Trondheim Norway
| | - Simon Jarman
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture Curtin University Perth Western Australia Australia
- Environomics Future Science Platform CSIRO National Collections and Marine Infrastructure Crawley Western Australia Australia
| | - Ari Jumpponen
- Division of Biology Kansas State University Manhattan Kansas
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE) University of Oslo Oslo Norway
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier Toulouse France
- Lundbeck Foundation GeoGenetics Center University of Copenhagen Copenhagen Denmark
| | - Johan Pansu
- Department of Biological Sciences Macquarie University Sydney New South Wales Australia
- Station Biologique de Roscoff CNRS UMR 7144, Sorbonne Université Roscoff France
- CSIRO Ocean & Atmosphere Lucas Heights New South Wales Australia
| | - Jan Pawlowski
- ID‐Gene Ecodiagnostics Geneva Switzerland
- Department of Genetics and Evolution University of Geneva Geneva Switzerland
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center University of Copenhagen Copenhagen Denmark
- Department of Zoology University of Cambridge Cambridge UK
- Wellcome Trust Sanger Institute Cambridge UK
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
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Bálint M, Pfenninger M, Grossart HP, Taberlet P, Vellend M, Leibold MA, Englund G, Bowler D. Environmental DNA Time Series in Ecology. Trends Ecol Evol 2018; 33:945-957. [DOI: 10.1016/j.tree.2018.09.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/28/2018] [Accepted: 09/05/2018] [Indexed: 12/13/2022]
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Bálint M, Nowak C, Márton O, Pauls SU, Wittwer C, Aramayo JL, Schulze A, Chambert T, Cocchiararo B, Jansen M. Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs. Mol Ecol Resour 2018; 18:1415-1426. [DOI: 10.1111/1755-0998.12934] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 06/20/2018] [Accepted: 07/05/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Miklós Bálint
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG); Frankfurt Germany
| | - Carsten Nowak
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG); Frankfurt Germany
| | - Orsolya Márton
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research; Hungarian Academy of Sciences; Budapest Hungary
| | - Steffen U. Pauls
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG); Frankfurt Germany
| | - Claudia Wittwer
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
| | - José Luis Aramayo
- Museo de Historia Natural Noel Kempff Mercado - Facultad Cs; Farmacéutica y Bioquímicas - UAGRM; Santa Cruz Bolivia
| | - Arne Schulze
- Hessisches Landesmuseum Darmstadt (HLMD); Darmstadt Germany
| | - Thierry Chambert
- Department of Ecosystem Science and Management; Pennsylvania State University; University Park Pennsylvania
| | - Berardino Cocchiararo
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG); Frankfurt Germany
| | - Martin Jansen
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
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Waringer J, Previšić A, Kučinić M, Graf W, Vitecek S, Keresztes L, Bálint M, Pauls SU. Larval morphology of the Western Balkans endemic caddisflies Drusus krusniki Malicky 1981, D. vernonensis Malicky 1989, and D. vespertinus Marinković 1976 (Trichoptera, Limnephilidae, Drusinae). Zootaxa 2018; 4083:483-500. [PMID: 26985141 DOI: 10.11646/zootaxa.4083.4.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Drusinae (Trichoptera, Limnephilidae) are highland caddisflies inhabiting high-gradient, turbulent running water and spring habitats. They are disjunctly distributed over the Eurasian mountain ranges, and the majority of species is endemic to particular mountain areas. The most diverse of three main groups of the Drusinae, the grazer clade, consists of species in which larvae feed on epiltihic biofilm and algae. In this paper we describe three previously unknown grazer-clade Drusinae larvae: Drusus krusniki Malicky 1981 (endemic to the Dinaric western Balkans), D. vernonensis Malicky 1989 (endemic to the Hellenic western Balkans), and D. vespertinus Marinković 1976 (endemic to the Dinaric western Balkans). The larvae of these species have toothless mandibles typical of the Drusinae grazer clade. Larvae and adults were unambiguously associated using molecular genetic data, i.e., the mitochondrial cytochrome oxidase I gene fragment (mtCOI3-P). Morphological characteristics of the larvae are described and the diagnostic features enabling species-level identification are illustrated. We further discuss the ecology and distribution of three Western Balkan endemic species.
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Affiliation(s)
- Johann Waringer
- Department of Limnology and Bio-Ocenaography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Ana Previšić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources and Life Sciences, Max Emanuel-Strasse 17, A-1180 Vienna, Austria
| | - Simon Vitecek
- Department of Limnology and Bio-Ocenaography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a.M., Germany
| | - Steffen U Pauls
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a.M., Germany
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Bálint M, Márton O, Schatz M, Düring R, Grossart H. Proper experimental design requires randomization/balancing of molecular ecology experiments. Ecol Evol 2018; 8:1786-1793. [PMID: 29435253 PMCID: PMC5792580 DOI: 10.1002/ece3.3687] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 04/04/2017] [Revised: 09/21/2017] [Accepted: 10/26/2017] [Indexed: 12/12/2022] Open
Abstract
Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.
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Affiliation(s)
- Miklós Bálint
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Orsolya Márton
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Soil Sciences and Agricultural ChemistryCentre for Agricultural ResearchHungarian Academy of SciencesBudapestHungary
| | | | | | - Hans‐Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland FisheriesStechlinGermany
- Institute of Biochemistry and BiologyPotsdam UniversityPotsdamGermany
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Schmidt PA, Schmitt I, Otte J, Bandow C, Römbke J, Bálint M, Rolshausen G. Season-Long Experimental Drought Alters Fungal Community Composition but Not Diversity in a Grassland Soil. Microb Ecol 2018; 75:468-478. [PMID: 28785816 DOI: 10.1007/s00248-017-1047-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/20/2017] [Indexed: 05/23/2023]
Abstract
Using terrestrial model ecosystems (TMEs), we investigated how reduced moisture conditions impact soil fungal communities from a temperate grassland over the course of an entire season. Starting at about 65% of the soil's maximum water holding capacity (WHCmax), TME soils were adjusted to three moisture levels for 15 weeks: 70% WHCmax, approximating starting conditions, 50% WHCmax, and 30% WHCmax, representing reduced moisture conditions. Diversity and abundances of soil fungi at the start and at the end of the experiment were characterized using Illumina meta-barcoding. Community diversity at the end of the experiment did not differ between experimental moisture levels and was comparable to diversity measures from the field. However, fungal communities did change compositionally in both abundances and presence/absence of species. Analyzing class-level and individual contributions of fungi to these changes revealed that only a minor portion reacted significantly, indicating that most compositional change was likely driven by many consistent small-scale shifts in presence/absences or abundances. Together, our results show that prolonged reduction in soil moisture conditions will trigger compositional changes in soil fungal communities but not necessarily change overall diversity. We highlight the cumulative contribution of minor but consistent changes among community members, as opposed to significant responses of individual species. We also detected a strong general experimental effect on soil fungi that are moved from the field to experimental TMEs, suggesting the importance of acclimatization effects in these communities under laboratory conditions.
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Affiliation(s)
- Philipp-André Schmidt
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
- Goethe Universität Frankfurt, Institut für Ökologie, Evolution und Diversität, Max-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
- Goethe Universität Frankfurt, Institut für Ökologie, Evolution und Diversität, Max-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
| | - Cornelia Bandow
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
- Goethe Universität Frankfurt, Institut für Ökologie, Evolution und Diversität, Max-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
- ECT Oekotoxikologie GmbH, 65439, Flörsheim/Main, Germany
| | - Jörg Römbke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
- ECT Oekotoxikologie GmbH, 65439, Flörsheim/Main, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany.
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany.
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Hagh-Doust N, Akbarinia M, Safaie N, Yousefzadeh H, Bálint M. Community analysis of Persian oak fungal microbiome under dust storm conditions. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Vitecek S, Kučinić M, Previšić A, Živić I, Stojanović K, Keresztes L, Bálint M, Hoppeler F, Waringer J, Graf W, Pauls SU. Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics. BMC Evol Biol 2017; 17:129. [PMID: 28587671 PMCID: PMC5461746 DOI: 10.1186/s12862-017-0972-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/18/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets. RESULTS Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy. CONCLUSIONS Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring.
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Affiliation(s)
- Simon Vitecek
- Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Senckenberg Research Institute and Natural History Museum, Frankfurt’ to ‘Frankfurt am Main, Germany
| | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ana Previšić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivana Živić
- Institute of Zoology, University of Belgrade-Faculty of Biology, Belgrade, Serbia
| | - Katarina Stojanović
- Institute of Zoology, University of Belgrade-Faculty of Biology, Belgrade, Serbia
| | - Lujza Keresztes
- Center for Systems Biology, Biodiversity and Bioresources, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre BIK-F, Frankfurt’ to ‘Frankfurt am Main, Germany
| | - Felicitas Hoppeler
- Senckenberg Biodiversity and Climate Research Centre BIK-F, Frankfurt’ to ‘Frankfurt am Main, Germany
| | - Johann Waringer
- Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Steffen U. Pauls
- Senckenberg Biodiversity and Climate Research Centre BIK-F, Frankfurt’ to ‘Frankfurt am Main, Germany
- Senckenberg Research Institute and Natural History Museum, Frankfurt’ to ‘Frankfurt am Main, Germany
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Oppold AM, Pedrosa JAM, Bálint M, Diogo JB, Ilkova J, Pestana JLT, Pfenninger M. Support for the evolutionary speed hypothesis from intraspecific population genetic data in the non-biting midge Chironomus riparius. Proc Biol Sci 2016; 283:20152413. [PMID: 26888029 DOI: 10.1098/rspb.2015.2413] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolutionary speed hypothesis (ESH) proposes a causal mechanism for the latitudinal diversity gradient. The central idea of the ESH is that warmer temperatures lead to shorter generation times and increased mutation rates. On an absolute time scale, both should lead to an acceleration of selection and drift. Based on the ESH, we developed predictions regarding the distribution of intraspecific genetic diversity: populations of ectothermic species with more generations per year owing to warmer ambient temperatures should be more differentiated from each other, accumulate more mutations and show evidence for increased mutation rates compared with populations in colder regions. We used the multivoltine insect species Chironomus riparius to test these predictions with cytochrome oxidase I (COI) sequence data and found that populations from warmer regions are indeed significantly more differentiated and have significantly more derived haplotypes than populations from colder regions. We also found a significant correlation of the annual mean temperature with the population mutation parameter θ that serves as a proxy for the per generation mutation rate under certain assumptions. This pattern could be corroborated with two nuclear loci. Overall, our results support the ESH and indicate that the thermal regime experienced may be crucially driving the evolution of ectotherms and may thus ultimately govern their speciation rate.
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Affiliation(s)
- Ann-Marie Oppold
- Molecular Ecology Group, Institute for Ecology, Evolution and Diversity, Goethe-University Frankfurt am Main, Hessen, Germany Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hessen, Germany
| | - João A M Pedrosa
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal Conservation Genetics Group, Senckenberg Research Institute, Gelnhausen, Hessen, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hessen, Germany
| | - João B Diogo
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hessen, Germany
| | - Julia Ilkova
- Institute of Biodiversity and Ecosystem research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - João L T Pestana
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Markus Pfenninger
- Molecular Ecology Group, Institute for Ecology, Evolution and Diversity, Goethe-University Frankfurt am Main, Hessen, Germany Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hessen, Germany
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Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol Rev 2016; 40:686-700. [DOI: 10.1093/femsre/fuw017] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
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Ibrahimi H, Kučinić M, Vitecek S, Waringer J, Graf W, Previšić A, Bálint M, Keresztes L, Pauls SU. New records for the Kosovo caddisfly fauna with the description of a new species, Drusus dardanicus sp. nov. (Trichoptera: Limnephilidae). Zootaxa 2015; 4032:551-68. [PMID: 26624385 DOI: 10.11646/zootaxa.4032.5.5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Indexed: 11/04/2022]
Abstract
The Balkan Peninsula is one of the most important European hotspots of freshwater biodiversity. The region is, however, to a large extent insufficiently investigated. Here we present data on distribution of caddisflies in one particularly understudied area, the Republic of Kosovo. Our data include the first records of Adicella altandroconia Botosaneanu & Novak and Halesus tessellatus (Rambur) for the Kosovo caddisfly fauna, and a new locality for the recently described Ecclisopteryx keroveci Previšić, Graf, & Vitecek. Further, we describe the new caddisfly species Drusus dardanicus sp. nov. from the Kopaonik Mountains. The new species belongs to the D. discophorus Species Group and differs morphologically from its most similar congeners (D. discophorus Radovanović, D. balcanicus Kumanski, and D. bureschi Kumanski) mainly in exhibiting (1) subtrianglar superior appendages; (2) a narrow, dorsal spinate area of tergite VIII; and (3) evenly rounded tips of intermediate appendages in caudal view. In phylogenetic analysis, D. dardanicus sp. nov. is well delineated and recovered as a sister taxon to D. osogovicus Kumanski, a species recorded from Bulgaria. The recent discovery of a new species and other rare or microendemic species presents important contributions to the knowledge on the rich freshwater biodiversity in Kosovo. These species face increasing anthropogenic pressure and threats to their conservation.
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Affiliation(s)
- Halil Ibrahimi
- Department of Biology, Faculty of Mathematical and Natural Sciences, University of Prishtina "Hasan Prishtina," "Mother Theresa" street p.n. 10000 Prishtina, Kosovo.;
| | - Mladen Kučinić
- Department of Biology, Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia.;
| | - Simon Vitecek
- Department of Limnology & Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.;
| | - Johann Waringer
- Department of Limnology & Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.;
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources and Life Sciences, Vienna, Austria.;
| | - Ana Previšić
- Department of Biology, Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia.;
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60388 Frankfurt a. M., Germany.;
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, Cluj-Napoca, Romania.;
| | - Steffen U Pauls
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60388 Frankfurt a. M., Germany.;
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Vitecek S, Kučinić M, Oláh J, Previšić A, Bálint M, Keresztes L, Waringer J, Pauls SU, Graf W. Description of two new filtering carnivore Drusus species (Limnephilidae, Drusinae) from the Western Balkans. Zookeys 2015:79-104. [PMID: 26257570 PMCID: PMC4524279 DOI: 10.3897/zookeys.513.9908] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 04/28/2015] [Accepted: 06/26/2015] [Indexed: 11/12/2022] Open
Abstract
Two new species of the genus Drusus (Trichoptera, Limnephilidae, Drusinae) from the Western Balkans are described. Additionally, observations on the biodiversity and threats to the region's endemic aquatic fauna are discussed. Drususkrpachi sp. n. is a micro-endemic of the Korab Mountains, Macedonia, and Drususmalickyi sp. n. is a micro-endemic of the Prokletije Mountains, Albania. Both new species are most similar to Drususmacedonicus but differ from the latter in the shape of segment IX, the shape of the tips of the intermediate appendages in lateral view, the shape of the inferior appendages, and the form and shape of the parameres. In addition, males of the European species of filtering carnivore Drusinae are diagnosed and illustrated, including Cryptothrixnebulicola McLachlan, Drususchrysotus Rambur, Drususdiscolor Rambur, Drususmacedonicus Schmid, Drususmeridionalis Kumanski, Drususmuelleri McLachlan, Drususromanicus Murgoci and Botosaneanu, and Drusussiveci Malicky. These additions to the Western Balkan fauna demonstrate the significance of this region for European biodiversity and further highlight the importance of faunistic studies in Europe.
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Affiliation(s)
- Simon Vitecek
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | | | - Ana Previšić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt a.M., Germany
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johann Waringer
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Steffen U Pauls
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt a.M., Germany
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources, Max-Emanuelstrasse 17, A-1180 Vienna, Austria
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Waringer J, Graf W, Bálint M, Kučinić M, Pauls SU, Previšić A, Keresztes L, Vitecek S. The larvae of Drusus franzressli Malicky 1974 and Drusus spelaeus (Ulmer 1920) (Trichoptera: Limnephilidae: Drusinae) with notes on ecology and zoogeography. Zootaxa 2015; 3637:1-16. [PMID: 26046172 DOI: 10.11646/zootaxa.3637.1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Water quality monitoring is greatly dependent on identification tools for aquatic and semi-aquatic insects. Species-level identification improves resolution and precision of water quality assessment and requires comprehensive keys. With the aim of increasing the suitability of Drusinae for such applications, this paper gives a description of the hitherto unknown larvae of Drusus franzressli Malicky 1974 and Drusus spelaeus (Ulmer 1920). Information on the morphology of the larvae is given and the most important diagnostic features are illustrated. In the context of already available keys, the larvae of D. franzressli and D. spelaeus key together with Metanoea flavipennis (Pictet 1834), M. rhaetica Schmid 1956, D. improvisus McLachlan 1884, D. nigrescens Meyer-Dür 1875 and Ecclisopteryx malickyi Moretti 1991. These species are easily separated by differences in larval morphology (dorsal outline and sculpturing of pronotum, presence/absence of lateral gills at 2nd and 3rd abdominal segments, start of lateral fringe) and their distribution ranges. Drusus franzressli is endemic to the Hellenic western Balkans whereas D. spelaeus is endemic to the western Alps (Grenoble area). In addition, ecological characteristics are briefly discussed.
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Affiliation(s)
- Johann Waringer
- Department of Limnology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
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Vitecek S, Previšić A, Kučinić M, Bálint M, Keresztes L, Waringer J, Pauls SU, Malicky H, Graf W. Description of a new species of Wormaldia from Sardinia and a new Drusus species from the Western Balkans (Trichoptera, Philopotamidae, Limnephilidae). Zookeys 2015; 496:85-103. [PMID: 25931956 PMCID: PMC4410158 DOI: 10.3897/zookeys.496.9169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/26/2015] [Indexed: 11/26/2022] Open
Abstract
New species are described in the genera Wormaldia (Trichoptera, Philopotamidae) and Drusus (Trichoptera, Limnephilidae, Drusinae). Additionally, the larva of the new species Drususcrenophylax sp. n. is described, and a key provided to larval Drusus species of the bosnicus-group, in which the new species belongs. Observations on the threats to regional freshwater biodiversity and caddisfly endemism are discussed. The new species Wormaldiasarda sp. n. is an endemic of the Tyrrhenian island of Sardinia and differs most conspicuously from its congeners in the shape of segment X, which is trilobate in lateral view. The new species Drususcrenophylax sp. n. is a micro-endemic of the Western Balkans, and increases the endemism rate of Balkan Drusinae to 79% of 39 species. Compared to other Western Balkan Drusus, males of the new species are morphologically most similar to Drususdiscophorus Radovanovic and Drususvernonensis Malicky, but differ in the shape of superior and intermediate appendages. The females of Drususcrenophylax sp. n. are most similar to those of Drususvernonensis, but differ distinctly in the outline of segment X. Larvae of Drususcrenophylax sp. n. exhibit toothless mandibles, indicating a scraping grazing-feeding ecology.
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Affiliation(s)
- Simon Vitecek
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Ana Previšić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt a.M., Germany
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, Clinicilor 5–7, 400006 Cluj-Napoca, Romania
| | - Johann Waringer
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Steffen U. Pauls
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt a.M., Germany
| | | | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources and Life Sciences, Max Emanuel-Strasse 17, A-1180 Vienna, Austria
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Bálint M, Bartha L, O'Hara RB, Olson MS, Otte J, Pfenninger M, Robertson AL, Tiffin P, Schmitt I. Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars. Mol Ecol 2014; 24:235-48. [DOI: 10.1111/mec.13018] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 11/19/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Miklós Bálint
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
| | - László Bartha
- Laboratory of Molecular Environmental Biology; Institute for Interdisciplinary Research in Bio-Nano Sciences; Babe-Bolyai University; Treboniu Laurian 42 400271 Cluj Romania
| | - Robert B. O'Hara
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
| | - Matthew S. Olson
- Department of Biological Sciences; Texas Tech University; P.O. Box 43131 Lubbock TX 79409-3131 USA
- Institute of Arctic Biology; University of Alaska Fairbanks; P.O. Box 757000 Fairbanks AK 99775 USA
| | - Jürgen Otte
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
| | - Markus Pfenninger
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
- Institut für Ökologie, Evolution und Diversität; Goethe Universität; Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Amanda L. Robertson
- Institute of Arctic Biology; University of Alaska Fairbanks; P.O. Box 757000 Fairbanks AK 99775 USA
- Science Applications; U.S. Fish & Wildlife Service; 101 12th Avenue Fairbanks AK 99701 USA
| | - Peter Tiffin
- Department of Plant Biology; University of Minnesota; 1445 Gortner Avenue St. Paul MN 55108 USA
| | - Imke Schmitt
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
- Institut für Ökologie, Evolution und Diversität; Goethe Universität; Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
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Previšić A, Graf W, Vitecek S, Kučinić M, Bálint M, Keresztes L, Pauls SU, Waringer J. Cryptic diversity of caddisflies in the Balkans: the curious case of Ecclisopteryx species (Trichoptera: Limnephilidae). Arthropod Syst Phylogeny 2014; 72:309-329. [PMID: 25810791 PMCID: PMC4370265] [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] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Adults and larvae of two new cryptic, endemic caddisflies, Ecclisopteryx keroveci sp.n. and Ecclisopteryx ivkae sp.n., are described and illustrated from the Western Balkans. Phylogenetic analysis (Bayesian MCMCMC) and association of different life history stages in both cryptic species were achieved through comparison of morphological characters and mitochondrial (mtCOI and mtLSU) and nuclear (nuWG) gene sequence data. The new species form a sister clade to the widely distributed E. dalecarlica and E. guttulata, with which they were formerly misidentified. Adults differ from each other and other species in the genus by the uniquely shaped inferior appendages in males and segment X in females. The larvae differ from each other and their congeners in the shape of the pronotum, and presence and constitution of additional spines on the parietalia. Larvae of both species are grazers and prefer stony substrate. Ecclisopteryx keroveci sp.n. has a wide distribution in the Western Balkans, while E. ivkae sp.n. is endemic to Dalmatia. Our findings demonstrate the significance of the Western Balkans as a freshwater biodiversity hotspot, and accentuate the importance of research focused on freshwater biodiversity and biogeography in southern Europe.
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Affiliation(s)
- Ana Previšić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Applied Life Sciences, Max Emanuel-Strasse 17, A-1180 Vienna, Austria
| | - Simon Vitecek
- Department of Limnology & Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Miklós Bálint
- Biodiversity and Climate Research Centre (LOEWE BiK-F), Senckenberganlage 25, D-60325 Frankfurt a.M., Germany
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, Clinicilor 5 – 7, 400006 Cluj-Napoca, Romania
| | - Steffen U. Pauls
- Biodiversity and Climate Research Centre (LOEWE BiK-F), Senckenberganlage 25, D-60325 Frankfurt a.M., Germany
| | - Johann Waringer
- Department of Limnology & Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
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Pfenninger M, Weigand A, Bálint M, Klussmann-Kolb A. Misperceived invasion: the Lusitanian slug (Arion lusitanicus auct. non-Mabille or Arion vulgaris Moquin-Tandon 1855) is native to Central Europe. Evol Appl 2014; 7:702-13. [PMID: 25067951 PMCID: PMC4105919 DOI: 10.1111/eva.12177] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [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: 10/31/2013] [Accepted: 05/06/2014] [Indexed: 11/29/2022] Open
Abstract
The Lusitanian slug, presumed to be native to south-west Europe, was ranked among the 100 worst invading species in Central Europe. However, from the very beginning of its recognition in the presumed invasion area, there was little evidence that the species was actually anthropogenically introduced. We investigated the invasive status of the species by comparing specific predictions on the population genetic structure in the invasion area with the pattern actually found. In a DNA-taxonomy approach, the species could not be found in its presumed native range. Using statistical phylogeographic techniques on a mitochondrial (COI) and nuclear (ZF) marker and species distribution modelling, we could show that the species is with very high probability not an invasor, but native to Central Europe. The study underlines the value of statistical phylogeography in rigorously testing hypotheses on the dynamics of biological invasions.
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Affiliation(s)
- Markus Pfenninger
- Biodiversity und Climate Research Centre by Senckenberg Naturforschende Gesellschaft, Goethe-Universität Frankfurt, Germany
| | - Alexander Weigand
- Institute for Ecology, Evolution and Diversity, J.W. Goethe-Universität Frankfurt, Germany
| | - Miklós Bálint
- Biodiversity und Climate Research Centre by Senckenberg Naturforschende Gesellschaft, Goethe-Universität Frankfurt, Germany
| | - Annette Klussmann-Kolb
- Institute for Ecology, Evolution and Diversity, J.W. Goethe-Universität Frankfurt, Germany
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Bálint M, Schmidt PA, Sharma R, Thines M, Schmitt I. An Illumina metabarcoding pipeline for fungi. Ecol Evol 2014; 4:2642-53. [PMID: 25077016 PMCID: PMC4113289 DOI: 10.1002/ece3.1107] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [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: 03/27/2014] [Revised: 04/14/2014] [Accepted: 04/23/2014] [Indexed: 11/07/2022] Open
Abstract
High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (1) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding; (2) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments; and (3) is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus giving the user maximum control over data treatment and avoiding a black-box approach. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.
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Affiliation(s)
- Miklós Bálint
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für NaturforschungSenckenberganlage 25, 60325, Frankfurt/Main, Germany
| | - Philipp-André Schmidt
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für NaturforschungSenckenberganlage 25, 60325, Frankfurt/Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe Universität FrankfurtMax-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
| | - Rahul Sharma
- Institut für Ökologie, Evolution und Diversität, Goethe Universität FrankfurtMax-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für NaturforschungSenckenberganlage 25, 60325, Frankfurt/Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe Universität FrankfurtMax-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
| | - Imke Schmitt
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für NaturforschungSenckenberganlage 25, 60325, Frankfurt/Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe Universität FrankfurtMax-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
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Dal Grande F, Alors D, Divakar PK, Bálint M, Crespo A, Schmitt I. Insights into intrathalline genetic diversity of the cosmopolitan lichen symbiotic green alga Trebouxia decolorans Ahmadjian using microsatellite markers. Mol Phylogenet Evol 2014; 72:54-60. [DOI: 10.1016/j.ympev.2013.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/20/2013] [Accepted: 12/30/2013] [Indexed: 11/28/2022]
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Meiser A, Bálint M, Schmitt I. Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns. New Phytol 2014; 201:623-635. [PMID: 24111803 DOI: 10.1111/nph.12532] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 08/27/2013] [Indexed: 06/02/2023]
Abstract
High-throughput amplicon sequencing gives new insights into fungal community ecology. Massively generated molecular data lead to the discovery of vast fungal diversity. However, it is unclear to what extent operational taxonomic units (OTUs) overlap among independent studies, because no comparative studies exist. We compared fungal diversity based on the internal transcribed spacer (ITS1) region among 10 published studies. Starting from the raw 454 pyrosequencing data, we used a uniform pipeline to prune the reads. We investigated fungal richness and taxonomic composition among phyllosphere and soil fungal communities, as well as biogeographic signals in the data. We did not find globally distributed OTUs, even when comparing fungal communities from similar habitats (phyllosphere or soil). This suggests that high local fungal diversity scales up to high global diversity. The most OTU-rich classes in the phyllosphere were Dothideomycetes (21%) and Sordariomycetes (14%), and in the soil were Sordariomycetes (13%) and Agaricomycetes (12%). The richness estimates suggest the presence of undiscovered fungal diversity even in deeply sequenced study systems. The small number of OTUs shared among studies indicates that globally distributed taxa and habitat generalists may be rare. Latitudinal diversity decline and distance decay relationships suggest the presence of biogeographic patterns similar to those in plants and animals.
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Affiliation(s)
- Anjuli Meiser
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Imke Schmitt
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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Sadowska-Deś AD, Bálint M, Otte J, Schmitt I. Corrigendum to “Assessing intraspecific diversity in a lichen-forming fungus and its green algal symbiont: Evaluation of eight molecular markers” [Fungal Ecology (2012) 141–151]. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2013.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kučinić M, Szivák I, Pauls SU, Bálint M, Delić A, Vučković I. Chaetopteryx bucari sp. n., a new species from the Chaetopteryx rugulosa group from Croatia (Insecta, Trichoptera, Limnephilidae) with molecular, taxonomic and ecological notes on the group. Zookeys 2013; 320:1-28. [PMID: 23950680 PMCID: PMC3744148 DOI: 10.3897/zookeys.320.4565] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 12/23/2012] [Accepted: 06/27/2013] [Indexed: 11/12/2022] Open
Abstract
We describe a new autumnal caddisfly species Chaetopteryx bucari sp. n. from 8 localities in the Banovina region of Croatia. We also present molecular, taxonomic and ecological notes (emergence, sex ratio and seasonal dynamics) on the new species and discuss the distribution of Chaetopteryx species in general and the Chaetopteryx rugulosa group in particular. Based on Bayesian phylogenetic analysis Chaetopteryx rugulosa schmidi was separated from the clade containing the other subspecies of Chaetopteryx rugulosa. Thus the subspecies Chaetopteryx rugulosa schmidi is here raised to species level, Chaetopteryx schmidi, as it was described originally. We further present distribution data on rare species in the genus Chaetopteryx in Croatia.
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Affiliation(s)
- Mladen Kučinić
- Department of Biology (Group for Systematic Zoology & Entomology), Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Ildikó Szivák
- Balaton Limnological Institute, Centre for Ecological Research, Hungarian Academy of Science, H-8237 Tihany, Klebelsberg Kuno u. 3, Hungary
| | - Steffen U. Pauls
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Miklós Bálint
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Antun Delić
- Faculty of Ecudation, Department in Petrinja, University of Zagreb, Matice Hrvatske 12, 44250, Petrinja, Croatia
| | - Ivan Vučković
- Elektroprojekt d.d., Civil and Architectural Engineering Department, Alexandera von Humboldta 4, 10000 Zagreb, Croatia
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Waringer J, Graf W, Bálint M, Kučinić M, Pauls SU, Previšić A, Keresztes L, Vitecek S. The larva of Drusus vinconi Sipahiler, 1992 (Trichoptera, Limnephilidae, Drusinae). Zookeys 2013:69-80. [PMID: 23950671 PMCID: PMC3744139 DOI: 10.3897/zookeys.317.5749] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 06/06/2013] [Accepted: 07/11/2013] [Indexed: 11/17/2022] Open
Abstract
This paper describes the previously unknown larva of Drusus vinconi Sipahiler, 1992. Information on the morphology of the 5th larval instar is given, and the most important diagnostic features are illustrated. In the context of existing identification keys the larva of Drusus vinconi keys together with Drusus annulatus (Stephens, 1837), Drusus biguttatus (Pictet, 1834), Drusus ingridae Sipahiler, 1993, Hadimina torosensis Sipahiler, 2002 and Leptodrusus budtzi (Ulmer, 1913). These species differ in the contours of the pronotum in lateral view, the presence/absence of the pronotal transverse groove, the shape of the median notch of the pronotum (in anterior view), pronotal sculpturing, presence/absence of the lateral carina of the head capsule, the number of proximo-dorsal setae on the mid-and hind femora, where the lateral fringe starts on the abdomen, and in geographic distribution. With respect to zoogeography, Drusus vinconi is a (micro-)endemic of the Western Pyrenees. The species prefers stony substratum in springs and springbrooks of the montane and subalpine region (Graf et al. 2008; Sipahiler 1992, 1993). As a grazer, the larvae of Drusus vinconi feed on biofilm and epilithic algae.
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Affiliation(s)
- Johann Waringer
- Department of Limnology, Faculty of Life Sciences, University of Vienna, Austria
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Sadowska-Deś AD, Bálint M, Otte J, Schmitt I. Assessing intraspecific diversity in a lichen-forming fungus and its green algal symbiont: Evaluation of eight molecular markers. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Pauls SU, Nowak C, Bálint M, Pfenninger M. The impact of global climate change on genetic diversity within populations and species. Mol Ecol 2012; 22:925-46. [DOI: 10.1111/mec.12152] [Citation(s) in RCA: 392] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 10/22/2012] [Accepted: 10/25/2012] [Indexed: 12/16/2022]
Affiliation(s)
- Steffen U. Pauls
- Biodiversity and Climate Research Centre (BiK‐F) by Senckenberg Gesellschaft für Naturforschung and Goethe University Senckenberganlage 25 D‐60325 Frankfurt/Main Germany
| | - Carsten Nowak
- Biodiversity and Climate Research Centre (BiK‐F) by Senckenberg Gesellschaft für Naturforschung and Goethe University Senckenberganlage 25 D‐60325 Frankfurt/Main Germany
- Conservation Genetics Group Senckenberg Research Institute and Natural History Museum Frankfurt Clamecystraße 12 D‐63571 Gelnhausen Germany
| | - Miklós Bálint
- Biodiversity and Climate Research Centre (BiK‐F) by Senckenberg Gesellschaft für Naturforschung and Goethe University Senckenberganlage 25 D‐60325 Frankfurt/Main Germany
- Molecular Biology Center, Babes‐Bolyai University Str. Treboniu Laurian 42 400271 Cluj Romania
| | - Markus Pfenninger
- Biodiversity and Climate Research Centre (BiK‐F) by Senckenberg Gesellschaft für Naturforschung and Goethe University Senckenberganlage 25 D‐60325 Frankfurt/Main Germany
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Pfenninger M, Bálint M, Pauls SU. Methodological framework for projecting the potential loss of intraspecific genetic diversity due to global climate change. BMC Evol Biol 2012; 12:224. [PMID: 23176586 PMCID: PMC3538604 DOI: 10.1186/1471-2148-12-224] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 10/30/2012] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND While research on the impact of global climate change (GCC) on ecosystems and species is flourishing, a fundamental component of biodiversity - molecular variation - has not yet received its due attention in such studies. Here we present a methodological framework for projecting the loss of intraspecific genetic diversity due to GCC. METHODS The framework consists of multiple steps that combines 1) hierarchical genetic clustering methods to define comparable units of inference, 2) species accumulation curves (SAC) to infer sampling completeness, and 3) species distribution modelling (SDM) to project the genetic diversity loss under GCC. We suggest procedures for existing data sets as well as specifically designed studies. We illustrate the approach with two worked examples from a land snail (Trochulus villosus) and a caddisfly (Smicridea (S.) mucronata). RESULTS Sampling completeness was diagnosed on the third coarsest haplotype clade level for T. villosus and the second coarsest for S. mucronata. For both species, a substantial species range loss was projected under the chosen climate scenario. However, despite substantial differences in data set quality concerning spatial sampling and sampling depth, no loss of haplotype clades due to GCC was predicted for either species. CONCLUSIONS The suggested approach presents a feasible method to tap the rich resources of existing phylogeographic data sets and guide the design and analysis of studies explicitly designed to estimate the impact of GCC on a currently still neglected level of biodiversity.
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Affiliation(s)
- Markus Pfenninger
- Biodiversity and Climate Research Centre (BiK-F) by Senckenberg Research Institut & Goethe University, Senckenberganlage 25, D-60325, Frankfurt/Main, Germany
| | - Miklós Bálint
- Biodiversity and Climate Research Centre (BiK-F) by Senckenberg Research Institut & Goethe University, Senckenberganlage 25, D-60325, Frankfurt/Main, Germany
- Molecular Biology Center, Babeş-Bolyai University, Str. Treboniu Laurian 42, 400271, Cluj, Romania
| | - Steffen U Pauls
- Biodiversity and Climate Research Centre (BiK-F) by Senckenberg Research Institut & Goethe University, Senckenberganlage 25, D-60325, Frankfurt/Main, Germany
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Magyari EK, Major A, Bálint M, Nédli J, Braun M, Rácz I, Parducci L. Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses. BMC Evol Biol 2011; 11:66. [PMID: 21392386 PMCID: PMC3068097 DOI: 10.1186/1471-2148-11-66] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [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: 10/07/2010] [Accepted: 03/10/2011] [Indexed: 12/04/2022] Open
Abstract
Background Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site. Results We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci. Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact. Conclusion Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene; however our limited sample size did not allow us to exclude sampling effect. This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetics analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species.
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Affiliation(s)
- Eniko K Magyari
- MTA-MTM Research Group for Paleontology, 1476 Budapest, P, O, Box 222, Hungary.
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Ujvárosi L, Bálint M, Schmitt T, Mészáros N, Ujvárosi T, Popescu O. Divergence and speciation in the Carpathians area: patterns of morphological and genetic diversity of the crane flyPedicia occulta(Diptera:Pediciidae). ACTA ACUST UNITED AC 2010. [DOI: 10.1899/09-099.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lujza Ujvárosi
- Department of Taxonomy and Ecology, Faculty of Biology and Geology, Babeş-Bolyai University, Clinicilor 5-7, 400002 Cluj, Romania
| | - Miklós Bálint
- Molecular Biology Center, Babeş-Bolyai University, Treboniu Laurian 42, 400271 Cluj, Romania
- Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Thomas Schmitt
- Department of Biogeography, Trier University, Am Wissenschaftspark 25–27, D-54286 Trier, Germany
| | - Noémi Mészáros
- Institute of Biochemistry, Biological Research Center, Temesvári krt. 62, H-6726 Szeged, Hungary
| | | | - Octavian Popescu
- Molecular Biology Center, Babeş-Bolyai University, Treboniu Laurian 42, 400271 Cluj, Romania
- Institute of Biology Bucharest, Romanian Academy, 296 Spl. Independenţei, Bucharest, Romania
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Lehrian S, Bálint M, Haase P, Pauls SU. Genetic population structure of an autumn-emerging caddisfly with inherently low dispersal capacity and insights into its phylogeography. ACTA ACUST UNITED AC 2010. [DOI: 10.1899/09-100.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stephanie Lehrian
- Department of Limnology and Conservation, Senckenberg, 63571 Gelnhausen, Germany
- Department Aquatic Ecotoxicology, Johann Wolfgang Goethe University Frankfurt am Main, 600054 Frankfurt am Main, Germany
| | - Miklós Bálint
- Biodiversity and Climate Research Centre (LOEWE BiK-F), Georg-Voigt-Straße 14-16, D-60325 Frankfurt am Main, Germany
- Molecular Biology Center, Babeş-Bolyai University, 400271 Cluj, Romania
| | - Peter Haase
- Department of Limnology and Conservation, Senckenberg, 63571 Gelnhausen, Germany
- Biodiversity and Climate Research Centre (LOEWE BiK-F), Georg-Voigt-Straße 14-16, D-60325 Frankfurt am Main, Germany
| | - Steffen U. Pauls
- Department of Limnology and Conservation, Senckenberg, 63571 Gelnhausen, Germany
- Biodiversity and Climate Research Centre (LOEWE BiK-F), Georg-Voigt-Straße 14-16, D-60325 Frankfurt am Main, Germany
- Department of Entomology, University of Minnesota, St Paul, Minnesota 55108, USA
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Magyari EK, Braun M, Buczkó K, Kern Z, László P, Hubay K, Bálint M. Radiocarbon chronology of glacial lake sediments in the Retezat Mts (South Carpathians, Romania): a window to Late Glacial and Holocene climatic and paleoenvironmental changes. ACTA ACUST UNITED AC 2009. [DOI: 10.1556/ceugeol.52.2009.3-4.2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Bálint M, Barnard PC, Schmitt T, Ujvárosi L, Popescu O. Differentiation and speciation in mountain streams: a case study in the caddisflyRhyacophila aquitanica(Trichoptera). J ZOOL SYST EVOL RES 2008. [DOI: 10.1111/j.1439-0469.2008.00480.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Barna M, Horvàth K, Bálint M, Antal M. Cardiovascular risks in childhood in Hungary. Forum Nutr 2003; 56:247-9. [PMID: 15806884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- M Barna
- Semmelweis University, College of Health Care, Department of Dietetics, Budapest, Hungary.
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