Author: "Lucie Zinger" / Topic: 03 medical and health sciences - Searchworks@Jio Institute Digital Library Search Results

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1. Cascading effects of moth outbreaks on subarctic soil food webs

Author: Heidy Schimann, Lucie Zinger, Mickaël Hedde, Wilfried Thuiller, Arnaud Foulquier, Irene Calderón-Sanou, Mélanie Roy, Marc Ohlmann, Sara Si-Moussi, Nigel G. Yoccoz, Tamara Münkemüller, Ludovic Gielly, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Arctic University of Norway [Tromsø, Norway] (UiT), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire de Mathématiques (LAMA), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Instituto Franco-Argentino sobre Estudios de Clima y sus Impactos [Buenos Aires] (IFAECI), Centro de Investigaciones del Mar y la Atmósfera (CIMA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas y Naturales [Buenos Aires] (FCEyN), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA)-Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas y Naturales [Buenos Aires] (FCEyN), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA)-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE02-0009,GlobNets,Biogéographie globale des réseaux écologiques des forêts du monde(2016), THUILLER, Wilfried, Biogéographie globale des réseaux écologiques des forêts du monde - - GlobNets2016 - ANR-16-CE02-0009 - AAPG2016 - VALID, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), The Arctic University of Norway (UiT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Facultad de Ciencias Exactas y Naturales [Buenos Aires] (FCEyN), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA)-Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Food Chain, Ecosystem ecology, Science, Biodiversity, Moths, Biology, Poaceae, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Mycorrhizae, Animals, Ecosystem, Relative species abundance, Betula, Trophic level, Multidisciplinary, Defoliants, Chemical, Ecology, Plant community, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, 15. Life on land, Subarctic climate, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, 030104 developmental biology, Disturbance (ecology), Ecological networks, Medicine, Omnivore, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental Pollution, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: The increasing severity and frequency of natural disturbances requires a better understanding of their effects on all compartments of biodiversity. In Northern Fennoscandia, recent large-scale moth outbreaks have led to an abrupt change in plant communities from birch forests dominated by dwarf shrubs to grass-dominated systems. However, the indirect effects on the belowground compartment remained unclear. Here, we combined eDNA survey of multiple trophic groups with network analyses to demonstrate that moth defoliation has far-reaching consequences on soil food webs. Following this disturbance, diversity and relative abundance of certain trophic groups declined (e.g. ectomycorrhizal fungi) while many others profited (e.g. bacterivores, omnivores) making soil food webs more diverse and structurally different. Overall, the direct and indirect consequences of moth outbreaks increased belowground diversity at different trophic levels. Our results highlight that a holistic view of ecosystems improves our understanding of cascading effects of major disturbances on soil food webs.
Published: 2021
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2. A robust approach to estimate relative phytoplankton cell abundance from metagenomes

Author: Patrick Wincker, Sébastien Colin, Chris Bowler, Pierella Karlusich Jj, Richard G. Dorrell, de Vargas C, Josep M. Gasol, Adriana Zingone, Eleonora Scalco, Fabien Lombard, Lucie Zinger, Eric Pelletier, and Silvia G. Acinas
Subjects: 0303 health sciences, Biomass (ecology), Phototroph, 030306 microbiology, fungi, 15. Life on land, Ribosomal RNA, Biology, Genome, 03 medical and health sciences, 13. Climate action, Evolutionary biology, Abundance (ecology), Metagenomics, Phytoplankton, 14. Life underwater, Relative species abundance, 030304 developmental biology
Abstract: Phytoplankton account for >45% of primary production on Earth, and hence have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found across many of the major clades of the tree of life, including prokaryotes (cyanobacteria) and multiple eukaryotic lineages. Phytoplankton communities are generally studied by PCR amplification of rRNA marker genes from the DNA extracted from environmental samples and high-throughput sequencing of the amplicons. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa and the fact that rRNA do not provide insights into metabolic traits such as photosynthesis (i.e., it is sometimes difficult to distinguish an rRNA sequence of a phytoplanktonic species from a phylogenetically close non-photosynthetic species). In addition, rRNA marker genes fail to capture both cyanobacteria and photosynthetic eukaryotes simultaneously, thus hampering assessment of the entire phytoplankton community. Here, we propose to use the core single-copy photosynthetic gene psbO extracted from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is present in both prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the Tara Oceans datasets, and showed in most cases improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these organisms, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine communities of dinoflagellates. To facilitate the incorporation of psbO in future molecular-based surveys, we released a curated database including >20,000 unique sequences. Overall, psbO appears to be a promising new gene marker for improving molecular-based evaluations of phytoplankton communities.
Published: 2021
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3. Decay of similarity across tropical forest communities: integrating spatial distance with soil nutrients

Author: Jordi Sardans, Jérôme Murienne, Lucie Zinger, Leandro Van Langenhove, Romà Ogaya, Albert Gargallo-Garriga, Amaia Iribar, Olga Margalef, Irene Ramirez-Rojas, Elodie A. Courtois, Lore T. Verryckt, Ivan A. Janssens, Jérôme Orivel, Guille Peguero, Josep Peñuelas, Andreas Richter, Erik Verbruggen, Dolores Asensio, Oriol Grau, Clément Stahl, Joan Llusià, Miquel Ferrín, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Guyane (UG)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: 0106 biological sciences, Soil biodiversity, scale-dependency, soil biodiversity, Rainforest, Forests, Biology, 010603 evolutionary biology, 01 natural sciences, Trees, Soil, 03 medical and health sciences, Propagule, nutrients, Sampling design, Ecosystem, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Ecological niche, 0303 health sciences, Community, Ecology, Biodiversity, environmental filtering, 15. Life on land, French Guiana, Chemistry, metabarcoding, Spatial ecology, Biological dispersal, community assembly, dispersion, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Altres ajuts: acords transformatius de la UAB Understanding the mechanisms that drive the change of biotic assemblages over space and time is the main quest of community ecology. Assessing the relative importance of dispersal and environmental species selection in a range of organismic sizes and motilities has been a fruitful strategy. A consensus for whether spatial and environmental distances operate similarly across spatial scales and taxa, however, has yet to emerge. We used censuses of four major groups of organisms (soil bacteria, fungi, ground insects, and trees) at two observation scales (1-m sampling point vs. 2,500-m plots) in a topographically standardized sampling design replicated in two tropical rainforests with contrasting relationships between spatial distance and nutrient availability. We modeled the decay of assemblage similarity for each taxon set and site to assess the relative contributions of spatial distance and nutrient availability distance. Then, we evaluated the potentially structuring effect of tree composition over all other taxa. The similarity of nutrient content in the litter and topsoil had a stronger and more consistent selective effect than did dispersal limitation, particularly for bacteria, fungi, and trees at the plot level. Ground insects, the only group assessed with the capacity of active dispersal, had the highest species turnover and the flattest nonsignificant distance−decay relationship, suggesting that neither dispersal limitation nor nutrient availability were fundamental drivers of their community assembly at this scale of analysis. Only the fungal communities at one of our study sites were clearly coordinated with tree composition. The spatial distance at the smallest scale was more important than nutrient selection for the bacteria, fungi, and insects. The lower initial similarity and the moderate variation in composition identified by these distance-decay models, however, suggested that the effects of stochastic sampling were important at this smaller spatial scale. Our results highlight the importance of nutrients as one of the main environmental drivers of rainforest communities irrespective of organismic or propagule size and how the overriding effect of the analytical scale influences the interpretation, leading to the perception of greater importance of dispersal limitation and ecological drift over selection associated with environmental niches at decreasing observation scales.
Published: 2021
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4. Sharing and reporting benefits from biodiversity research

Author: Emily Marden, Megan L. Smith, Nicholas M. Fountain-Jones, Annabel Whibley, Nolan C. Kane, Ana L. Caicedo, Rosemary G. Gillespie, Kathryn A. Hodgins, Paul A. Hohenlohe, Benjamin Sibbett, Loren H. Rieseberg, Joanna L. Kelley, Andrew P. Kinziger, Graham N. Stone, Lisette P. Waits, Aurélie Bonin, Luke Browne, C. Alex Buerkle, Daniel Ortiz-Barrientos, Jeremy B. Yoder, David W. Coltman, Cynthia Riginos, Brent C. Emerson, Alex J. Dumbrell, Suhua Shi, Jacob A. Russell, Pim Bongaerts, Sébastien Renaut, Michael Møller Hansen, Emily Warschefsky, Tara A. Pelletier, Naiara Rodríguez-Ezpeleta, Regina S. Baucom, Valerie J. McKenzie, Sean D. Schoville, Frédéric Austerlitz, Janna R. Willoughby, Elin Videvall, Victoria L. Sork, Richard J. Abbott, J. Andrew DeWoody, Lucie Zinger, Pierre Taberlet, Mitchell B. Cruzan, Sean M. Rogers, Robert K. Wayne, Josephine M. Pemberton, Tatiana Giraud, Yanhua Qu, Alison G. Nazareno, Myriam Heuertz, Camille Bonneaud, Corrie S. Moreau, Angus Davison, Shawn R. Narum, Shotaro Hirase, Rebecca Hooper, Centre National de la Recherche Scientifique (CNRS), AgroParisTech, Université Paris-Saclay, Biodiversité, Gènes & Communautés (BioGeCo), and Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Conservation of Natural Resources, Knowledge management, Biodiversity research, [SDV]Life Sciences [q-bio], MEDLINE, Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 11. Sustainability, Genetics, 14. Life underwater, Nagoya Protocol, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, business.industry, 15. Life on land, 13. Climate action, business
Abstract: The most remarkable feature of our planet is the diversity of its life forms, ranging from viruses and nanobacteria to blue whales and giant sequoias to satanic leaf‐tailed geckos and leafy seadragons (look them up!). Life is found in essentially all environments on earth, and the number of species living on our planet is many times greater than we could have imagined a century ago. A well‐regarded estimate pegs the number of eukaryotic species on earth at 8.7 million (±1.3 million), of which fewer than 15% are currently described (Mora et al., 2011). The diversity of prokaryotes is less clear (and highly controversial), but an analysis of 1.6 billion 16S ribosomal RNA sequences estimated that 0.8–1.6 million prokaryotic operational taxonomic units exist globally (Louca et al., 2019). While we do not know how many species are currently extant, or have existed in the past, we do know that this biodiversity is valuable, providing food, fibre and medicine, furnishing ecosystem services such as water and air purification, nutrient cycling, pollination and carbon uptake, and contributing to technological innovations ranging from biotechnology to robotics to material science. Moreover, biodiversity underlies the cultural identity of human populations and is important to human health and well‐being. Geographically, species richness increases from the Polar Regions to the tropics in terrestrial and surface marine ecosystems. Thus, some countries, especially those in tropical and subtropical regions, are endowed with much greater biodiversity than others. Unfortunately, benefits arising from the access and utilization of this biodiversity have been unequally shared, with (paradoxically) biodiversity‐poor countries often accruing the lion's share of economic gains. There can be imbalances within countries as well, wherein some segments of the population obtain greater economic benefits from biodiversity and associated traditional knowledge than indigenous peoples. The “Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization,” which came into force in 2014, is an international agreement designed to ensure that the benefits arising from biodiversity are shared equitably (https://www.cbd.int/abs/). However, few scientific journals require compliance with the Nagoya Protocol or the reporting of benefits from biodiversity research. In this editorial, we (the editors of Molecular Ecology and Molecular Ecology Resources) express support for the Nagoya Protocol and the principle of benefit sharing. We believe that scientific journals publishing research on biodiversity can play an important role in implementing the Nagoya Protocol and in reporting on benefits generated from such research. Below, we provide background on the Nagoya Protocol, discuss the kinds of benefits that may arise from biodiversity research, describe the rationale for reporting on these benefits and introduce changes to the journals’ Data Accessibility Statements to incorporate the requirements and goals of the Nagoya Protocol.
Published: 2020
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5. Disentangling the assembly mechanisms of ant cuticular bacterial communities of two Amazonian ant species sharing a common arboreal nest

Author: Lucie Zinger, Caroline Birer, Christophe Duplais, Niklas Tysklind, Corrie S. Moreau, School of Biological Sciences [Bangor], Bangor University, Ecologie des forêts de Guyane (UMR ECOFOG), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: DNA, Bacterial, 0106 biological sciences, 0301 basic medicine, Arboreal locomotion, Cuticle, Zoology, Arthropod cuticle, Environment, 010603 evolutionary biology, 01 natural sciences, Host Specificity, Trees, 03 medical and health sciences, Species Specificity, Nest, Animal Shells, RNA, Ribosomal, 16S, Genetics, Animals, DNA Barcoding, Taxonomic, Phylogeny, reproductive and urinary physiology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Bacteria, biology, Ants, Host (biology), fungi, biology.organism_classification, ANT, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Metabolome, behavior and behavior mechanisms, Epiphyte, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Bacteria living on the cuticle of ants are generally studied for their protective role against pathogens, especially in the clade of fungus-growing ants. However, little is known regarding the diversity of cuticular bacteria in other ant host species, as well as the mechanisms leading to the composition of these communities. Here, we used 16S rRNA gene amplicon sequencing to study the influence of host species, species interactions and the pool of bacteria from the environment on the assembly of cuticular bacterial communities on two phylogenetically distant Amazonian ant species that frequently nest together inside the roots system of epiphytic plants, Camponotus femoratus and Crematogaster levior. Our results show that (a) the vast majority of the bacterial community on the cuticle is shared with the nest, suggesting that most bacteria on the cuticle are acquired through environmental acquisition, (b) 5.2% and 2.0% of operational taxonomic units (OTUs) are respectively specific to Ca. femoratus and Cr. levior, probably representing their respective core cuticular bacterial community, and (c) 3.6% of OTUs are shared between the two ant species. Additionally, mass spectrometry metabolomics analysis of metabolites on the cuticle of ants, which excludes the detection of cuticular hydrocarbons produced by the host, were conducted to evaluate correlations among bacterial OTUs and m/z ion mass. Although some positive and negative correlations are found, the cuticular chemical composition was weakly species-specific, suggesting that cuticular bacterial communities are prominently environmentally acquired. Overall, our results suggest the environment is the dominant source of bacteria found on the cuticle of ants.
Published: 2020
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6. From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices?

Author: Wilfried Thuiller, Lucie Zinger, Irene Calderón-Sanou, Frédéric Boyer, Tamara Münkemüller, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire Biologie, Informatique et Mathématiques, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and ANR-16-CE02-0009,GlobNets,Biogéographie globale des réseaux écologiques des forêts du monde(2016)
Subjects: 0106 biological sciences, Distance decay, 0303 health sciences, Ecology, [SDV]Life Sciences [q-bio], Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Environmental DNA, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience
Published: 2020
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7. Advances and prospects of environmental DNA in neotropical rainforests

Author: Amaia Iribar, Mailyn Gonzalez, Céline Leroy, Sébastien Brosse, Julian Donald, Jérôme Murienne, Lucie Zinger, Carla Martins Lopes, Pierre Taberlet, Jérôme Orivel, Heidy Schimann, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE02-0009,GlobNets,Biogéographie globale des réseaux écologiques des forêts du monde(2016), ANR-17-CE02-0007,DEBIT,Decouplage des dimensions de la biodiversité dans les écosystèmes tropicaux(2017), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, Neotropics, conservation biology, amazon, Biodiversity, Climate change, microbial communities, Rainforest, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, diversity, DNA metabarcoding, 03 medical and health sciences, Goods and services, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Deforestation, land-use, Environmental DNA, Ecosystem, Environmental planning, real-time pcr, 030304 developmental biology, biodiversity, Rainforests, 0303 health sciences, endophytic fungi, environmental genomics, Aquatic ecosystem, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, soil bacterial, Geography, 13. Climate action, biomonitoring, phylogenetic community ecology, eDNA, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, extracellular DNA
Abstract: International audience; The rainforests of the Neotropics shelter a vast diversity of plant, animal and microscopic species that provide critical ecosystem goods and services for both local and worldwide populations. These environments face a major crisis due to increased deforestation, pollution, and climate change, emphasizing the need for more effective conservation efforts. The adequate monitoring of these ecosystems has proven a complex and time consuming endeavour, which depends on ever dwindling taxonomic expertise. To date, many species remain undiscovered, let alone described, with otherwise limited information regarding known species population distributions and densities. Overcoming these knowledge shortfalls and practical limitations is becoming increasingly possible through techniques based on environmental DNA (eDNA), i.e., DNA that can be obtained from environmental samples (e.g. tissues, soil, sediment, water, etc.). When coupled with high-throughput sequencing, these techniques now enable realistic, cost-effective, and standardisable biodiversity assessments. This opens up enormous opportunities for advancing our understanding of complex and species-rich tropical communities, but also in facilitating large-scale biomonitoring programs in the neotropics. In this review, we provide a brief introduction to eDNA methods, and an overview of their current and potential uses in both terrestrial and aquatic ecosystems of neotropical rainforests. We also discuss the limits and challenges of these methods for our understanding and monitoring of biodiversity, as well as future research and applied perspectives of these techniques in neotropical rainforests, and beyond.
Published: 2020
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8. Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA‐based census of soil biodiversity from a tropical forest

Author: Jérôme Chave, Heidy Schimann, Guilhem Sommeria-Klein, Lucie Zinger, Amaia Iribar, Pierre Taberlet, Eric Coissac, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA), and Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA)
Subjects: 0106 biological sciences, 0301 basic medicine, Topic model, Soil biodiversity, Biodiversity, Initialization, Biology, 010603 evolutionary biology, 01 natural sciences, Latent Dirichlet allocation, topic modelling, 03 medical and health sciences, symbols.namesake, Soil, OTU presence-absence, Genetics, Environmental DNA, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Soil Microbiology, Bacteria, Dimensionality reduction, Fungi, Computational Biology, Eukaryota, High-Throughput Nucleotide Sequencing, 15. Life on land, environmental DNA, soil microbione, 030104 developmental biology, Taxon, metabarcoding, [SDE]Environmental Sciences, symbols, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biological system, community ecology, Biotechnology
Abstract: International audience; High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retriev-ing and interpreting the structure of such data sets requires efficient methods for di-mensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical for-est and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, con-firming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiver-sity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity.
Published: 2019
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9. The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution

Author: Juan F. Dueñas, Lucie Zinger, Florent Mazel, Julien Roy, Stefan Hempel, Matthias C. Rillig, and Moisés A. Sosa-Hernández
Subjects: 0106 biological sciences, 0301 basic medicine, Operational taxonomic unit, Databases, Factual, Physiology, Biogeography, phylogenetic scale, Beta diversity, arbuscular mycorrhizal fungi, Plant Science, Biology, 01 natural sciences, 03 medical and health sciences, 500 Naturwissenschaften und Mathematik::580 Pflanzen (Botanik)::580 Pflanzen (Botanik), Mycorrhizae, DNA, Fungal, biogeography, Phylogeny, Soil Microbiology, Phylotype, Ecological niche, operational taxonomic units (OTUs), taxonomic resolution, Phylogenetic tree, Ecology, exactsequence variants (ESVs), environmental filtering, Biodiversity, Sequence Analysis, DNA, 030104 developmental biology, Taxon, Genetic distance, amplicon sequence variants (ASVs), 010606 plant biology & botany, Mycobiome
Abstract: The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic unit (OTU) delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) to resolve phylotypes at resolutions finer than provided by traditional sequence clustering and analyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUs or at higher genetic distances. However, the correlation between environmental predictors and community turnover steeply increased at a genetic distance of c. 0.03 substitutions per site. Furthermore, we observed a turnover of either closely or distantly related taxa (respectively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at different phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences should screen different phylogenetic resolutions to better elucidate the factors that shape communities and predict the fate of AM symbioses in a changing environment.
Published: 2019

10. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

Author: Inger Greve Alsos, Lucie Zinger, Gentile Francesco Ficetola, Aurélie Bonin, Frédéric Boyer, Marta De Barba, Simon N. Jarman, M. Thomas P. Gilbert, Ian A. Dickie, Leho Tedersoo, Anthony A. Chariton, Bruce E. Deagle, Philip Francis Thomsen, Johan Pansu, Alex J. Dumbrell, Ari Jumpponen, Håvard Kauserud, Holly M. Bik, Eske Willerslev, Pierre Taberlet, Luca Fumagalli, Simon Creer, Eric Coissac, Miklós Bálint, Jan Pawlowski, Ludovic Orlando, Noah Fierer, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, New York University [New York] (NYU), NYU System (NYU), Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, emlyon business school, Politecnico di Milano [Milan] (POLIMI), University of Copenhagen = Københavns Universitet (KU), Microbial Evolution Research Group (MERG), Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Genetics and Evolution, Université de Genève (UNIGE), University of Tartu, JP was supported by the Marie Skłodowska-Curie actions (TEAM-Coast project, MSCA-GF 750570), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Robotique Et Vivant (ReV), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques
Subjects: 0106 biological sciences, replication, Ecology (disciplines), [SDV]Life Sciences [q-bio], experimental controls, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Dna genetics, Replication (statistics), Genetics, DNA Barcoding, Taxonomic, data quality, Environmental DNA, Ecology, Evolution, Behavior and Systematics, Sound (geography), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, geography, geography.geographical_feature_category, Ecology, Biodiversity, DNA, environmental DNA, chemistry, Evolutionary biology, [SDE]Environmental Sciences
Abstract: International audience
Published: 2019
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11. Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA

Author: Eliane Louisanna, Lucie Zinger, Jérôme Chave, Pierre Taberlet, Amaia Iribar, Eric Coissac, Guilhem Sommeria-Klein, Sophie Manzi, Heidy Schimann, Vincent Schilling, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Ecologie des forêts de Guyane (UMR ECOFOG), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Molécules, Biomolécules et Objets Supramoléculaires. Synthèse, structure, applications thérapeutiques. (MBOSSSAT), Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), Projet Metabar ANR 11 BSV7 0020, Investissement d'avenir ANR 10 LABX 2501, LABX 0041, ANR 11 INBS 0001, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: tropical forest, 0301 basic medicine, DNA extraction protocol, Soil test, Soil biodiversity, [SDV]Life Sciences [q-bio], Biodiversity, Soil Science, Computational biology, Biology, Microbiology, Bottleneck, DNA metabarcoding, diversity, biodiversité, communauté, 03 medical and health sciences, chemistry.chemical_compound, Relative species abundance, diversité, Ecology, Extraction (chemistry), multi-taxa biodiversity, 15. Life on land, DNA extraction, 030104 developmental biology, chemistry, fungi, DNA
Abstract: DNA metabarcoding on soil samples is increasingly used for large-scale and multi-taxa biodiversity studies. However, DNA extraction may be a major bottleneck for such wide uses. It should be cost/time effective and allow dealing with large sample volumes so as to maximise the representativeness of both micro- and macro-organisms diversity. Here, we compared the performances of a fast and cheap extracellular DNA extraction protocol with a total DNA extraction method in retrieving bacterial, eukaryotic and plant diversity from tropical soil samples of ca. 10 g. The total DNA extraction protocol yielded more high-quality DNA. Yet, the extracellular DNA protocol provided similar diversity assessments although it presented some differences in clades relative abundance and undersampling biases. We argue that extracellular DNA is a good compromise between cost, labor, and accuracy for high-throughput DNA metabarcoding studies of soil biodiversity.
Published: 2016
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12. Body size determines soil community assembly in a tropical forest

Author: Cyril Zouiten, Heidy Schimann, Amaia Iribar, Ludovic Gielly, Delphine Rioux, Gilles Rayé, Maxime Réjou-Méchain, Charline Giguet-Covex, Marta De Barba, Frédéric Boyer, Wilfried Thuiller, Vincent Schilling, Blaise Tymen, Aurélie Bonin, Philippe Gaucher, Jérôme Viers, Pierre Taberlet, Eric Coissac, Lucie Zinger, Jérôme Chave, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Ecologie des forêts de Guyane (UMR ECOFOG), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), ANR : 11-INBS-0001, CEBA ANR 10-LABX-25-01- METABAR, ANR-11-BSV7-0020 OSUG@2020, ANR-10LABX-56 and TULIP, and ANR-10-LABX-0041
Subjects: 0106 biological sciences, 0301 basic medicine, Assembly rules, Food Chain, Rainforest, Ecological selection, propagule size, Soil biology, Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, DNA metabarcoding, 03 medical and health sciences, Propagule, soil diversity, Genetics, Animals, Body Size, DNA Barcoding, Taxonomic, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, Soil mesofauna, 2. Zero hunger, Tropical Climate, Bacteria, Community, Ecology, Fungi, niche determinism, Plants, 15. Life on land, Biota, French Guiana, 030104 developmental biology, neutral assembly, [SDE]Environmental Sciences, multitaxa, Species richness, eDNA, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Tropical forests shelter an unparalleled biological diversity. The relative influence of environmental selection (i.e., abiotic conditions, biotic interactions) and stochastic-distance-dependent neutral processes (i.e., demography, dispersal) in shaping communities has been extensively studied for various organisms, but has rarely been explored across a large range of body sizes, in particular in soil environments. We built a detailed census of the whole soil biota in a 12-ha tropical forest plot using soil DNA metabarcoding. We show that the distribution of 19 taxonomic groups (ranging from microbes to mesofauna) is primarily stochastic, suggesting that neutral processes are prominent drivers of the assembly of these communities at this scale. We also identify aluminium, topography and plant species identity as weak, yet significant drivers of soil richness and community composition of bacteria, protists and to a lesser extent fungi. Finally, we show that body size, which determines the scale at which an organism perceives its environment, predicted the community assembly across taxonomic groups, with soil mesofauna assemblages being more stochastic than microbial ones. These results suggest that the relative contribution of neutral processes and environmental selection to community assembly directly depends on body size. Body size is hence an important determinant of community assembly rules at the scale of the ecological community in tropical soils and should be accounted for in spatial models of tropical soil food webs. K E Y W O R D S DNA metabarcoding, eDNA, French Guiana, multitaxa, neutral assembly, niche determinism, propagule size, soil diversity
Published: 2019
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13. One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

Author: Charles C.Y. Xu, David Duneau, Lucie Zinger, Rémi Chappaz, Françoise D. Messu Mandeng, Jean-François Agnèse, Gaït Archambaud-Suard, Emese Meglécz, Emmanuel Corse, Charles Félix Bilong Bilong, Christelle Tougard, Vincent Dubut, Dubut, Vincent, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Yaoundé I, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), McGill University = Université McGill [Montréal, Canada], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: 0106 biological sciences, PCR primers, In silico, Locus (genetics), [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, s eDNA, 03 medical and health sciences, diet analysis, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Taxonomic rank, Ecology, Evolution, Behavior and Systematics, Original Research, 030304 developmental biology, Nature and Landscape Conservation, 0303 health sciences, Ecology, cytochrome c oxidase subunit I gene, false negatives, Cytochrome c oxidase subunit I, Phylogeography, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Taxon, Evolutionary biology, Complementarity (molecular biology), diet analysi, metabarcoding, eDNA, Primer (molecular biology), [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets’ complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the “one‐locus‐several‐primer‐sets” (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey–predator interactions.
Published: 2019
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14. Coalescing molecular evolution and DNA barcoding

Author: Lucie Zinger, Hervé Philippe, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), and Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, 0301 basic medicine, Specimen identification, Ecology, posterior predictive simulations, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, Molecular ecology, 03 medical and health sciences, species delimitation, 030104 developmental biology, Taxon, Evolutionary biology, Molecular evolution, clustering methods, [SDE]Environmental Sciences, Genetics, genetic distances, Taxonomy (biology), Species richness, Ecology, Evolution, Behavior and Systematics
Abstract: The DNA barcoding concept (Woese et al. ; Hebert et al. ) has considerably boosted taxonomy research by facilitating the identification of specimens and discovery of new species. Used alone or in combination with DNA metabarcoding on environmental samples (Taberlet et al. ), the approach is becoming a standard for basic and applied research in ecology, evolution and conservation across taxa, communities and ecosystems (Scheffers et al. ; Kress et al. ). However, DNA barcoding suffers from several shortcomings that still remain overlooked, especially when it comes to species delineation (Collins & Cruickshank ). In this issue of Molecular Ecology, Barley & Thomson () demonstrate that the choice of models of sequence evolution has substantial impacts on inferred genetic distances, with a propensity of the widely used Kimura 2-parameter model to lead to underestimated species richness. While DNA barcoding has been and will continue to be a powerful tool for specimen identification and preliminary taxonomic sorting, this work calls for a systematic assessment of substitution models fit on barcoding data used for species delineation and reopens the debate on the limitation of this approach.
Published: 2016
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15. Ubiquitous abundance distribution of non-dominant plankton across the world’s ocean

Author: Lucie Zinger, Chris Bowler, Shruti Malviya, Eric Karsenti, Silvia De Monte, Enrico Ser-Giacomi, and Colomban de Vargas
Subjects: 0106 biological sciences, 0303 health sciences, Ecology, business.industry, Ecology (disciplines), Distribution (economics), Context (language use), Plankton, 010603 evolutionary biology, 01 natural sciences, Cell size, 03 medical and health sciences, Geography, Abundance (ecology), 14. Life underwater, Species richness, business, Relative species abundance, 030304 developmental biology
Abstract: Species Abundance Distributions (SADs) bear the imprint of ecological processes that shape biological communities, and are therefore used to discriminate among different scenarios of community assembly. Even though empirical distributions appear to follow a handful of qualitative laws, it is still unclear if and how quantitative variation in SADs reflects peculiar features of the communities and their environmental context. Here, we use the extensive dataset generated by theTaraOceans expedition for marine microbial eukaryotes (protists) and an adaptive algorithm to explore how SADs vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant OTUs, comprising over 99% of local richness, is commonly governed by a power-law. The power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Our findings suggest that large-scale ubiquitous ecological processes govern the assembly of non-dominant plankton throughout the global ocean.
Published: 2018
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16. Chemical regulation of body feather microbiota in a wild bird

Author: Louis Sallé, Lucie Zinger, Alexis S. Chaine, Léa Boutault, Christine Ducamp, Andrew F. Russell, Staffan Jacob, Philipp Heeb, UCL - SST/ELI/ELIB - Biodiversity, Evolution et Diversité Biologique (EDB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Earth and Life Institute, Biodiversity Research Centre, Université Catholique de Louvain = Catholic University of Louvain (UCL), Toulouse School of Economics (TSE), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Exeter, ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: Male, 0106 biological sciences, 0301 basic medicine, animal structures, skin microbiota, Defence mechanisms, Zoology, microbiome, Animals, Wild, Environment, 010603 evolutionary biology, 01 natural sciences, Nesting Behavior, 03 medical and health sciences, Nest, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Parus major, Genetics, Animals, Colonization, Passeriformes, Ecology, Evolution, Behavior and Systematics, biology, Host (biology), Microbiota, Biodiversity, Preen gland, Feathers, biology.organism_classification, 030104 developmental biology, Feather, visual_art, [SDE]Environmental Sciences, visual_art.visual_art_medium, Uropygial gland, host–microbiota interactions, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bacteria, Function (biology)
Abstract: International audience; The microbiota has a broad range of impacts on host physiology and behaviour, pointing out the need to improve our comprehension of the drivers of host–microbiota composition. Of particular interest is whether the microbiota is acquired passively, or whether and to what extent hosts themselves shape the acquisition and maintenance of their microbiota. In birds, the uropygial gland produces oily secretions used to coat feathers that have been suggested to act as an antimicrobial defence mechanism regulating body feather microbiota. However, our comprehension of this process is still limited. In this study, we for the first time coupled high‐throughput sequencing of the microbiota of both body feathers and the direct environment (i.e., the nest) in great tits with chemical analyses of the composition of uropygial gland secretions to examine whether host chemicals have either specific effects on some bacteria or nonspecific broad‐spectrum effects on the body feather microbiota. Using a network approach investigating the patterns of co‐occurrence or co‐exclusions between chemicals and bacteria within the body feather microbiota, we found no evidence for specific promicrobial or antimicrobial effects of uropygial gland chemicals. However, we found that one group of chemicals was negatively correlated to bacterial richness on body feathers, and a higher production of these chemicals was associated with a poorer body feather bacterial richness compared to the nest microbiota. Our study provides evidence that chemicals produced by the host might function as a nonspecific broad‐spectrum antimicrobial defence mechanism limiting colonization and/or maintenance of bacteria on body feathers, providing new insight about the drivers of the host's microbiota composition in wild organisms.
Published: 2018
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17. Mapping the imprint of biotic interactions on β-diversity

Author: Loïc Chalmandrier, Vincent Schilling, Wilfried Thuiller, Ludovic Gielly, Jérôme Chave, Marc Ohlmann, Johan Pansu, Lucie Zinger, Stéphane Bec, Pierre Taberlet, Florent Mazel, Eric Coissac, THUILLER, Wilfried, Laboratoire d'Ecologie Alpine (LECA ), and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0106 biological sciences, 0301 basic medicine, [SDE] Environmental Sciences, Species groups, Biodiversity, Distribution (economics), 010603 evolutionary biology, 01 natural sciences, Structuring, β diversity, 03 medical and health sciences, Soil, Interaction network, Graphical model, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Trophic level, Spatial Analysis, Bacteria, business.industry, Ecology, Fungi, 15. Life on land, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, 030104 developmental biology, Geography, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: Investigating how trophic interactions influence the β-diversity of meta-communities is of paramount importance to understanding the processes shaping biodiversity distribution. Here, we apply a statistical method for inferring the strength of spatial dependencies between pairs of species groups. Using simulated community data generated from a multi-trophic model, we showed that this method can approximate biotic interactions in multi-trophic communities based on β-diversity patterns across groups. When applied to soil multi-trophic communities along an elevational gradient in the French Alps, we found that fungi make a major contribution to the structuring of β-diversity across trophic groups. We also demonstrated that there were strong spatial dependencies between groups known to interact specifically (e.g. plant-symbiotic fungi, bacteria-nematodes) and that the influence of environment was less important than previously reported in the literature. Our method paves the way for a better understanding and mapping of multi-trophic communities through space and time.
Published: 2018

18. Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: A case study with ant cuticular bacteria

Author: Niklas Tysklind, Christophe Duplais, Lucie Zinger, Caroline Birer, Ecologie des forêts de Guyane (UMR ECOFOG), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), ANR 10-LABX-25-01, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire d'Ecologie Alpine (LECA), and Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA)
Subjects: 0301 basic medicine, DNA, Bacterial, cuticular microbiome, media_common.quotation_subject, Zoology, Arthropod cuticle, Cephalotes, Insect, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 03 medical and health sciences, Botany, insect cuticle, Genetics, Animals, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, media_common, Bacteria, Ants, Microbiota, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Atta cephalotes, biology.organism_classification, 16S ribosomal RNA, bacterial communities, DNA extraction, 030104 developmental biology, metabarcoding, Species richness, Metagenomics, Biotechnology
Abstract: International audience; High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behaviour of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties of working with low bacterial DNA quantities as with individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (similar to 15mm) and Pseudomyrmex penetrator (similar to 5mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial community characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in terms of bacterial diversity and composition for A.cephalotes (similar to 15mm). In contrast, greater amounts of artefactual sequences and contaminations, as well as noticeable differences in bacterial community characteristics were observed between extraction methods for P.penetrator (similar to 5mm). We also found that large (similar to 15mm) and small (similar to 5mm) A.cephalotes individuals harbour different bacterial communities. Our benchmark suggests that cuticular microbiota of single individual insects can be reliably retrieved provided that blank controls, appropriate data cleaning, and individual body size and functional role within insect society are considered in the experiment.
Published: 2017
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19. Evaluation of short mitochondrial metabarcodes for the identification of Amazonian mammals

Author: Mailis Huguin, Arthur Kocher, Jérôme Murienne, Lucie Zinger, Sophie Valière, François Catzeflis, Anne-Laure Bañuls, Benoit de Thoisy, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Association Kwata (Kwata), Kwata, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Département de Génétique Animale [Toulouse], Institut National de la Recherche Agronomique (INRA), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Du gène à l'écosystème (MIVEGEC-GeneSys), Pathogènes, Environnement, Santé Humaine (EPATH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Investissement d'Avenir CEBA: ANR-10-LABX-25-01 TULIP: ANR-10-LABX-41 ANR-11-IDEX-0002-02 / project METABAR ANR-11-BSV7-0020, Université de Toulouse (UT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Amazonian, blood meals, Biology, MT-RNR1, Barcode, DNA barcoding, law.invention, COI, 03 medical and health sciences, law, parasitic diseases, mitochondrial 12S rRNA gene, Ecology, Evolution, Behavior and Systematics, Ecology, Ecological Modeling, Ribosomal RNA, French Guiana, 030104 developmental biology, Evolutionary biology, Reference database, Identification (biology), Primer (molecular biology), sand fly, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; 1. DNA barcoding and metabarcoding are increasingly used as alternatives to traditional morphological identifications. For animals, the standard barcode is a c. 658-bp portion of the COI gene, for which reference libraries now cover a large proportion of described mammal species. Unfortunately, because its sequence is too long and does not contain highly conserved primer binding sites, this marker is not adapted for metabarcoding. Although alternative metabarcodes have been developed, their performances are generally seldom assessed. 2. We evaluate the reliability of a short metabarcode located in the mitochondrial 12S ribosomal RNA for the identifications of Amazonian mammals. We (i) constitute a nearly exhaustive reference library for species found in French Guiana, (ii) assess the taxonomic resolution of the marker and validate its use with dipteran blood meal analyses, (iii) assess the conservation of the primer binding sites, and (iv) compare its theoretical performances with that of a newly designed metabarcode located within the standard COI barcode. 3. About 576 specimens representing 164 species were gathered and sequenced. We show that the 12S marker allows remarkably accurate taxonomic assignations despite its very short size, and that primer binding sites are highly conserved, which is important to avoid PCR amplification bias potentially leading to detection failure. Additionally, our results stress that the identifications should only be considered at the generic level when they are based on incomplete reference libraries, even when a stringent similarity cutoff is used. A new short COI metabarcode was designed based on 569 reference sequences of mammals retrieved on BOLD. Our results clearly show that, while both markers provide similar taxonomic resolution, much higher rates of primer mismatches are found with COI. 4. Besides demonstrating the accuracy of the short 12S marker for the identification of Amazonian mammals and providing a reliable molecular reference database, this study emphasizes that the accuracy of taxonomic assignations highly depends on the comprehensiveness of the reference library and that great caution should be taken for interpreting metabarcoding results based on scarce reference libraries. The comparison with a short COI metabarcode also provides novel evidence in support for the use of ribosomal markers in metabarcoding studies.
Published: 2017
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20. Soil community assembly varies across body sizes in a tropical forest

Author: Pierre Taberlet, Amaia Iribar, Eric Coissac, Marta De Barba, Philippe Gaucher, Lucie Zinger, Wilfried Thuiller, Jérôme Chave, Heidy Schimann, Ludovic Gielly, Vincent Schilling, Cyril Zouiten, Delphine Rioux, Charline Giguet-Covex, Aurélie Bonin, Maxime Réjou-Méchain, Frédéric Boyer, Blaise Tymen, Jérôme Viers, and Gilles Rayé
Subjects: 0106 biological sciences, Abiotic component, 0303 health sciences, Ecology, Soil biology, 15. Life on land, Biology, Spatial distribution, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Spatial ecology, Biological dispersal, Species richness, Soil mesofauna, 030304 developmental biology, Trophic level
Abstract: The relative influence of deterministic niche-based (i.e. abiotic conditions, biotic interactions) and stochastic-distance dependent neutral processes (i.e. demography, dispersal) in shaping communities has been extensively studied for various organisms, but is far less explored jointly across the tree of life, in particular in soil environments. Here, using a thorough DNA-based census of the whole soil biota in a large tropical forest plot, we show that soil aluminium, topography, and plant species identity are all important drivers of soil richness and community composition. Body size emerges as an important feature of the comparative ecology of the different taxa at the studied spatial scale, with microorganisms being more importantly controlled by environmental factors, while soil mesofauna rather display random spatial distribution. We infer that niche-based processes contribute differently to community assembly across trophic levels due to spatial scaling. Body size could hence help better quantifying important properties of multitrophic assemblages.
Published: 2017
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21. Ubiquitous abundance distribution of non-dominant plankton across the global ocean

Author: Silvia De Monte, Chris Bowler, Enrico Ser-Giacomi, Eric Karsenti, Shruti Malviya, Lucie Zinger, Colomban de Vargas, Institute for Cross-Disciplinary Physics and Complex Systems [Mallorca] (IFISC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universitat de les Illes Balears (UIB), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Heidelberg] (EMBL), Universitat de les Illes Balears (UIB)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Biogeochemical cycle, Rare biosphere, Oceans and Seas, Distribution (economics), Cell size, 03 medical and health sciences, Abundance (ecology), Plankton ecology, DNA Barcoding, Taxonomic, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Ecology, business.industry, fungi, 15. Life on land, Plankton, Models, Theoretical, 030104 developmental biology, 13. Climate action, Environmental science, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Algorithms
Abstract: International audience; Marine plankton populate 70% of Earth's surface, providing the energy that fuels ocean food webs and contributing to global biogeochemical cycles. Plankton communities are extremely diverse and geographically variable, and are overwhelmingly composed of low-abundance species. The role of this rare biosphere and its ecological underpinnings are however still unclear. Here, we analyse the extensive dataset generated by the Tara Oceans expedition for marine microbial eukaryotes (protists) and use an adaptive algorithm to explore how metabarcoding-based abundance distributions vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant operational taxonomic units, which comprise over 99% of local richness, is commonly governed by a power-law. Despite the high spatial turnover in species composition, the power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Such striking regularity suggests that the assembly of plankton communities in the dynamic and highly variable ocean environment is governed by large-scale ubiquitous processes. Understanding their origin and impact on plankton ecology will be important for evaluating the resilience of marine biodiversity in a changing ocean.
Published: 2017
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22. Altered trophic interactions in warming climates: consequences for predator diet breadth and fitness

Author: Staffan Jacob, Lucie Di Gesu, Andrea Soriano-Redondo, Lucie Zinger, Joël White, Julien Cote, Lisa Fourtune, Julien Cucherousset, Elvire Bestion, Aimeric Teyssier, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), University of Exeter, Evolution et Diversité Biologique (EDB), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-11-INBS-0001AnaEE-Services, Agence Nationale de la Recherche, European Project: ERC-2018-CoG-817779,ECOFEED, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), 817779, H2020 European Research Council, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Food Chain, Biodiversity, Climate change, Zootoca vivipara, Generalist and specialist species, 010603 evolutionary biology, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, diet specialization, Predation, 03 medical and health sciences, niche breadth, biology.animal, stable isotope analysis, Animals, skin and connective tissue diseases, Predator, 030304 developmental biology, General Environmental Science, Isotope analysis, Trophic level, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, gut microbiota, General Immunology and Microbiology, biology, Lizard, Ecology, General Medicine, 15. Life on land, Biological Evolution, Diet, climate change, 13. Climate action, Predatory Behavior, [SDE]Environmental Sciences, sense organs, General Agricultural and Biological Sciences
Abstract: International audience; Species interactions are central in predicting the impairment of biodiversity with climate change. Trophic interactions may be altered through climate-dependent changes in either predator food preferences or prey communities. Yet, climate change impacts on predator diets remain surprisingly poorly understood. We experimentally studied the consequences of 2°C-warmer climatic conditions on the trophic niche of a generalist lizard predator. We used a system of semi-natural mesocosms housing a variety of invertebrate species and in which climatic conditions were manipulated. Lizards in warmer climatic conditions ate a greater predatory to phytophagous invertebrate ratio and had smaller individual dietary breadths. These shifts mainly arose from direct impacts of climate on lizard diets rather than from changes in prey communities. Dietary changes were associated with negative changes in fitness-related traits (body condition, gut microbiota) and survival. We demonstrate that climate change alters trophic interactions through top-predator dietary shifts which might disrupt eco-evolutionary dynamics.
Published: 2019
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23. Vector soup : high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding

Author: Jérôme Murienne, Lucie Zinger, Romain Girod, Pascal Gaborit, Isabelle Dusfour, Sophie Valière, Hélène Holota, Arthur Kocher, Anne-Laure Bañuls, Jean-Charles Gantier, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Lab Identificat Fong & Entomoparasitol, Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Du gène à l'écosystème (MIVEGEC-GeneSys), Pathogènes, Environnement, Santé Humaine (EPATH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0301 basic medicine, dna barcode, [SDV]Life Sciences [q-bio], ADN, mitochondrial 16S rRNA gene, Zoology, DNA, Mitochondrial, DNA, Ribosomal, DNA barcoding, GENETIQUE DE POPULATION, 03 medical and health sciences, LEISHMANIOSE, vector monitoring, RNA, Ribosomal, 16S, Bulk samples, parasitic diseases, Genetics, Animals, Cluster Analysis, DNA Barcoding, Taxonomic, Psychodidae, leishmaniasis, Phylogeny, Ecology, Evolution, Behavior and Systematics, biology, french guiana, Ecology, VECTEUR, fungi, Sequence Analysis, DNA, biology.organism_classification, Multiple species, Insect Vectors, 030104 developmental biology, Vector (epidemiology), psychodidae, OBSERVATOIRE, Reference database, Identification (biology), Metagenomics, ECOLOGIE, Biotechnology
Abstract: Phlebotomine sand flies are haematophagous dipterans of primary medical importance. They represent the only proven vectors of leishmaniasis worldwide and are involved in the transmission of various other pathogens. Studying the ecology of sand flies is crucial to understand the epidemiology of leishmaniasis and further control this disease. A major limitation in this regard is that traditional morphological-based methods for sand fly species identifications are time-consuming and require taxonomic expertise. DNA metabarcoding holds great promise in overcoming this issue by allowing the identification of multiple species from a single bulk sample. Here, we assessed the reliability of a short insect metabarcode located in the mitochondrial 16S rRNA for the identification of Neotropical sand flies, and constructed a reference database for 40 species found in French Guiana. Then, we conducted a metabarcoding experiment on sand flies mixtures of known content and showed that the method allows an accurate identification of specimens in pools. Finally, we applied metabarcoding to field samples caught in a 1-ha forest plot in French Guiana. Besides providing reliable molecular data for species-level assignations of phlebotomine sand flies, our study proves the efficiency of metabarcoding based on the mitochondrial 16S rRNA for studying sand fly diversity from bulk samples. The application of this high-throughput identification procedure to field samples can provide great opportunities for vector monitoring and eco-epidemiological studies.
Published: 2017
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24. Climate warming reduces gut microbiota diversity in a vertebrate ectotherm

Author: JoÃ«l White, Murielle Richard, Staffan Jacob, Elvire Bestion, Julien Cote, Lucie Zinger, Lucie Di Gesu, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, ANR-12-JSV7-0004,FRADISYN,Populations fragmentées et syndromes dispersants : des gènes à la dynamique des métapopulations(2012), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Ecology, biology, Global warming, Biodiversity, Climate change, microbiome, ectotherms, 15. Life on land, Gut flora, biology.organism_classification, Ecological network, lizards, 03 medical and health sciences, 030104 developmental biology, climate change, Microbial ecology, 13. Climate action, Ectotherm, host-microbiota interactions, Microbiome, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, Ecology, Evolution, Behavior and Systematics, biodiversity
Abstract: International audience; Climate change is now considered as the greatest threat to biodiversity and ecological networks, but its impacts on the bacterial communities associated with plant or animals remain largely unknown. Here, we studied the consequences of climate warming on gut bacterial communities of an ectotherm, the common lizard (Zootoca vivipara), using a semi-natural experimental approach. We found that +2/3°C warmer climates cause a 34% loss of populations' microbiota diversity, with possible negative consequences for host survival.
Published: 2017
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25. Not only mosses: lemming winter diets as described by DNA metabarcoding

Author: Rolf A. Ims, Ludovic Gielly, Eeva M. Soininen, John-André Henden, Lucie Zinger, and Nigel G. Yoccoz
Subjects: 0106 biological sciences, 0301 basic medicine, education.field_of_study, Ecology, Food availability, Population, Biology, Snow, 010603 evolutionary biology, 01 natural sciences, Tundra, VDP::Mathematics and natural science: 400::Basic biosciences: 470, Spatial heterogeneity, 03 medical and health sciences, 030104 developmental biology, Arctic, VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470, Population growth, Bryophyte, General Agricultural and Biological Sciences, education
Abstract: This is a post-peer-review, pre-copyedit version of an article published in Polar Biology. The final authenticated version is available online at: http://dx.doi.org/10.1007/s00300-017-2114-3. The temporal dynamics of most tundra food webs are shaped by the cyclic population dynamics of lemmings. While processes during winter may be behind the recent disruptions of lemming cycles, lemming winter ecology is poorly known. We present here the first DNA metabarcoding data on the winter diet of Norwegian lemmings (Lemmus lemmus), based on feces collected after a winter of population increase. Prostrate willows, mosses, and graminoids dominated the species winter diet, indicating that the conventional idea of lemmings as moss‐specialists should be revised. The behavior of lemming‐plant models in theoretical studies is conditional on the assumptions of mosses being their main winter food item. As shrubs have been excluded from the framework of these models, incorporating them in future modeling studies should nuance our understanding on how plants affect lemmings. We also sampled diet of a few individuals found dead on top of the snow. These individuals had relatively empty stomachs and had, prior to death, relied heavily on mosses. This apparent lack of abundant good quality indicates spatial heterogeneity in local food availability during the population increase phase.
Published: 2017

26. Inferring neutral biodiversity parameters using environmental DNA data sets

Author: Pierre Taberlet, Eric Coissac, Guilhem Sommeria-Klein, Lucie Zinger, and Jérôme Chave
Subjects: 0301 basic medicine, Biodiversity, Inference, Biology, Biostatistics, computer.software_genre, Barcode, Polymerase Chain Reaction, Article, law.invention, 03 medical and health sciences, Abundance (ecology), law, DNA Barcoding, Taxonomic, Environmental DNA, Computer Simulation, Ecosystem, Multidisciplinary, Robustness (evolution), DNA, Noise, 030104 developmental biology, Data mining, Metagenomics, computer, Neutral theory of molecular evolution
Abstract: The DNA present in the environment is a unique and increasingly exploited source of information for conducting fast and standardized biodiversity assessments for any type of organisms. The datasets resulting from these surveys are however rarely compared to the quantitative predictions of biodiversity models. In this study, we simulate neutral taxa-abundance datasets, and artificially noise them by simulating noise terms typical of DNA-based biodiversity surveys. The resulting noised taxa abundances are used to assess whether the two parameters of Hubbell’s neutral theory of biodiversity can still be estimated. We find that parameters can be inferred provided that PCR noise on taxa abundances does not exceed a certain threshold. However, inference is seriously biased by the presence of artifactual taxa. The uneven contribution of organisms to environmental DNA owing to size differences and barcode copy number variability does not impede neutral parameter inference, provided that the number of sequence reads used for inference is smaller than the number of effectively sampled individuals. Hence, estimating neutral parameters from DNA-based taxa abundance patterns is possible but requires some caution. In studies that include empirical noise assessments, our comprehensive simulation benchmark provides objective criteria to evaluate the robustness of neutral parameter inference.
Published: 2016

27. Macroecological patterns of marine bacteria on a global scale

Author: Linda A. Amaral-Zettler, Jed A. Fuhrman, Lucie Zinger, David B. Mark Welch, Jennifer B. H. Martiny, Alban Ramette, Anthony S. Amend, Susan M. Huse, Mitchell L. Sogin, M. Claire Horner-Devine, Thomas A. Oliver, Adam C. Martiny, and Antje Boetius
Subjects: 0106 biological sciences, 0303 health sciences, Ecology, Range (biology), Pelagic zone, Bacterioplankton, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, International Census of Marine Microbes, 13. Climate action, Abundance (ecology), 14. Life underwater, Rapoport's rule, Southern Hemisphere, Ecology, Evolution, Behavior and Systematics, Macroecology, 030304 developmental biology
Abstract: Aim To test whether within-species and among-species patterns of abundance and latitudinal range in marine bacteria resemble those found for macro-organisms, and whether these patterns differ along latitudinal clines. Location Global pelagic marine environments. Methods Taxon-specific sequence abundance and location were retrieved from the open-access V6-rRNA pyrotag sequence data base VAMPS (http://vamps.mbl.edu/), which holds a massive collection of marine bacterial community data sets from the International Census of Marine Microbes sampling effort of global ocean water masses. Data were randomly subsampled to correct for spatial bias and for differences in sampling effort. Results We show that bacterial latitudinal ranges are narrower than expected by chance. When present in both Northern and Southern hemispheres, taxa occupy restricted ranges at similar latitudes on both sides of the equator. A significant and positive relationship exists between sequence abundance and latitudinal range, although this pattern contains a large amount of variance. Abundant taxa in the tropics and in the Northern Hemisphere generally have smaller ranges than those in the Southern Hemisphere. We show that the mean latitudinal range of bacterial taxa increases with latitude, supporting the existence of a Rapoport effect in marine bacterioplankton. Finally, we show that bacterioplankton communities contain a higher proportion of abundant taxa as they approach the poles. Main conclusions Macroecological patterns such as the abundance–range relationship, in general, extend to marine bacteria. However, differences in the shape of these relationships between bacteria and macro-organisms call into question whether the processes and their relative importance in shaping global marine bacteria and macro-organism distributions are the same.
Published: 2012
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28. Phylogenetic Clustering Reveals Selective Events Driving the Turnover of Bacterial Community in Alpine Tundra Soils

Author: Se´bastien Lavergne, Bahar Shahnavaz, Roberto A. Geremia, Philippe Choler, and Lucie Zinger
Subjects: 0106 biological sciences, 0301 basic medicine, Global and Planetary Change, Biomass (ecology), Phylogenetic tree, biology, Ecology, Beta diversity, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Tundra, 03 medical and health sciences, 030104 developmental biology, Snowmelt, Temperate climate, Ecosystem, Ecology, Evolution, Behavior and Systematics, Earth-Surface Processes, Acidobacteria
Abstract: Soil bacterial communities play a determining role in snow-covered ecosystems' response to global warming because of their role in nutrient recycling. However, little is known about how changes in snow-cover dynamics could affect bacterial community assembly in the short or long term. We examined the phylogenetic structure of soil bacterial communities sampled seasonally from early snowmelt (ESM) and late snowmelt locations (LSM) in temperate alpine tundra. Most of the variation in phylogenetic structure (i.e. β-diversity) was temporal rather than spatial and most observed deviations from random community assembly were towards phylogenetic clustering. Indeed, we observed phylogenetic clustering of Acidobacteria, Actinobacteria, and α-Proteobacteria during late winter in ESM locations, and a phylogenetic clustering of β-,γ-Proteobacteria, and Bacteroidetes during autumn in ESM and LSM locations probably linked to the onset of plant senescence and biomass decomposition. Interestingly, Acidobacteria...
Published: 2012
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29. Two decades of describing the unseen majority of aquatic microbial diversity

Author: Lucie Zinger, Thomas Pommier, and Angélique Gobet
Subjects: 0303 health sciences, 030306 microbiology, business.industry, Ecology, Microbial diversity, Aquatic ecosystem, Environmental resource management, Biodiversity, Context (language use), 15. Life on land, Biology, 6. Clean water, 03 medical and health sciences, 13. Climate action, Sustainability, Genetics, Degree of precision, 14. Life underwater, business, Ecology, Evolution, Behavior and Systematics, Water sampling, 030304 developmental biology
Abstract: Aquatic environments harbour large and diverse microbial populations that ensure their functioning and sustainability. In the current context of global change, characterizing microbial diversity has become crucial, and new tools have been developed to overcome the methodological challenges posed by working with microbes in nature. The advent of Sanger sequencing and now next-generation sequencing technologies has enabled the resolution of microbial communities to an unprecedented degree of precision. However, to correctly interpret microbial diversity and its patterns this revolution must also consider conceptual and methodological matters. This review presents advances, gaps and caveats of these recent approaches when considering microorganisms in aquatic ecosystems. We also discuss potentials and limitations of the available methodologies, from water sampling to sequence analysis, and suggest alternative ways to incorporate results in a conceptual and methodological framework. Together, these methods will allow us to gain an unprecedented understanding of microbial diversity in aquatic ecosystems.
Published: 2011
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30. CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies

Author: Jérôme Gury, Lucie Zinger, Lucile Sage, François Pompanon, Roberto A. Geremia, Olivier Alibeu, Delphine Rioux, Ludovic Gielly, Laboratoire d'Ecologie Alpine (LECA), and Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])
Subjects: microbial, t-rflp, Biodiversity, registered designation, chemistry.chemical_compound, Molecular marker, DNA, Fungal, high-throughput, Polymorphism, Single-Stranded Conformational, Soil Microbiology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, Community structure, keratitis, gradient gel-electrophoresis, community structure, origin salers, Polymorphism, Restriction Fragment Length, Microbiology (medical), ribosomal-rna genes, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Sensitivity and Specificity, Microbiology, soil, cheese, 03 medical and health sciences, Capillary electrophoresis, CE-FLA, Ecosystem, CE-SSCP, Molecular Biology, 030304 developmental biology, 030306 microbiology, Fungi, Electrophoresis, Capillary, Reproducibility of Results, Single-strand conformation polymorphism, 15. Life on land, DNA Fingerprinting, soil bacterial, genomic DNA, capillary-electrophoresis, Agronomy, chemistry, mycotic, Soil water, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Strand-conformation polymorphism
Abstract: International audience; Fungal communities are key components of soil, but the study of their ecological significance is limited by a lack of appropriated methods. For instance, the assessment of fungi occurrence and spatio-temporal variation in soil requires the analysis of a large number of samples. The molecular signature methods provide a useful tool to monitor these microbial communities and can be easily adapted to capillary electrophoresis (CE) allowing high-throughput studies. Here we assess the suitability of CE-FLA (Fragment Length Polymorphism, denaturing conditions) and CE-SSCP (Single-Stranded Conformation Polymorphism, native conditions) applied to environmental studies since they require a short molecular marker and no post-PCR treatments. We amplified the ITSI region from 22 fungal strains isolated from an alpine ecosystem and from total genomic DNA of alpine and infiltration basin soils. The CE-FLA and CE-SSCP separated 17 and 15 peaks respectively from a mixture of 19 strains. For the alpine soil-metagenomic DNA, the FLA displayed more peaks than the SSCP and the converse result was found for infiltration basin sediments. We concluded that CE-FLA and CE-SSCP of ITS I region provided complementary information. In order to improve CE-SSCP sensitivity. we tested its resolution according to migration temperature and found 32 degrees C to be optimal. Because of their simplicity, quickness and reproducibility. we found that these two methods were promising for high-throughput studies of soil fungal communities. (c) 2007 Elsevier B.V All rights reserved.
Published: 2008
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31. Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands

Author: Roberto A. Geremia, Lucie Zinger, Philippe Choler, Mihai Pușcaș, Jean-Marc Bonneville, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and ANR-13-ISV7-0004,ODYSSEE,De nouvelles voies pour la modélisation des dynamiques d'assemblages d'espèces intégrant l'écologie et l'évolution: le cas des écosystèmes de montagne des Alpes et des Carpates(2013)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Beta diversity, Plant Science, Biology, complex mixtures, 010603 evolutionary biology, 01 natural sciences, Natural (archaeology), Grassland, Soil, 03 medical and health sciences, Humans, Human Activities, natural sciences, Keystone species, Illumina dye sequencing, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, geography, geography.geographical_feature_category, Bacteria, Ecology, Fungi, food and beverages, Plants, 15. Life on land, Phylogeography, 030104 developmental biology, Habitat, Disturbance (ecology), Multivariate Analysis, Linear Models, Montane ecology
Abstract: Summary The effect of plant species composition on soil microbial communities was studied at the multiregional level. We compared the soil microbial communities of alpine natural grasslands dominated by Carex curvula and anthropogenic subalpine pastures dominated by Nardus stricta. We conducted paired sampling across the Carpathians and the Alps and used Illumina sequencing to reveal the molecular diversity of soil microbes. We found that bacterial and fungal communities exhibited contrasting regional distributions and that the distribution in each grassland is well discriminated. Beta diversity of microbial communities was much higher in C. curvula grasslands due to a marked regional effect. The composition of grassland-type core microbiomes suggest that C. curvula, and N. stricta to a lesser extent, tend to select a cohort of microbes related to antibiosis/exclusion, pathogenesis and endophytism. We discuss these findings in light of the postglacial history of the studied grasslands, the habitat connectivity and the disturbance regimes. Human-induced disturbance in the subalpine belt of European mountains has led to homogeneous soil microbial communities at large biogeographical scales. Our results confirm the overarching role of the dominant grassland plant species in the distribution of microbial communities and highlight the relevance of biogeographical history.
Published: 2016
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32. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria

Author: Alban Ramette, Lucie Zinger, Christina Bienhold, and Antje Boetius
Subjects: 0301 basic medicine, Geologic Sediments, lcsh:Medicine, Marine and Aquatic Sciences, Bathyal zone, Deep Sea, Abyssal zone, RNA, Ribosomal, 16S, Oceans, lcsh:Science, Sedimentary Geology, Multidisciplinary, Ecology, Geography, Microbiota, Community structure, Geology, Genomics, Biodiversity, Marine Bacteria, Seafloor spreading, Productivity (ecology), Community Ecology, Biogeography, Medical Microbiology, Research Article, 030106 microbiology, 610 Medicine & health, Microbial Genomics, Biology, Deep sea, Microbiology, 03 medical and health sciences, Genetics, Seawater, 14. Life underwater, Endemism, Petrology, Community, Bacteria, lcsh:R, Ecology and Environmental Sciences, Organisms, Biology and Life Sciences, Bodies of Water, 13. Climate action, Earth Sciences, 570 Life sciences, biology, lcsh:Q, Sediment, Microbiome
Abstract: The deep ocean floor covers more than 60% of the Earth’s surface, and hosts diverse bacterial communities with important functions in carbon and nutrient cycles. The identification of key bacterial members remains a challenge and their patterns of distribution in seafloor sediment yet remain poorly described. Previous studies were either regionally restricted or included few deep-sea sediments, and did not specifically test biogeographic patterns across the vast oligotrophic bathyal and abyssal seafloor. Here we define the composition of this deep seafloor microbiome by describing those bacterial operational taxonomic units (OTU) that are specifically associated with deep-sea surface sediments at water depths ranging from 1000–5300 m. We show that the microbiome of the surface seafloor is distinct from the subsurface seafloor. The cosmopolitan bacterial OTU were affiliated with the clades JTB255 (class Gammaproteobacteria, order Xanthomonadales) and OM1 (Actinobacteria, order Acidimicrobiales), comprising 21% and 7% of their respective clades, and about 1% of all sequences in the study. Overall, few sequence-abundant bacterial types were globally dispersed and displayed positive range-abundance relationships. Most bacterial populations were rare and exhibited a high degree of endemism, explaining the substantial differences in community composition observed over large spatial scales. Despite the relative physicochemical uniformity of deep-sea sediments, we identified indicators of productivity regimes, especially sediment organic matter content, as factors significantly associated with changes in bacterial community structure across the globe.
Published: 2016
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33. Using metabarcoding to reveal and quantify plant-pollinator interactions

Author: Roselyne Etienne, Christophe Andalo, Hélène Holota, Lucie Zinger, Aurélie Khimoun, Nathalie Escaravage, Charlène Pellizzari, Jérôme Mariette, Pierre Taberlet, Monique Burrus, André Pornon, Marie Vidal, Amaia Iribar, Peter Winterton, Evolution et Diversité Biologique ( EDB ), Institut de Recherche pour le Développement ( IRD ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Unité de Mathématiques et Informatique Appliquées de Toulouse ( MIAT INRA ), Institut National de la Recherche Agronomique ( INRA ), Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), GeT PlaGe, Genotoul, Université Paul Sabatier - Toulouse 3 ( UPS ), Work supported by the French Laboratory of Excellence project 'TULIP' and by the Centre National de la Recherche Scientifique-INEE (ERESA program: DJ/ST/IP/2013/D-112)., ANR-11-IDEX-0002-02/10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental ( 2011 ), ANR : ANR-11-IDEX-0002-02, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, ANR-11-IDEX-0002-02/10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2011), ANR: ANR-11-IDEX-0002-02, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Pornon, André, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Toulouse (UT)
Subjects: 0106 biological sciences, 0301 basic medicine, Insecta, DNA, Plant, Pollination, media_common.quotation_subject, Insect, Biology, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Species Specificity, Pollinator, Pollen, medicine, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Animals, DNA Barcoding, Taxonomic, Plant Physiological Phenomena, media_common, [SDV.GEN]Life Sciences [q-bio]/Genetics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Multidisciplinary, Community, Ecology, Plant community, Sequence Analysis, DNA, Plants, 15. Life on land, Ecological genetics, 030104 developmental biology, Taxon, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole.
Published: 2016
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34. Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA

Author: Ludovic Gielly, Jérôme Poulenard, Lucie Zinger, Fabien Arnaud, Charline Giguet-Covex, Frédéric Boyer, Gentile Francesco Ficetola, Pierre Taberlet, Philippe Choler, Johan Pansu, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Geologic Sediments, DNA, Plant, Climate Change, [SDE.MCG]Environmental Sciences/Global Changes, Population Dynamics, Biodiversity, Climate change, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetics, DNA Barcoding, Taxonomic, Humans, Ecosystem, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, High-Throughput Nucleotide Sequencing, Plant community, Agriculture, [SHS.GEO]Humanities and Social Sciences/Geography, 15. Life on land, Plants, [SDE.ES]Environmental Sciences/Environmental and Society, Lakes, Ancient DNA, 13. Climate action, Paleoecology, Plant cover, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Landscape history
Abstract: International audience; Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA‐based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high‐elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall‐herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long‐term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long‐term ecosystem dynamics under the influence of human‐induced and environmental drivers.
Published: 2015
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35. Bacterial taxa-area and distance-decay relationships in marine environments

Author: Lucie Zinger, Alban Ramette, and Antje Boetius
Subjects: 0106 biological sciences, Geologic Sediments, Range (biology), Biodiversity, 610 Medicine & health, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Marine bacteriophage, 360 Social problems & social services, Genetics, Ecosystem, Seawater, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, Distance decay, 0303 health sciences, Bacteria, Models, Genetic, Ecology, Tar, Pelagic zone, Original Articles, distance-decay, body regions, pyrosequencing, species-area, methodological biases, 13. Climate action, global scale, Pyrosequencing, 570 Life sciences, biology, microbes
Abstract: The taxa-area relationship (TAR) and the distance-decay relationship (DDR) both describe spatial turnover of taxa, and are central patterns of biodiversity. Here, we compared TAR and DDR of bacterial communities across different marine realms and ecosystems at the global scale. To obtain reliable global estimates for both relationships, we quantified the poorly assessed effects of sequencing depth, rare taxa removal, and number of sampling sites. Slope coefficients of bacterial TARs were within the range of those of plants and animals, whereas slope coefficients of bacterial DDR were much lower. Slope coefficients were mostly affected by removing rare taxa and by the number of sampling sites considered in the calculations. TAR and DDR slope coefficients were overestimated at sequencing depth < 4,000 sequences per sample. Noticeably bacterial TAR and DDR patterns did not correlate with each other both within and across ecosystem types, suggesting that (i) TAR cannot be directly derived from DDR and (ii) TAR and DDR may be influenced by different ecological factors. Nevertheless, we found marine bacterial TAR and DDR to be steeper in ecosystems associated with high environmental heterogeneity or spatial isolation, namely marine sediments and coastal environments compared to pelagic ecosystems. Hence, our study provides information on macroecological patterns of marine bacteria, as well as methodological and conceptual insights to ecologists at a time when biodiversity surveys increasingly make use of high-throughput sequencing technologies.
Published: 2013
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36. Changes in root-associated microbial communities are determined by species-specific plant growth responses to stress and disturbance

Author: Tarfa Mustafa, Abderrahim Bouasria, Lucie Zinger, Philippe Choler, Roberto A. Geremia, Guy Lempérière, Francesco de Bello, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: Microbial diversity, Plant growth, Beta diversity, Soil Science, Microbiology, 03 medical and health sciences, Botany, Herbivory, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Rhizosphere, Herbivore, Biomass (ecology), Drought, biology, Grass, fungi, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, Disturbance (ecology), Microbial population biology, Agronomy, Insect Science, Environmental changes, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, human activities, Bacteria, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; The diversity changes in the rhizosphere microbial communities of four grass species submitted to a stress (drought) and/or a disturbance (defoliation) were examined in a full factorial common garden experiment. The diversity of bacterial and fungal communities was determined using Single Strand Conformation Polymorphism (SSCP) and multivariate analyses of variance were performed to test for the effect of experimental factors on microbial beta diversity, i.e. the variation of microbial community composition among pots. Plant species identity contributed the most to microbial beta diversity with 22% of the total variance explained and this effect was stronger for fungi than for bacteria. The effect of defoliation was significant for fungal communities, and more pronounced for plant species that exhibited an increased root biomass following defoliation. Drought had a higher effect on bacterial beta diversity, and this was particularly noticeable for plant species that were the least able to tolerate water shortage. Our results showed that both plant species identity and characteristics of plant growth response captured the plant-mediated effects on microbial diversity. They illustrate the biotic cascade between plants responding to a changing environment and the dynamics of rhizosphere microbial communities.
Published: 2012
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37. Exonuclease activity of proofreading DNA polymerases is at the origin of artifacts in molecular profiling studies

Author: Pierre Taberlet, Lucie Zinger, Jérôme Gury, Roberto A. Geremia, Ludovic Gielly, Laboratoire d'Ecologie Alpine (LECA), and Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])
Subjects: Exonucleases, DNA polymerase II, Clinical Biochemistry, microbial communities, [SDV.BID]Life Sciences [q-bio]/Biodiversity, DNA-Directed DNA Polymerase, Biochemistry, Polymerase Chain Reaction, Analytical Chemistry, 03 medical and health sciences, chemistry.chemical_compound, Polymerase chain reaction optimization, Polymerase, Polymorphism, Single-Stranded Conformational, biodiversity, 030304 developmental biology, Klenow fragment, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, multiple peaks, biology, 030306 microbiology, Multiple displacement amplification, Electrophoresis, Capillary, Molecular biology, DNA Fingerprinting, enzymes and coenzymes (carbohydrates), capillary electrophoresis-single-strand conformation polymorphism, chemistry, environmental microbiology, biology.protein, Proofreading, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Artifacts, Taq polymerase, Hot start PCR
Abstract: International audience; CE fingerprint methods are commonly used in microbial ecology. We have previously noticed that the position and number of peaks in CE-SSCP (single-strand conformation polymorphism) profiles depend on the DNA polymerase used in PCR [1]. Here, we studied the fragments produced by Taq polymerase as well as four commercially available proofreading polymerases, using the V3 region of the Escherichia coli rss gene as a marker. PCR products rendered multiple peaks in denaturing CE; Taq polymerase was observed to produce the longest fragments. Incubation of the fragments with T4 DNA polymerase indicated that the 3'-ends of the proofreading polymerase amplicons were recessed, while the Taq amplicon was partially +A tailed. Treatment of the PCR product with proofreading DNA polymerase rendered trimmed fragments. This was due to the 3'-5' exonuclease activity of these enzymes, which is essential for proofreading. The nuclease activity was reduced by increasing the concentration of dNTP. The Platinum (R) Pfx DNA polymerase generated very few artifacts and could produce 85% of blunted PCR products. Nevertheless, despite the higher error rate, we recommend the use of Taq polymerase rather than proofreading in the framework for molecular fingerprint studies. They are more cost-effective and therefore ideally suited for high-throughput analysis; the +A tail artifact rate can be controlled by modifying the PCR primers and the reaction conditions.
Published: 2008
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38. Tannin impacts on microbial diversity and the functioning of alpine soils: a multidisciplinary approach

Author: Roberto A. Geremia, Jean-Christophe Clément, Florence Baptist, Christiane Gallet, Bahar Shahnavaz, Lucile Sage, Ph. Choler, Jean M.F. Martins, R. Guillemin, Lucie Zinger, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Laboratoire d'étude des transferts en hydrologie et environnement (LTHE), Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Station alpine Joseph Fourier - UMS 3370 (SAJF), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Grenoble (INPG)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), and Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)
Subjects: Nutrient cycle, Biogeochemical cycle, [SDE.MCG]Environmental Sciences/Global Changes, availability, polymerase-chain-reaction, litter decomposition, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Microbiology, bacterial community, nitrogen, 03 medical and health sciences, Soil, Nutrient, Botany, Tannin, Ecosystem, Dryas octopetala, condensed tannin, Nitrogen cycle, Ecology, Evolution, Behavior and Systematics, Soil Microbiology, chemistry.chemical_classification, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, biology, Bacteria, 030306 microbiology, tundra soils, nutrient, Fungi, Conformation polymorphism analysis, 04 agricultural and veterinary sciences, Mineralization (soil science), Biodiversity, dynamics, 15. Life on land, carbon storage, biology.organism_classification, Carbon, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, 13. Climate action, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tannins
Abstract: International audience; In alpine ecosystems, tannin-rich-litter decomposition occurs mainly under snow. With global change, variations in snowfall might affect soil temperature and microbial diversity with biogeochemical consequences on ecosystem processes. However, the relationships linking soil temperature and tannin degradation with soil microorganisms and nutrients fluxes remain poorly understood. Here, we combined biogeochemical and molecular profiling approaches to monitor tannin degradation, nutrient cycling and microbial communities (Bacteria, Crenarcheotes, Fungi) in undisturbed wintertime soil cores exposed to low temperature (0 degrees C/-6 degrees C), amended or not with tannins, extracted from Dryas octopetala. No toxic effect of tannins on microbial populations was found, indicating that they withstand phenolics from alpine vegetation litter. Additionally at -6 degrees C, higher carbon mineralization, higher protocatechuic acid concentration (intermediary metabolite of tannin catabolism), and changes in fungal phylogenetic composition showed that freezing temperatures may select fungi able to degrade D. octopetala's tannins. In contrast, negative net nitrogen mineralization rates were observed at -6 degrees C possibly due to a more efficient N immobilization by tannins than N production by microbial activities, and suggesting a decoupling between C and N mineralization. Our results confirmed tannins and soil temperatures as relevant controls of microbial catabolism which are crucial for alpine ecosystems functioning and carbon storage.
Published: 2008
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39. Improvements of polymerase chain reaction and capillary electrophoresis single-strand conformation polymorphism methods in microbial ecology: Toward a high-throughput method for microbial diversity studies in soil

Author: Frédéric Giraud, Jérôme Gury, Ludovic Gielly, Lucie Zinger, S. Krivobok, Roberto A. Geremia, Pierre Taberlet, Laboratoire d'Ecologie Alpine (LECA), and Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])
Subjects: 0106 biological sciences, DNA polymerase, Soil Science, Genomics, DNA-Directed DNA Polymerase, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Polymerase Chain Reaction, 01 natural sciences, law.invention, 03 medical and health sciences, Capillary electrophoresis, BACTERIAL-POPULATIONS, law, 010608 biotechnology, RIBOSOMAL-RNA GENE, ORIGIN SALERS CHEESE, Ecosystem, Polymorphism, Single-Stranded Conformational, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, Polymerase chain reaction, DNA Primers, 2. Zero hunger, Genetics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Bacteria, Ecology, biology, IDENTIFICATION, 030306 microbiology, Electrophoresis, Capillary, REGISTERED DESIGNATION, Single-strand conformation polymorphism, AMPLIFICATION, Biodiversity, DNA, COMMUNITY DYNAMICS, DNA extraction, genomic DNA, Terminal restriction fragment length polymorphism, PCR, BIAS, biology.protein, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biological system
Abstract: Times Cited: 1; International audience; The molecular signature of bacteria from soil ecosystems is an important tool for studying microbial ecology and biogeography. However, a high-throughput technology is needed for such studies. In this article, we tested the suitability of available methods ranging from soil DNA extraction to capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) for high-throughput studies. Our results showed that the extraction method does not dramatically influence CE-SSCP profiles, and that DNA extraction of a 0.25 g soil sample is sufficient to observe overall bacterial diversity in soil matrices. The V3 region of the 16S rRNA gene was amplified by PCR, and the extension time was found to be critical. We have also found that proofreading DNA polymerases generate a better signal in CE-SSCP profiles. Experiments performed with different soil matrices revealed the repeatability, efficiency, and consistency of CE-SSCP. Studies on PCR and CE-SSCP using single-species genomic DNA as a matrix showed that several ribotypes may migrate at the same position, and also that single species can produce double peaks. Thus, the extrapolation between number of peaks and number of species remains difficult. Additionally, peak detection is limited by the analysis software. We conclude that the presented method, including CE-SSCP and the analyzing step, is a simple and effective technique to obtain the molecular signature of a given soil sample.
Published: 2007
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40. Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis

Author: Thomas J. Creedy, Henrik Krehenwinkel, Susan Kennedy, Brent C. Emerson, Víctor Noguerales, Kristine Bohmann, Florian Leese, Douglas W. Yu, Anna Papadopoulou, Jeremy R deWaard, Vasco Elbrecht, Martin I. Bidartondo, Hélène Morlon, Carmelo Andújar, Lucie Zinger, Simon Creer, Gentile Francesco Ficetola, Paula Arribas, Eric Coissac, Alfried P. Vogler, Emmanouil Meramveliotakis, Vojtech Novotny, Fredrik Ronquist, Isaac Overcast, Marta Goberna, European Research Council, European Commission, Estacion Volcanologica de Canarias IPNA-CSIC, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), and Natural Environment Research Council (NERC)
Subjects: 0106 biological sciences, 0301 basic medicine, Biochemistry & Molecular Biology, Global integration, Exploit, Test data generation, Ecology (disciplines), [SDV]Life Sciences [q-bio], Biodiversity, Throughput, Environmental Sciences & Ecology, Biology, 010603 evolutionary biology, 01 natural sciences, harmonized data generation, Domain (software engineering), DNA metabarcoding, 03 medical and health sciences, High‐throughput sequencing, Harmonized data generation, Genetics, DNA Barcoding, Taxonomic, Biodiversity assessment, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Evolutionary Biology, Science & Technology, Ecology, business.industry, Environmental resource management, high‐throughput sequencing, high-throughput sequencing, Reproducibility of Results, Genomics, 15. Life on land, 06 Biological Sciences, Meeting Review, biodiversity assessment, Genomic Observatories, 030104 developmental biology, Cyprus, business, Biologie, Life Sciences & Biomedicine, Global biodiversity
Abstract: Departamento de Medio Ambiente y Agronomía (INIA)., High‐throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site‐based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled “Next Generation Biodiversity Monitoring” was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3‐day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS‐based strategy to collectively build an integrative framework for site‐based biodiversity data generation., The international symposium “Next Generation Biodiversity Monitoring” held in November 2019 in Nicosia (Cyprus) was organized by the iBioGen project, which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 810729. G.F.F. is funded by the European Research Council under the European Union’s Horizon 2020 programme, grant agreement No. 772284 (IceCommunities).
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