Lucie Zinger

Lucie Zinger
Ecole Normale Supérieure de Paris | ENS · Institut de Biologie de l’Ecole Normale Supérieure (IBENS)

PhD
community ecology & macroecology of small organisms, eDNA, metabarcoding

About

88
Publications
35,042
Reads
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3,689
Citations
Introduction
Lucie Zinger currently works at the Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure de Paris. Lucie does research in Ecology, Molecular Biology and Microbiology. See more at luciezinger.wordpress.com
Additional affiliations
September 2016 - present
Ecole Normale Supérieure de Paris
Position
  • Professor (Assistant)
April 2013 - August 2016
Paul Sabatier University - Toulouse III
Position
  • Post Doc - Soil tropical diversity through metabarcoding
October 2011 - March 2013
French National Centre for Scientific Research
Position
  • Post Doc - Soil Eukarya Metatranscriptomes

Publications

Publications (88)
Article
Full-text available
Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems. The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface...
Book
Environmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to t...
Article
Full-text available
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 acros...
Article
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity...
Article
Full-text available
1. In soils, plants and fungi can form complex mycorrhizal networks allowing nutrient transfers between plant individuals and species. It is less clear, however, whether such networks exist on the bark of trees where epiphytic plant communities thrive in rainforests. Previous work showed that tropical epiphytic orchids especially, harbor symbiotic...
Article
Full-text available
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-sca...
Article
Soil trophic networks are key to biogeochemical cycles, in particular decomposition. However, few studies have yet quantified how microbial decomposition activity along environmental gradients is jointly driven by bacteria, fungi, and their respective consumers. Here, we quantified these direct and indirect effects on decomposition and contrasted t...
Article
Full-text available
Aim Although soil biodiversity is extremely rich and spatially variable, both in terms of species and trophic groups, we still know little about its main drivers. Here, we contrast four long‐standing hypotheses to explain the spatial variation of soil multi‐trophic diversity: energy, physiological tolerance, habitat heterogeneity and resource heter...
Article
Full-text available
The development of high‐throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational ana...
Article
Full-text available
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacte...
Article
Full-text available
The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potentia...
Article
Full-text available
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 distance...
Preprint
Full-text available
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview about current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational...
Article
Full-text available
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 indire...
Article
Full-text available
Urban expansion and associated habitat transformation drives shifts in biodiversity, with declines in taxonomic and functional diversity. Forests fragments within urban landscapes offer a number of ecosystem services, and help to maintain biodiversity and ecosystem functions. Here, we focus on a tropical forest environment, and on the soil biota. U...
Preprint
Full-text available
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Phytoplankton communities are generally studied by PCR amplification of bacterial (16S), nuc...
Preprint
Full-text available
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 indire...
Article
1. DNA metabarcoding is becoming the tool of choice for biodiversity assessment across taxa and environments. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines to remove experimental noise exist. However, these often only partially target produced artefacts, o...
Article
Full-text available
High‐throughput sequencing (HTS) is increasingly being used for the characterisation and monitoring of biodiversity. If applied in a structured way, across broad geographic scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated indepe...
Preprint
Full-text available
DNA metabarcoding is becoming the tool of choice for biodiversity studies across taxa and large-scale environmental gradients. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines removing experimental noise have been designed to address this issue. However, thes...
Article
Full-text available
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 of the diversity of cuticular bacteria in other ant host species, as well as of the mechanisms leading to the composition of these communities. Here, we used 16S rRNA gene...
Chapter
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 ef...
Book
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 ef...
Article
Full-text available
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 consequen...
Article
Full-text available
High‐throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such datasets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA sampl...
Article
Full-text available
Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are...
Article
Full-text available
Environmental DNA (eDNA) is increasingly used for analysing and modelling all‐inclusive biodiversity patterns. However, the reliability of eDNA‐based diversity estimates is commonly compromised by arbitrary decisions for curating the data from molecular artefacts. Here, we test the sensitivity of common ecological analyses to these curation steps,...
Article
Full-text available
•The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic units (OTUs) delineation from sequence data and the study of their biogreography. •We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU p...
Article
Full-text available
1.Much effort has been devoted to better understanding the effects of environment and biodiversity on ecosystem functioning. However, few studies have moved beyond measuring biodiversity as species richness of a single group and/or focusing on a single ecosystem function. While there is a growing recognition that along environmental gradients, the...
Article
Full-text available
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 cy-tochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an i...
Article
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...
Article
Full-text available
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 mult...
Article
Full-text available
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 howe...
Article
Full-text available
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 microbio...
Preprint
Full-text available
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 r...
Article
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 hig...
Preprint
Full-text available
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. H...
Article
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 behavior of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties to working with low bacterial DNA quantities as in individ...
Article
Full-text available
Climate change is now considered to be the greatest threat to biodiversity and ecological networks, but its impacts on the bacterial communities associated with plants and animals remain largely unknown. Here, we studied the consequences of climate warming on the gut bacterial communities of an ectotherm, the common lizard (Zootoca vivipara), using...
Article
Full-text available
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 fec...
Article
Full-text available
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...
Article
Full-text available
Phlebotomine sand flies are hematophagous 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...
Article
Full-text available
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 intera...
Article
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...
Article
Full-text available
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...
Article
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 I...
Article
It is now well recognized that considering species evolutionary history is crucial for understanding the processes driving community assembly (Cavender-Bares et al. ). Considerable efforts have been made to integrate phylogenetics and community ecology into a single theoretical framework. Yet, assessing phylogenetic structure at the community scale...
Article
Full-text available
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...
Presentation
Paleoenvironmental studies provides crucial long-term data to study both anthropogenic disturbance and/or climate changes, and their effects on the environment. We used a multi-disciplinary approach to reconstruct past landscapes in Lake Anterne watershed (Haute-Savoie, French Alps) over the Holocene. In a previous study, DNA metabarcoding approach...
Article
Full-text available
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 quantifi...
Chapter
Environmental RNA-based metatranscriptomics is assumed to better reflect ongoing biological activities. This type of metatranscriptomics has been developed for environments as diverse as freshwater and seawater or soils. The eukaryotic 3’ polyadenylated messenger RNAs can be isolated from ribosomal, noncoding RNAs and bacterial mRNAs that dominate...
Article
Full-text available
Lemmings are key herbivores in many arctic food webs and their population dynamics have major impacts on the functioning of tundra systems. However, current knowledge of lemming diet is limited, hampering evaluation of lemming-vegetation interactions. This lack of knowledge is mainly due to methodological challenges, as previously used microhistolo...
Conference Paper
This paper considers a statistical modelling approach to investigate spatial cross-correlations between species in an ecosystem. A special feature is the origin of the data from high-troughput environmental DNA sequencing of soil samples. Here we use data collected at the Nourague CNRS Field Station in French Guiana. We describe bivariate spatial r...