A5017795667- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Identification and Quantification in Food
- Protist diversity and phylogeny
- Fish biology, ecology, and behavior
- Fish Ecology and Management Studies
- Nematode management and characterization studies
- Species Distribution and Climate Change
- International Maritime Law Issues
- Wildlife-Road Interactions and Conservation
- Genetic diversity and population structure
- Aluminum Alloy Microstructure Properties
- Mycorrhizal Fungi and Plant Interactions
- Polar Research and Ecology
- Genome Rearrangement Algorithms
- DNA and Biological Computing
- Freshwater macroinvertebrate diversity and ecology
- Forest Ecology and Biodiversity Studies
- Aquatic Ecosystems and Biodiversity
- Isotope Analysis in Ecology
- Bayesian Methods and Mixture Models
- Wildlife Ecology and Conservation
- Genomics and Phylogenetic Studies
- Conservation, Biodiversity, and Resource Management
- Marine and fisheries research
University of Milan
2022-2024
Université Toulouse III - Paul Sabatier
2015-2023
Institut de Recherche pour le Développement
2019-2023
Centre National de la Recherche Scientifique
2019-2023
Laboratoire Evolution et Diversite Biologique
2019-2023
Laboratoire d'Écologie Alpine
2023
Université de Toulouse
2015-2019
Laboratoire Écologie Fonctionnelle et Environnement
2015
Ecolab (France)
2015
Abstract Environmental DNA (eDNA) metabarcoding is a promising tool to estimate aquatic biodiversity. It based on the capture of from water sample. The sampled volume, crucial aspect for efficient species detection, has been empirically variable (ranging few centiliters tens liters). This results in high variability sampling effort across studies, making comparisons difficult and raising uncertainties about completeness eDNA inventories. Our aim was determine (filtered volume) needed get...
Abstract Species trees have traditionally been inferred from a few selected markers, and genome‐wide investigations remain largely restricted to model organisms or small groups of species for which sampling fresh material is available, leaving out most the existing historical diversity. The genomes an increasing number species, including specimens extracted natural history collections, are being sequenced at low depth. While these data sets widely used analyse organelle genomes, nuclear...
Abstract Assessing the impact of human activity on ecosystems often links local biodiversity to disturbances measured within same locality. However, remote may also affect biodiversity. Here, we used environmental DNA metabarcoding evaluate relationships between vertebrate (fish and mammals) disturbance intensity in two Amazonian rivers. Measurements anthropic -here forest cover losses- were made from immediate vicinity sampling sites up 90 km upstream. The findings suggest that...
Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about spatial extent downstream transport eDNA. Here, we assessed ability eDNA inventories retrieve patterns fish assemblages along two large species-rich Neotropical rivers. We first examined overall community variation with distance through decay similarity compared this pattern capture-based...
Freshwater ecosystems are among the most endangered ecosystem in world. Understanding how human activities affect these requires disentangling and quantifying contribution of factors driving community assembly. While it has been largely studied temperate freshwaters, tropical remain challenging to study due high species richness lack knowledge on distribution. Here, use eDNA-based fish inventories combined a community-level modelling approach allowed depicting assembly rules relative...
Aquatic insects represent the majority of freshwater biodiversity, yet they are less studied than other taxa. Responses aquatic communities to stressors rarely assessed and usually measured in terms taxonomic richness derived from presence-absence data, despite certain mechanisms that may cause a reduction biomass species, without causing their disappearance. The integration functional measures with is often disregarded due methodological difficulties, particularly concerning insects....
Abstract Environmental DNA (eDNA) metabarcoding has recently gain much attention to assess aquatic environment biodiversity. A great variety of protocols have been developed collect, extract, and analyze eDNA, some which are continuously evolving optimized with technological improvements. Such shifts might deprecate the biological data produced earlier protocols, leading a loss knowledge. Here, we investigated robustness an eDNA method through comparison two biodiversity datasets generated...
Summary The development of terrestrial ecosystems depends greatly on plant mutualists such as mycorrhizal fungi. global retreat glaciers exposes nutrient‐poor substrates in extreme environments and provides a unique opportunity to study early successions fungi by assessing their dynamics drivers. We combined environmental DNA metabarcoding measurements local conditions assess the succession communities during soil 46 glacier forelands around globe, testing whether drivers differ between...
Ice-free areas are expanding worldwide due to dramatic glacier shrinkage and undergoing rapid colonization by multiple lifeforms, thus representing key environments study ecosystem development. It has been proposed that the dynamics of deglaciated terrains is different between surface deep soils but heterogeneity communities inhabiting decreases through time. Nevertheless, tests this hypothesis remain scarce, it unclear whether patterns consistent among taxonomic groups. Here, we used...
Protists are major actors of soil communities and play key roles in shaping food webs, community assembly, ecosystem processes, yet their functional diversity is understudied. High-throughput sequencing data have revealed ubiquity diversity, but lack standardized traits has hampered the integration information, limiting our understanding ecosystems. Here we propose a framework for protists, identify set common to characterize apply on broad-scale, real-world dataset. We reviewed studies...
Understanding how anthropization impacts the assembly of species onto communities is pivotal to go beyond observation biodiversity changes and reveal disturbances affect environmental biotic processes shaping biodiversity. Here, we propose a simple framework measure underpinning functional convergence/divergence patterns. We applied this northern Amazonian fish inventoried using DNA in 35 stream sites 64 river sites. found that harsh unstable conditions characterizing streams conveyed...
Abstract Background Deforestation is a widespread disturbance for neotropical freshwater ecosystems. While biodiversity declines have been associated with deforestation, its functional consequences stream and river fish faunas remain poorly understood. In this study, we explored how deforestation affects the different facets of structure communities inventoried using environmental DNA metabarcoding in 64 35 sites French Guiana. Specifically, investigated richness, divergence, evenness...
Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity morphological identification has limited broad-scale monitoring nematode biodiversity. DNA metabarcoding is increasingly used to assess diversity requires universal primers with high taxonomic coverage resolution. Several have been proposed for diversity, many which target 18S rRNA gene. In silico analyses a great potential key parameters primers, including coverage, resolution specificity. Based on...
Dietary plasticity of populations can be associated to ontogenetic diet preferences and depends on the size‐structure populations. niche characterizes functional role organisms in a food web, as it reflects both resources' diversity used by consumer trophic interactions system. niches are controlled biotic abiotic factors, but their natural systems remain poorly studied. Here, we investigated variability dietary salmonid wild focusing inter‐population intra‐population (through time) changes,...
Environmental DNA [eDNA] metabarcoding has recently emerged as a non-destructive alternative to traditional sampling for characterising species assemblages. We here provide consistent dataset synthetising all eDNA sites in French Guiana date. Field collections have been initiated 2014 and continued until 2019. This is however work progress will be updated after each collecting campaign. also taxon by site matrix fishes presence / absence inferred from eDNA. Our aim allow transparent...
Abstract The worldwide retreat of glaciers is causing a faster than ever increase in ice‐free areas that are leading to the emergence new ecosystems. Understanding dynamics these environments critical predicting consequences climate change on mountains and at high latitudes. Climatic differences between regions world could modulate biodiversity functionality after glacier retreat, yet global tests this hypothesis lacking. Nematodes most abundant soil animals, with keystone roles ecosystem...
Abstract Mechanisms underlying plant succession remain highly debated. A global quantification of the relative importance species addition versus replacement is lacking due to local scope most studies. We quantified their role in variation communities colonizing forelands 46 retreating glaciers distributed worldwide, using both environmental DNA and traditional surveys. Both mechanisms concur determining community changes over time but varied along successions. Taxa predominated immediately...
Abstract Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about spatial extent downstream transport eDNA. Here, we assessed ability eDNA inventories retrieve patterns fish assemblages along two large species rich Neotropical rivers. We first examined overall community variation with distance through decay similarity compared this pattern...
Abstract Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity morphological identification has limited broad-scale monitoring their biodiversity. DNA metabarcoding is increasingly used to assess nematode biodiversity requires universal primers with high taxonomic coverage resolution. Several have been proposed for diversity, many which target 18S rRNA gene. In-silico analyses a great potential key parameters primers, including coverage, resolution...
Soil hosts key components of terrestrial biodiversity providing essential services to the below- and above-ground ecosystems. The worldwide retreat glaciers is exposing new deglaciated terrains, offering a unique opportunity understand development soil ecosystems under changing climate. Many studies have investigated how biotic communities change after deglaciation, but protists often been overlooked despite their role in multiple ecosystem functions. Here, we aim protist develop along...
Ice-free areas are increasing worldwide due to the dramatic glacier shrinkage and undergoing rapid colonization by multiple lifeforms, thus representing key environments study ecosystem development. Soils have a complex vertical structure. However, we know little about how microbial animal communities differ across soil depths development stages during of deglaciated terrains, these differences evolve through time, whether patterns consistent among different taxonomic groups. Here, used...