Résumé
Contemporary climate change affects population dynamics, but its influence varies with landscape structure. It is still unclear whether landscape fragmentation buffers or amplifies the effects of climate on population size and the age and body size of individuals composing these populations. This study aims to investigate the impacts of warm climates on lizard life-history traits and population dynamics in habitats that vary in their connectivity. We monitored common lizard Zootoca vivipara populations for 3 years in an experimental system in which both climatic conditions and connectivity among habitats were simultaneously manipulated. We considered two climatic treatments (i.e. present-day climate and warm climate [+1.4°C than present-day climate]) and two connectivity treatments (i.e. a connected treatment in which individuals could move from one climate to the other and an isolated treatment in which movement between climates was not possible). We monitored survival, reproduction, growth, dispersal, age and body size of each individual in the system as well as population density through time. We found that the influence of warm climates on life-history traits and population dynamics depended on connectivity among thermal habitats. Populations in warm climates were (i) composed of younger individuals only when isolated; (ii) larger in population size only in connected habitats and (iii) composed of larger age-specific individuals independently of the landscape configuration. The connectivity among habitats altered population responses to climate warming likely through asymmetries in the flow and phenotype of dispersers between thermal habitats. Our results demonstrate that landscape fragmentation can drastically change the dynamics and persistence of populations facing climate change.
Auteurs, date et publication :
Auteurs Félix Pellerin , Elvire Bestion , Laurane Winandy , Lucie Di Gesu , Murielle Richard , Robin Aguilée , Julien Cote
Publication : Journal of Animal Ecology
Date : 2025
Volume : 91
Issue : 11
Pages : 2301-2313
Catégorie(s)
#ANR-Citation #CNRS #Metatron terrestreRésumé
Abstract. The CANOPEE project aims to better understand the biosphere–atmosphere exchanges of biogenic volatile organic compounds (BVOCs) in the case of Mediterranean ecosystems and the impact of in-canopy processes on the atmospheric chemical composition above the canopy. Based on an intensive field campaign, the objective of our work was to determine the chemical composition of the air inside a canopy as well as the net fluxes of reactive species between the canopy and the boundary layer. Measurements were carried out during spring 2012 at the field site of the Oak Observatory of the Observatoire de Haute Provence (O3HP) located in the southeast of France. The site is a forest ecosystem dominated by downy oak, Quercus pubescens Willd., a typical Mediterranean species which features large isoprene emission rates. Mixing ratios of isoprene, its degradation products methylvinylketone (MVK) and methacrolein (MACR) and several other oxygenated VOC (OxVOC) were measured above the canopy using an online proton transfer reaction mass spectrometer (PTR-MS), and fluxes were calculated by the disjunct eddy covariance approach. The O3HP site was found to be a very significant source of isoprene emissions, with daily maximum ambient concentrations ranging between 2–16 ppbv inside and 2–5 ppbv just above the top of the forest canopy. Significant isoprene fluxes were observed only during daytime, following diurnal cycles with midday net emission fluxes from the canopy ranging between 2.0 and 9.7 mg m−2 h1. Net isoprene normalized flux (at 30 °C, 1000 μmol quanta m−2 s−1) was estimated at 7.4 mg m−2 h−1. Evidence of direct emission of methanol was also found exhibiting maximum daytime fluxes ranging between 0.2 and 0.6 mg m−2 h−1, whereas flux values for monoterpenes and others OxVOC such as acetone and acetaldehyde were below the detection limit.
The MVK+MACR-to-isoprene ratio provided useful information on the oxidation of isoprene, and is in agreement with recent findings proposing weak production yields of MVK and MACR, in remote forest regions where the NOx concentrations are low. In-canopy chemical oxidation of isoprene was found to be weak and did not seem to have a significant impact on isoprene concentrations and fluxes above the canopy.
Auteurs, date et publication :
Auteurs C. Kalogridis , V. Gros , R. Sarda-Esteve , B. Langford , B. Loubet , B. Bonsang , N. Bonnaire , E. Nemitz , A.-C. Genard , C. Boissard , C. Fernandez , E. Ormeño , D. Baisnée , I. Reiter , J. Lathière
Publication : Atmospheric Chemistry and Physics
Date : 2014
Volume : 14
Issue : 18
Pages : 10085-10102
Catégorie(s)
#CNRS #FORET O3HPRésumé
Abstract Site occupancy-detection models (SODMs) are statistical models widely used for biodiversity surveys where imperfect detection of species occurs. For instance, SODMs are increasingly used to analyse environmental DNA (eDNA) data, taking into account the occurrence of both false-positive and false-negative errors. However, species occurrence data are often characterized by spatial and temporal autocorrelation, which might challenge the use of standard SODMs. Here we reviewed the literature of eDNA biodiversity surveys and found that most of studies do not take into account spatial or temporal autocorrelation. We then demonstrated how the analysis of data with spatial or temporal autocorrelation can be improved by using a conditionally autoregressive SODM, and show its application to environmental DNA data. We tested the autoregressive model on both simulated and real data sets, including chronosequences with different degrees of autocorrelation, and a spatial data set on a virtual landscape. Analyses of simulated data showed that autoregressive SODMs perform better than traditional SODMs in the estimation of key parameters such as true-/false-positive rates and show a better discrimination capacity (e.g., higher true skill statistics). The usefulness of autoregressive SODMs was particularly high in data sets with strong autocorrelation. When applied to real eDNA data sets (eDNA from lake sediment cores and freshwater), autoregressive SODM provided more precise estimation of true-/false-positive rates, resulting in more reasonable inference of occupancy states. Our results suggest that analyses of occurrence data, such as many applications of eDNA, can be largely improved by applying conditionally autoregressive specifications to SODMs.
Auteurs, date et publication :
Auteurs Wentao Chen , Gentile Francesco Ficetola
Publication : Molecular Ecology Resources
Date : 2019
Volume : 19
Issue : 1
Pages : 163–175
Catégorie(s)
#CNRS #eDNARésumé
There is a growing demand for spatially explicit assessment of multiple ecosystem services (ES) and remote sensing (RS) can provide valuable data to meet this challenge. In this study, located in the Central French Alps, we used high spatial and spectral resolution RS images to assess multiple ES based on underpinning ecosystem properties (EP) of subalpine grasslands. We estimated five EP (green biomass, litter mass, crude protein content, species diversity and soil carbon content) from RS data using empirical RS methods and maps of ES were calculated as simple linear combinations of EP. Additionally, the RSbased results were compared with results of a plant trait-based statistical modelling approach that predicted EP and ES from land use, abiotic and plant trait data (modelling approach). The comparison between the RS and the modelling approaches showed that RS-based results provided better insight into the fine-grained spatial distribution of EP and thereby ES, whereas the modelling approach reflected the land use signal that underpinned trait-based models of EP. The spatial agreement between the two approaches at a 20-m resolution varied between 16 and 22% for individual EP, but for the total ecosystem service supply it was only 7%. Furthermore, the modelling approach identified the alpine grazed meadows land use class as areas with high values of multiple ES (hot spots) and mown-grazed permanent meadows as areas with low values and only few ES (cold spots). Whereas the RS-based hot spots were a small subset of those predicted by the modelling approach, cold spots were rather scattered, small patches with limited overlap with the modelling results. Despite limitations associated with timing of assessment campaigns and field data requirements, RS offers valuable data for spatially continuous mapping of EP and can thus supply RS-based proxies of ES. Although the RS approach was applied to a limited area and for one type of ecosystem, we believe that the broader availability of high fidelity airborne and satellite RS data will promote RS-based assessment of ES to larger areas and other ecosystems.
Auteurs, date et publication :
Auteurs L. Homolová , M. E. Schaepman , P. Lamarque , J. G. P. W. Clevers , F. de Bello , W. Thuiller , S. Lavorel
Publication : Ecosphere
Date : 2025
Volume : 5
Issue : 8
Pages : art100
Catégorie(s)
#CNRS #Lautaret #UGAAuteurs, date et publication :
Auteurs Hannah Loranger , Gerhard Zotz , Maaike Y. Bader
Publication : Oikos
Date : 2025
Volume : 126
Issue : 11
Pages : 1625-1636
Catégorie(s)
#CNRS #Lautaret #UGAAuteurs, date et publication :
Auteurs Nicolas Legay , F. Grassein , T. M. Robson , Emmanuelle Personeni , Marie-Paule Bataillé , S. Lavorel , J.-C. Clement
Publication : Biogeosciences
Date : 2025
Volume : 10
Issue : 11
Catégorie(s)
#CNRS #Lautaret #UGARésumé
Abstract Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2-COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.
Auteurs, date et publication :
Auteurs Gentile Francesco Ficetola , Frédéric Boyer , Alice Valentini , Aurélie Bonin , Albin Meyer , Tony Dejean , Coline Gaboriaud , Philippe Usseglio-Polatera , Pierre Taberlet
Publication : Molecular Ecology
Date : 2025
Volume : 30
Issue : 13
Pages : 3189–3202
Catégorie(s)
#CNRS #eDNARésumé
Flowing surface waters (rivers, creeks, streams) are integrators of biological, chemical and physical processes occurring in a catchment and they link catchment land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present - nor about their dynamics - along the full course of a catchment. We do not know if they are confined to regions close to crops or if they are present throughout a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 10e5 bacteria/L. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 x 10e4 bacteria/L. Among the aquatic parameters that were characterized at each sampling site (total culturable bacteria, temperature, conductivity, concentrations of dissolved organic carbon (DOC), PO43-, NH4+, NO2- and NO3-), temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. These results suggest that strains of SRP with pathogenic potential to plants have lower competence for saprophytic survival (in freshwaters) than do potentially pathogenic strains of Psy and that their presence in river water is probably much more dependent on specific vegetative sources than are pathogenic strains of Psy. Nevertheless, their vegetative sources have not yet been identified. We discuss how to incorporate knowledge of the abundance and diversity of these two groups of plant pathogens in river water into a strategy for anticipating risk for disease outbreaks on crops in a catchment.
Auteurs, date et publication :
Auteurs Cindy E. Morris , Christelle Lacroix , Charlotte Chandeysson , Caroline Guilbaud , Cécile Monteil , Sylvain Piry , Emma Rochelle-Newall , Sarah Fiorini , Frédérique Van Gijsegem , Marie-Anne Barny , Odile Berge
Date : 2022
Catégorie(s)
#CNRS #PLANAQUARésumé
Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pisum to compare the performances of two widely used PCR primer pairs with DNA capture, based on solution hybrid selection. All methods produced an exhaustive description of the 8 bacterial taxa known to be present in this sample. In addition, the methods yielded similar quantitative results, with the number of reads strongly correlating with quantitative PCR controls. Both methods can thus be considered as qualitatively and quantitatively robust on such a sample with low microbial complexity.
Auteurs, date et publication :
Auteurs Marie Cariou , Céline Ribière , Stéphanie Morlière , Jean-Pierre Gauthier , Jean-Christophe Simon , Pierre Peyret , Sylvain Charlat
Publication : BMC Research Notes
Date : 2018
Volume : 11
Issue : 1
Pages : 1-5
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Abstract The rapidly growing field of molecular diet analysis is becoming increasingly popular among ecologists, especially when investigating methodologically challenging groups, such as invertebrate generalist predators. Prey DNA detection success is known to be affected by multiple factors; however, the type of dietary sample has rarely been considered. Here, we address this knowledge gap by comparing prey DNA detection success from three types of dietary samples. In a controlled feeding experiment, using the carabid beetle Pterostichus melanarius as a model predator, we collected regurgitates, faeces and whole consumers (including their gut contents) at different time points postfeeding. All dietary samples were analysed using multiplex PCR, targeting three different length DNA fragments (128, 332 and 612 bp). Our results show that both the type of dietary sample and the size of the DNA fragment contribute to a significant part of the variation found in the detectability of prey DNA. Specifically, we observed that in both regurgitates and whole consumers, prey DNA was detectable significantly longer for all fragment sizes than for faeces. Based on these observations, we conclude that prey DNA detected from regurgitates and whole consumers DNA extracts are comparable, whereas prey DNA detected from faeces, though still sufficiently reliable for ecological studies, will not be directly comparable to the former. Therefore, regurgitates and faeces constitute a useful, nonlethal source for dietary information that could be applied to field studies in situations when invertebrate predators should not be killed.
Auteurs, date et publication :
Auteurs Stefaniya Kamenova , Rebecca Mayer , Oskar R Rubbmark , Eric Coissac , Manuel Plantegenest , Michael Traugott
Publication : Molecular Ecology Resources
Date : 2018
Volume : 18
Issue : 5
Pages : 966–973