Résumé
Experiments comparing diploids with polyploids and in single grassland sites show that nitrogen and/or phosphorus availability influences plant growth and community composition dependent on genome size; specifically, plants with larger genomes grow faster under nutrient enrichments relative to those with smaller genomes. However, it is unknown if these effects are specific to particular site localities with speciifc plant assemblages, climates, and historical contingencies. To determine the generality of genome size-dependent growth responses to nitrogen and phosphorus fertilization, we combined genome size and species abundance data from 27 coordinated grassland nutrient addition experiments in the Nutrient Network that occur in the Northern Hemisphere across a range of climates and grassland communities. We found that after nitrogen treatment, species with larger genomes generally increased more in cover compared to those with smaller genomes, potentially due to a release from nutrient limitation. Responses were strongest for C3 grasses and in less seasonal, low precipitation environments, indicating that genome size effects on water-use-efficiency modulates genome size–nutrient interactions. Cumulatively, the data suggest that genome size is informative and improves predictions of species’ success in grassland communities.
Auteurs, date et publication :
Auteurs Joseph A. Morton , Carlos Alberto Arnillas , Lori Biedermann , Elizabeth T. Borer , Lars A. Brudvig , Yvonne M. Buckley , Marc W. Cadotte , Kendi Davies , Ian Donohue , Anne Ebeling , Nico Eisenhauer , Catalina Estrada , Sylvia Haider , Yann Hautier , Anke Jentsch , Holly Martinson , Rebecca L. McCulley , Xavier Raynaud , Christiane Roscher , Eric W. Seabloom
Publication : PLOS Biology
Date : 2025
Volume : 22
Issue : 12
Pages : e3002927
Catégorie(s)
#ANR-Citation #CEREEP #CNRS #ENSRésumé
Climatic variation is a key driver of genetic differentiation and phenotypic traits evolution, and local adaptation to temperature is expected in widespread species. We investigated phenotypic and genomic changes in the native range of the Asian tiger mosquito, Aedes albopictus. We first refine the phylogeographic structure based on genome-wide regions (1,901 double-digest restriction-site associated DNA single nucleotide polymophisms [ddRAD SNPs]) from 41 populations. We then explore the patterns of cold adaptation using phenotypic traits measured in common garden (wing size and cold tolerance) and genotype-temperature associations at targeted candidate regions (51,706 exon-capture SNPs) from nine populations. We confirm the existence of three evolutionary lineages including clades A (Malaysia, Thailand, Cambodia, and Laos), B (China and Okinawa), and C (South Korea and Japan). We identified temperature-associated differentiation in 15 out of 221 candidate regions but none in ddRAD regions, supporting the role of directional selection in detected genes. These include genes involved in lipid metabolism and a circadian clock gene. Most outlier SNPs are differently fixed between clades A and C, whereas clade B has an intermediate pattern. Females are larger at higher latitude yet produce no more eggs, which might favor the storage of energetic reserves in colder climate. Nondiapausing eggs from temperate populations survive better to cold exposure than those from tropical populations, suggesting they are protected from freezing damages but this cold tolerance has a fitness cost in terms of egg viability. Altogether, our results provide strong evidence for the thermal adaptation of A. albopictus across its wide temperature range.
Auteurs, date et publication :
Auteurs Stephanie Sherpa , Jordan Tutagata , Thierry Gaude , Frederic Laporte , Shinji Kasai , Intan H. Ishak , Xiang Guo , Jiyeong Shin , Sebastien Boyer , Sebastien Marcombe , Theeraphap Chareonviriyaphap , Jean-Philippe David , Xiao-Guang Chen , Xiaohong Zhou , Laurence Despres
Publication : MOLECULAR BIOLOGY AND EVOLUTION
Date : 2022
Volume : 39
Issue : 5
Catégorie(s)
#ANR-Citation #CNRS #Lautaret #UGARésumé
Water use efficiency (WUE), the amount of assimilated carbon per amount of transpired water is central to assess how trees and forests respond to the ongoing climate changes and, particularly, to increasing drought severity. We concurrently evaluated leaf- and ecosystem-scale intrinsic WUE (WUEi) of a Mediterranean evergreen oak (Quercus ilex) forest in southern France using stable carbon isotopic discrimination, leaf gas exchange and eddy covariance fluxes. Nine years of continuous daily eddy fluxes were converted into 7-day composite chronicle of WUEi and then into δ13C input to check, is there a link between eddy and bulk leaf δ13C? The relationship between ecosystem-scale WUEi and water limitation, assessed by the predawn tree potential (ψpd), followed a trapezoidal curve with a plateau value of 158.0 ± 4.0 µmol CO2 mol-1 H2O. WUEi began to decline from -2.4 MPa with gas exchange ceasing at -4.4 MPa. WUEi measured at leaf scale followed a bi-linear relationship with ψpd that peaked at ψpd = -3.15 MPa, reaching 120.5 ± 16.4 µmol CO2 mol-1 H2O. Current year leaf δ13C is linearly related to the averaged δ13C input over the leaf expansion period. In 1-year old leaves, adjustment in bulk δ13C was dependent on the degree of water limitation. Whole-isotopic mass balance at tree or ecosystem scales continue to be a major challenge because large gaps remain in understanding all the processes that influence δ13C of fluxes and C pools.
Auteurs, date et publication :
Auteurs Serge Rambal , Jeannine Cavender-Bares , Jean-Marc Limousin , Yann Salmon
Publication : Agricultural and Forest Meteorology
Date : 2026
Volume : 361
Pages : 110283
Catégorie(s)
#CNRS #FORET PuechabonRésumé
Satellite radar backscatter contains unique information on land surface moisture, vegetation features, and surface roughness and has thus been used in a range of Earth science disciplines. However, there is no single global radar data set that has a relatively long wavelength and a decades-long time span. We here provide the first long-term (since 1992), high-resolution ( similar to 8 :9 km instead of the commonly used similar to 25 km resolution) monthly satellite radar backscatter data set over global land areas, called the long-term, high-resolution scatterometer (LHScat) data set, by fusing signals from the European Remote Sensing satellite (ERS; 1992-2001; C-band; 5.3 GHz), Quick Scatterometer (QSCAT, 1999-2009; Ku-band; 13.4 GHz), and the Advanced SCATterometer (ASCAT; since 2007; C-band; 5.255 GHz). The 6-year data gap between C-band ERS and ASCAT was filled by modelling a substitute C-band signal during 1999-2009 from Ku-band QSCAT signals and climatic information. To this end, we first rescaled the signals from different sensors, pixel by pixel. We then corrected the monthly signal differences between the C-band and the scaled Ku-band signals by modelling the signal differences from climatic variables (i.e. monthly precipitation, skin temperature, and snow depth) using decision tree regression. The quality of the merged radar signal was assessed by computing the Pearson r, root mean square error (RMSE), and relative RMSE (rRMSE) between the C-band and the corrected Ku-band signals in the overlapping years (1999-2001 and 2007-2009). We obtained high Pearson r values and low RMSE values at both the regional ( r >= 0 :92, RMSE <= 0.11 dB, and rRMSE = 0.64, median RMSE <= 0.34 dB, and median rRMSE <= 0.88), suggesting high accuracy for the data-merging procedure. The merged radar signals were then validated against the European Space Agency (ESA) ERS-2 data, which provide observations for a subset of global pixels until 2011, even after the failure of on-board gyroscopes in 2001. We found highly concordant monthly dynamics between the merged radar signals and the ESA ERS-2 signals, with regional Pearson r values ranging from 0.79 to 0.98. These results showed that our merged radar data have a consistent C-band signal dynamic. The LHScat data set (https://doi.org/10.6084/m9.figshare.20407857; Tao et al., 2023) is expected to advance our understanding of the long-term changes in, e.g., global vegetation and soil moisture with a high spatial resolution. The data set will be updated on a regular basis to include the latest images acquired by ASCAT and to include even higher spatial and temporal resolutions.
Auteurs, date et publication :
Auteurs Shengli Tao , Zurui Ao , Jean-Pierre Wigneron , Sassan Saatchi , Philippe Ciais , Jerome Chave , Thuy Le Toan , Pierre-Louis Frison , Xiaomei Hu , Chi Chen , Lei Fan , Mengjia Wang , Jiangling Zhu , Xia Zhao , Xiaojun Li , Xiangzhuo Liu , Yanjun Su , Tianyu Hu , Qinghua Guo , Zhiheng Wang
Publication : EARTH SYSTEM SCIENCE DATA
Date : 2023
Volume : 15
Issue : 4
Pages : 1577-1596
Catégorie(s)
#ANR-Citation #CNRS #FORET NouraguesRésumé
Biochar is the product of intentional pyrolysis of organic feedstocks. It is made under controlled conditions in order to achieve desired physico-chemical characteristics. These characteristics ultimately affect biochar properties as a soil amendment. When biochar is used for carbon storage, an important property is its persistence in soil, often described by the proportion of biochar carbon remaining in soil after a 100 years (Fperm mathrmF_mathrmperm ). We analyzed published data on 1230 biochars to re-evaluate the effect of pyrolysis parameters on biochar characteristics and the possibility to predict Fperm mathrmF_mathrmperm from the maximum temperature reached during pyrolysis (HTT). We showed that biochar ash and nitrogen (N) contents were mostly affected by feedstock type. The oxygen to carbon (O:C) and hydrogen to carbon (H:C) ratios were mostly affected by the extent of pyrolysis (a combination of HTT and pyrolysis duration), except for non (ligno)cellulosic feedstocks (plastic waste, sewage sludge). The volatile matter (VM) content was affected by both feedstock type and the extent of pyrolysis. We demonstrated that HTT is the main driver of H:C – an indicator of persistence – but that it is not measured accurately enough to precisely predict H:C, let alone persistence. We examined the equations to estimate Fperm mathrmF_mathrmperm available in the literature and showed that Fperm mathrmF_mathrmperm calculated from HTT presented little agreement with Fperm mathrmF_mathrmperm calculated from H:C. The sign and magnitude of the bias depended on the equation used to calculate Fperm mathrmF_mathrmperm and the dispersion was usually large. This could lead to improper compensation of carbon emissions and wrong reporting of carbon sinks in national carbon accounting schemes. We recommend not to use HTT as a predictor for persistence and stress the importance to rapidly develop more accurate proxies of biochar C persistence in soil.
Auteurs, date et publication :
Auteurs Johanne Lebrun Thauront , Gerhard Soja , Hans-Peter Schmidt , Samuel Abiven
Publication : GCB Bioenergy
Date : 2025
Volume : 16
Issue : 11
Pages : e13170
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENSRésumé
Earthworms represent a crucial taxon in soil ecosystems in terms of biomass and ecological functions. Knowledge of their diversity is growing, but the understanding of the ecological and evolutionary mechanisms underlying this diversity and its distribution patterns remains poorly understood. This is partly due to a lack of community data available on a large scale, particularly in the natural ecosystems of the most diverse tropical regions. Here we describe a large dataset containing records of 3555 georeferenced earthworm specimens, sampled in 125 one-hectare plots distributed in different habitats and localities across French Guiana. Each of these specimens was DNA barcoded targeting the cytochrome C Oxidase I subunit barcode region (COI), and these sequences were clustered into molecular operational taxonomic units (OTUs) that we used as species proxy to describe community taxonomic composition and diversity. Each community is associated in the dataset with climate and elevation data, and soil properties are also available for part of them. This dataset represents a unique opportunity for analyzing community diversity and phylogeographic patterns in neotropical rainforests.
Auteurs, date et publication :
Auteurs Arnaud Goulpeau , Mickaël Hedde , Marie-Eugénie Maggia , Sylvain Gérard , Emmanuel Lapied , Thibaud Decaens
Publication : Soil Organisms
Date : 2024
Volume : 96
Issue : 2
Pages : 79–90
Catégorie(s)
#CNRS #FORET NouraguesRésumé
The accurate separation between leaf and woody components from terrestrial laser scanning (TLS) data is vital for the estimation of leaf area index (LAI) and wood area index (WAI). Here, we present the application of deep learning time series separation of leaves and wood from TLS point clouds collected from broad-leaved trees. First, we use a multiple radius nearest neighbor approach to obtain a time series of the geometric features. Second, we compare the performance of Fully Convolutional Neural Network (FCN), Long Short-Term Memory Fully Convolutional Neural Network (LSTM-FCN), and Residual Network (ResNet) on leaf and wood classification. We also compare the effect of univariable (UTS) and multivariable (MTS) time series on classification accuracy. Finally, we explore the utilization of a class activation map (CAM) to reduce the black-box effect of deep learning. The average overall accuracy of the MTS method across the training data is 0.96, which is higher than the UTS methods (0.67 to 0.88). Meanwhile, ResNet spent much more time than FCN and LSTM-FCN in model development. When testing our method on an independent dataset, the MTS models based on FCN, LSTM-FCN, and ResNet all demonstrate similar performance. Our method indicates that the CAM can explain the black-box effect of deep learning and suggests that deep learning algorithms coupled with geometric feature time series can accurately separate leaf and woody components from point clouds. This provides a good starting point for future research into estimation of forest structure parameters.
Auteurs, date et publication :
Auteurs Tao Han , Gerardo Arturo Sánchez-Azofeifa
Publication : Remote Sensing
Date : 2022
Volume : 14
Issue : 13
Pages : 3157
Catégorie(s)
#CNRS #FORET NouraguesRésumé
The genus Culex is one of the most diverse in the world and includes numerous known vector species of parasites and viruses to humans. Morphological identification of Culex species is notoriously difficult and rely mostly on the examination of properly dissected male genitalia which largely prevents female and immature identification during entomological, ecological or arboviral surveys. The aims of this study were (i) to establish a DNA barcode library for Culex mosquitoes of French Guiana based on the mitochondrial gene cytochrome c oxidase I (COI) marker, (ii) to compare three approaches of molecular delimitation of species to morphological identification, and (iii) to test the effectiveness of the COI marker at a broader geographical scale across South America. Mosquitoes used in this study were sampled in French Guiana between 2013 and 2023. We provide 246 COI sequences for 90 morphologically identified species of Culex, including five new country records and two newly described species. Overall, congruence between morphological identification and molecular delimitations using the COI barcode were high. The Barcode of Life Data clustering approach into Barcode Index Numbers gives the best result in terms of species delimitation, followed by the muti-rate Poisson Tree Processes and the Assemble Species by Automatic Partitioning methods. Inconsistencies between morphological identification and molecular delimitation can be explained by introgression, incomplete lineage sorting, imperfect taxonomy or the effect of the geographical scale of sampling. This increases by almost two-fold the number of mosquito species for which a DNA barcode is available in French Guiana, including 75% of the species of Culex currently known in the territory. Finally, this study confirms the usefulness of the COI barcode in identifying Culex mosquitoes of South America, but also points the limits of this marker for some groups of species within the subgenera Culex and Melanoconion.Competing Interest StatementThe authors have declared no competing interest.
Auteurs, date et publication :
Auteurs Stanislas Talaga , Amandine Guidez , Benoît de Thoisy , Anne Lavergne , Romuald Carinci , Pascal Gaborit , Jean Issaly , Isabelle Dusfour , Jean-Bernard Duchemin
Publication : bioRxiv
Date : 2024
Pages : 2024.09.04.611342
Catégorie(s)
#CNRS #FORET NouraguesRésumé
Estimating the overall number of species for a given taxon is a central issue in ecology and conservation biology. It should be particularly topical in the case of soil organisms, which represent the majority of known species, but still suffer from a considerable taxonomic knowledge deficit. We propose here an estimation of the global number of earthworm species based on the Joppa approach, which models taxonomic effort over time in order to estimate the total number of known and as yet unknown species in a given taxa. Our Bayesian estimation of this model allows us to propose a global diversity of the order of 30,000 species. However, the uncertainty around this estimate is considerable due to severe undersampling and as the model cannot unambiguously decide whether we are describing few species because of a small pool of as yet unknown species, or because of a lack of taxonomic efficiency. This means that the 5,679 species and subspecies already described only represent around 20% of the global number of earthworm species. Considering the current rate of new species description, we calculate that it would take at least 120 years to describe all the species existing on Earth. We discuss the strategies that could be developed to reduce the magnitude of this taxonomic deficit.Competing Interest StatementThe authors have declared no competing interest.
Auteurs, date et publication :
Auteurs Thibaud Decaëns , George G. Brown , Erin K. Cameron , Csaba Csuzdi , Nico Eisenhauer , Sylvain Gérard , Arnaud Goulpeau , Mickaël Hedde , Samuel W. James , Emmanuel Lapied , Marie-Eugénie Maggia , Daniel F. Marchán , Jérôme Mathieu , Helen R. P. Phillips , Eric Marcon
Publication : bioRxiv
Date : 2024
Pages : 2024.09.08.611896
Catégorie(s)
#CNRS #FORET NouraguesRésumé
Abstract
Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species Ferriphaselus amnicola and is strikingly similar to Ferriphaselus amnicola strain OYT1 which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species Ferriphaselus amnicola.
Auteurs, date et publication :
Auteurs M Garry , J Farasin , L Drevillon , A Quaiser , C Bouchez , T Le Borgne , S Coffinet , A Dufresne
Publication : FEMS Microbiology Ecology
Date : 2024
Pages : fiae047