Résumé
Recent advances in next-generation sequencing (NGS) technologies spur progress in determining the microbial diversity in various ecosystems by highlighting, for example, the rare biosphere. Currently, high-throughput pyrotag sequencing of PCR-amplified SSU rRNA gene regions is mainly used to characterize bacterial and archaeal communities, and rarely to characterize protist communities. In addition, although taxonomic assessment through phylogeny is considered as the most robust approach, similarity and probabilistic approaches remain the most commonly used for taxonomic affiliation. In a first part of this work, a tree-based method was compared with different approaches of taxonomic affiliation (BLAST and RDP) of 18S rRNA gene sequences and was shown to be the most accurate for near full-length sequences and for 400 bp amplicons, with the exception of amplicons covering the V5-V6 region. Secondly, the applicability of this method was tested by running a full scale test using an original pyrosequencing dataset of 18S rRNA genes of small lacustrine protists (0.2–5 mm) from eight freshwater ecosystems. Our results revealed that i) fewer than 5% of the operational taxonomic units (OTUs) identified through clustering and phylogenetic affiliation had been previously detected in lakes, based on comparison to sequence in public databases; ii) the sequencing depth provided by the NGS coupled with a phylogenetic approach allowed to shed light on clades of freshwater protists rarely or never detected with classical molecular ecology approaches; and iii) phylogenetic methods are more robust in describing the structuring of under-studied or highly divergent populations. More precisely, new putative clades belonging to Mamiellophyceae, Foraminifera, Dictyochophyceae and Euglenida were detected. Beyond the study of protists, these results illustrate that the tree-based approach for NGS based diversity characterization allows an in-depth description of microbial communities including taxonomic profiling, community structuring and the description of clades of any microorganisms (protists, Bacteria and Archaea).
Auteurs, date et publication :
Auteurs Najwa Taib , Jean-François Mangot , Isabelle Domaizon , Gisèle Bronner , Didier Debroas , Stefan J. Green
Publication : Plos One
Date : 2013
Volume : 8
Issue : 3
Pages : e58950
Catégorie(s)
#INRAE #OLARésumé
Pesticide usage has been expanding since the 1950s. Their use has been known to harm human and environmental health for decades. Pesticide volatilisation to the atmosphere is a known process which is however not well documented, especially for periods beyond a few days after pesticide application. This is partly due to the difficulty to measure gaseous pesticides concentration in the atmosphere continuously for long time periods. Indeed, current state-of-the-art measurements is made by thermo-desorption gaseous chromatography involving semi-manual sampling with cartridges.In this study, we report first monthly outdoor online measurement of concentrations and volatilisation of one fungicide and two herbicides by proton transfer reaction, quadrupole injection, time of flight, mass spectrometry (PTR-QI-TOF-MS). The fungicide Chlorothalonil was measured over a wheat field in spring, while the herbicides Prosulfocarb and Pendimethalin were measured over a bare soil in autumn. Comparison with state-of-the-art TD-GC-MS and calibration by a home-made permeation system proved the PTRMS to be adapted for pesticides measurements.Maximum measured concentrations ranged from 12 ppt for Chlorothalonil to 600 ppt Prosulfocarfb. Maximum daily volatilisation fluxes ranged from 35 ng m-2 s-1 for Chlorothalonil to 350 ng m-2 s-1 for Prosulfocarb. We found that volatilisation of Chlorothalonil lasted more than three weeks, leading to up to 50% of the applied quantity volatilised, a duration and an amount much larger that what has been reported before.Volatilisation of pesticides may contribute much more significantly than expected to atmospheric burden, and be wet and dry deposited over larger areas. Further PTRMS pesticides measurements should be done to gain insight into pesticide transfer to the environment, and better characterize human exposure to these harmful compounds.
Auteurs, date et publication :
Auteurs Benjamin Loubet , Florence Lafouge , Sandy Bsaibes , Carole Bedos , Céline Decuq , Baptiste Esnault , Raluca Ciuraru , Julien Kammer , Raffaella Vuolo , Valérie Gros
Date : 2024
Catégorie(s)
#INRAE #PT-RMSAuteurs, date et publication :
Auteurs Benjamin Loubet
Date : 1970
Catégorie(s)
#INRAE #PT-RMSRésumé
Local glacial fluctuations and flood occurrences were investigated in the sediment sequence of proglacial Lake Muzelle. Based on geochemical analysis and organic matter content established using loss on ignition and reflectance spectroscopy, we identified six periods of increased glacial activity over the last 1700 yr. Each is in accordance with records from reference glaciers in the Alps. A total of 255 graded layers were identified and interpreted as flood deposits. Most of these occurred during glacial advances such as the Little Ice Age period and exhibit thicker deposits characterized by an increase in the fine grain-size fraction. Fine sediment produced by glacial activity is transported to the proglacial lake during heavy rainfall events. The excess of glacial flour during these periods seems to increase the watershed’s tendency to produce flood deposits in the lake sediment, suggesting a strong influence of the glacier on flood reconstruction records. Thus, both flood frequency and intensity, which is estimated based on layer thickness as a proxy, cannot be used in reconstruction of past extreme events because of their variability. There is a need to take into account changes in sediment supply in proglacial areas that could preclude satisfactory interpretation of floods in terms of past climate variability.
Auteurs, date et publication :
Auteurs Laurent Fouinat , Pierre Sabatier , Jérôme Poulenard , David Etienne , Christian Crouzet , Anne-Lise Develle , Elise Doyen , Emmanuel Malet , Jean-Louis Reyss , Clotilde Sagot , Richard Bonet , Fabien Arnaud
Publication : Quaternary Research
Date : 2025
Volume : 87
Issue : 03
Pages : 407-422
Catégorie(s)
#INRAE #OLARésumé
Pesticide usage has been expanding since the 1950s. However, their use has been known to harm human and environmental health for decades. Recent studies have shown that these two factors are impacted by pesticide diffusion in the atmosphere. The gaseous diffusion of pesticides in the atmosphere is known as volatilization. Although it is a known process, pesticide volatilization has been scarcely measured, especially for periods beyond a few days after pesticide application. Pesticide concentration is usually measured mainly by offline gas-chromatography mass spectrometry, which makes it difficult to deploy in the field for long-term studies. In this study, we report the first online concentration measurements of Chlorothalonil, a fungicide, over a wheat field using a highly sensitive proton transfer reaction, quadrupole injection, time of flight, mass spectrometer (PTR-QI-TOF-MS) for several weeks after its application. The volatilization computed by inverse dispersion modeling was sustained over more than three weeks, leading to up to 50% of the applied quantity being lost by volatilization. High-temporal volatilization dynamics indicate that the understorey contributes significantly to the emissions. Our findings suggest that Chlorothalonil volatilization may contribute significantly to atmospheric exposure, and transfer by deposition to nearby fields and over larger areas. Online PTR-QI-TOF-MS measurements should be developed further to quantify human exposure and the spread of pesticides through the atmosphere.
Auteurs, date et publication :
Auteurs Benjamin Loubet , Carole Bedos , Julien Kammer , Céline Decuq , Florence Lafouge , Baptiste Esnault , Raluca Ciuraru , Sandy Bsaibes , Pauline Buysse , Enrique Barriuso , Maria Raffaella Vuolo , Valérie Gros
Date : 2024
Catégorie(s)
#INRAE #PT-RMSAuteurs, date et publication :
Auteurs Lafouge Florence , Bsaibes Sandy , Decuq Céline , Esnault Baptiste , Buysse Pauline , Durand Brigitte , Truong François , Gros Valérie , Ciuraru Raluca , Bedos Carole , Loubet Benjamin
Date : 1970
Catégorie(s)
#INRAE #PT-RMSRésumé
Green infrastructures play a key role in the functionality and resilience of urban ecosystems. The physical, including thickness, chemical and biological properties of the Technosols of green infrastructures on rooftops are highly variable, leading to more or less favourable conditions for soil biodiversity. The aim of this study was to investigate the abundance and diversity of bacteria, fungi, nematodes, collembola and plants communities in relation with abiotic parameters of Technosols on 12 productive and extensive green roofs of the Paris region (France). Results showed that green roofs harboured a high level of abundance and diversity from microorganisms to micro and mesofauna. Microbial biomass ranged between 16.3 and 419.8 μg DNA g−1, with a predominance of bacteria, nematodes represented 820–60,700 individuals per kg of soil and between 1000 and 60,700 collembolan were present per m2 of soil. A total of 13,986 bacterial OTU (Operational Taxonomic Unit), 33,559 fungal OTU, 47 Collembola species, 28 nematodes families, 16 cultivated plant species and 48 spontaneous plant species was identified on all the green roofs studied. Microbial, animals and plants communities were significantly different between the two types of green roofs. Productive and extensive rooftops represent contrasted habitats, which can strongly influence the soil biota. Any voluntary action to enhance soil biodiversity in cities would need to take-into-account both soil properties and the landscape around.
Auteurs, date et publication :
Auteurs Sophie Joimel , Baptiste Grard , Claire Chenu , Pénélope Cheval , Samuel Mondy , Mélanie Lelièvre , Apolline Auclerc , Laure Vieublé Gonod
Publication : Ecological Engineering
Date : 2025
Volume : 175
Pages : 106475
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs A. Deredjian , N. Alliot , L. Blanchard , E. Brothier , M. Amane , P. Cambier , C. Jolivet , M.N. Khelil , S. Nazaret , N. Saby , J. Thioulouse , S. Favre-Bonté
Publication : Research in Microbiology
Date : 2025
Volume : 167
Issue : 4
Pages : 313–324
Catégorie(s)
#INRAE #PRO #PRO Colmar #PRO EFELERésumé
Plan de Gestion de Données de l'infrastructure OLA (Umr Carrtel - INRAE)
Auteurs, date et publication :
Auteurs Ghislaine Monet , Denis Barbet , Viet Tran-Khac , Ghislaine Monet
Date : 2025
Catégorie(s)
#INRAE #OLARésumé
We developed a process-oriented model called NutsFor that simulates nutrient cycling of major cations (Ca, Mg, K, Al, NH4, Na) and anions (NO3, SO4, Cl) and the stable isotope tracers for each of the respective elements at the scale of an ecosystem (isotopic fractionation are not simulated). We tested the ability of NutsFor to reproduce major element and stable isotope tracer (Mg-26 and Ca-44) cycling with the data from 35-yr old beech stand in France. NutsFor correctly reproduced the measured trends in soil solution chemistry for most major elements. The high similarity between modeled and measured distribution of Mg-26 and Ca-44 tracers in the ecosystem provided a unique and robust way to evaluate the hypotheses grounding the model and study the efficiency of Mg and Ca cycling at this very nutrient-poor site. (C) 2017 Elsevier Ltd. All rights reserved.
Auteurs, date et publication :
Auteurs G. van der Heijden , S. Belyazid , E. Dambrine , Jacques Ranger , A. Legout
Publication : Environmental Modelling & Software
Date : 2017
Volume : 95
Pages : 365-380