Résumé
BACKGROUND: The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.
RESULTS: BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.
CONCLUSIONS: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.
Auteurs, date et publication :
Auteurs Christophe Djemiel , Samuel Dequiedt , Battle Karimi , Aurélien Cottin , Thibault Girier , Yassin El Djoudi , Patrick Wincker , Mélanie Lelièvre , Samuel Mondy , Nicolas Chemidlin Prévost-Bouré , Pierre-Alain Maron , Lionel Ranjard , Sébastien Terrat
Publication : BMC bioinformatics
Date : 2020
Volume : 21
Issue : 1
Pages : 492
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
The stability of ecological communities is critical for the stable provisioning of ecosystem services, such as food and forage production, carbon sequestration, and soil fertility. Greater biodiversity is expected to enhance stability across years by decreasing synchrony among species, but the drivers of stability in nature remain poorly resolved. Our analysis of time series from 79 datasets across the world showed that stability was associated more strongly with the degree of synchrony among dominant species than with species richness. The relatively weak influence of species richness is consistent with theory predicting that the effect of richness on stability weakens when synchrony is higher than expected under random fluctuations, which was the case in most communities. Land management, nutrient addition, and climate change treatments had relatively weak and varying effects on stability, modifying how species richness, synchrony, and stability interact. Our results demonstrate the prevalence of biotic drivers on ecosystem stability, with the potential for environmental drivers to alter the intricate relationship among richness, synchrony, and stability.
Auteurs, date et publication :
Auteurs Enrique Valencia , Francesco de Bello , Thomas Galland , Peter B. Adler , Jan Lepš , Anna E-Vojtkó , Roel van Klink , Carlos P. Carmona , Jiří Danihelka , Jürgen Dengler , David J. Eldridge , Marc Estiarte , Ricardo García-González , Eric Garnier , Daniel Gómez‐García , Susan P. Harrison , Tomáš Herben , Ricardo Ibáñez , Anke Jentsch , Norbert Juergens
Publication : Proceedings of the National Academy of Sciences
Date : 2020
Volume : 117
Issue : 39
Pages : 24345-24351
Catégorie(s)
#ACBB #ACBB Theix #INRAERésumé
The knowledge of tree species dependent turnover of soil organic matter (SOM) is limited, yet required to understand the carbon sequestration function of forest soil. We combined investigations of 13C and 15N and its relationship to elemental stoichiometry along soil depth gradients in 35-year old monocultural stands of Douglas fir (Pseudotsuga menziesii), black pine (Pinus nigra), European beech (Fagus sylvatica) and red oak (Quercus rubra) growing on a uniform post-mining soil. We investigated the natural abundance of 13C and 15N and the carbon:nitrogen (C:N) and oxygen:carbon (O:C) stoichiometry of litterfall and fine roots as well as SOM in the forest floor and mineral soil. Tree species had a significant effect on SOM δ13C and δ15N reflecting significantly different signatures of litterfall and root inputs. Throughout the soil profile, δ13C and δ15N were significantly related to the C:N and O:C ratio which indicates that isotope enrichment with soil depth is linked to the turnover of organic matter (OM). Significantly higher turnover of OM in soils under deciduous tree species depended to 46% on the quality of litterfall and root inputs (N content, C:N, O:C ratio), and the initial isotopic signatures of litterfall. Hence, SOM composition and turnover also depends on additional—presumably microbial driven—factors. The enrichment of 15N with soil depth was generally linked to 13C. In soils under pine, however, with limited N and C availability, the enrichment of 15N was decoupled from 13C. This suggests that transformation pathways depend on litter quality of tree species.
Auteurs, date et publication :
Auteurs Marcel Lorenz , Delphine Derrien , Bernd Zeller , Thomas Udelhoven , Willy Werner , Sören Thiele-Bruhn
Publication : Biogeochemistry
Date : 2020
Volume : 151
Issue : 2
Pages : 203-220
Catégorie(s)
#ANR-Citation #INRAE #M-POETERésumé
L’initiative « 4 ‰ sur les sols pour la sécurité alimentaire et le climat », lancée par la France à l’occasion de la Conférence de Paris sur le climat (COP-21), propose d’augmenter chaque année d’un quatre millième le stock de carbone présent dans tous les sols du monde afin de compenser les émissions anthropiques de CO2. Cet objectif, très ambitieux, nécessite des évolutions profondes des pratiques agricoles et des modes de gestion sylvicoles, certaines pouvant s’accompagner de modifications de systèmes de production et, éventuellement, des modes d’usage des sols. C'est dans ce contexte que le Ministère de l’Agriculture et de l’Alimentation (MAA) et l’Agence De l'Environnement et de la Maîtrise de l'Energie (ADEME) ont demandé à l'INRA de conduire la présente étude "4 pour mille France". Les objectifs étaient : i) d’identifier des pratiques agricoles et sylvicoles plus "stockantes" que les pratiques actuellement mises en œuvre ; ii) de chiffrer le potentiel de stockage additionnel associé, de le cartographier, de quantifier les autres effets induits liés à l’adoption de ces pratiques stockantes (pertes ou gains de rendement, émissions de N2O, lixiviation de nitrate, utilisation de produits phytosanitaires...) ; iii) de chiffrer leur coût de mise en œuvre et de proposer une stratégie coût-efficace de stockage. Le présent document constitue le rapport scientifique de cette étude.
Ce travail a fait l'objet de documents de synthèse et d'un colloque public de restitution, qui s'est tenu à Paris le 13 juin 2019.
Auteurs, date et publication :
Auteurs Sylvain Pellerin , Laure Bamière , Camille Launay , Raphaël Martin , Michele Schiavo , Denis Angers , Laurent Augusto , Jérôme Balesdent , Isabelle BASILE-DOELSCH , Valentin Bellassen , Rémi Cardinael , Lauric Cécillon , Eric Ceschia , Claire Chenu , Julie Constantin , Joël Daroussin , Philippe Delacote , Nathalie Delame , Francois Gastal , Daniel Gilbert
Date : 2020
Pages : 528 p.
Catégorie(s)
#INRAERésumé
The intensity and frequency of storms are projected to increase in many regions of the world because of climate change. Storms can alter environmental conditions in many ecosystems. In lakes and reservoirs, storms can reduce epilimnetic temperatures from wind-induced mixing with colder hypolimnetic waters, direct precipitation to the lake's surface, and watershed runoff. We analyzed 18 long-term and high-frequency lake datasets from 11 countries to assess the magnitude of wind- vs. rainstorm-induced changes in epilimnetic temperature. We found small day-to-day epilimnetic temperature decreases in response to strong wind and heavy rain during stratified conditions. Day-to-day epilimnetic temperature decreased, on average, by 0.28°C during the strongest windstorms (storm mean daily wind speed among lakes: 6.7 ± 2.7 m s−1, 1 SD) and by 0.15°C after the heaviest rainstorms (storm mean daily rainfall: 21.3 ± 9.0 mm). The largest decreases in epilimnetic temperature were observed ≥2 d after sustained strong wind or heavy rain (top 5th percentile of wind and rain events for each lake) in shallow and medium-depth lakes. The smallest decreases occurred in deep lakes. Epilimnetic temperature change from windstorms, but not rainstorms, was negatively correlated with maximum lake depth. However, even the largest storm-induced mean epilimnetic temperature decreases were typically <2°C. Day-to-day temperature change, in the absence of storms, often exceeded storm-induced temperature changes. Because storm-induced temperature changes to lake surface waters were minimal, changes in other limnological variables (e.g., nutrient concentrations or light) from storms may have larger impacts on biological communities than temperature changes.
Auteurs, date et publication :
Auteurs Jonathan P. Doubek , Orlane Anneville , Gaël Dur , Aleksandra M. Lewandowska , Vijay P. Patil , James A. Rusak , Nico Salmaso , Christian Torsten Seltmann , Dietmar Straile , Pablo Urrutia-Cordero , Patrick Venail , Rita Adrian , María B. Alfonso , Curtis L. DeGasperi , Elvira de Eyto , Heidrun Feuchtmayr , Evelyn E. Gaiser , Scott F. Girdner , Jennifer L. Graham , Hans-Peter Grossart
Publication : Limnology and Oceanography
Date : 2025
Volume : 66
Issue : 5
Pages : 1979-1992
Catégorie(s)
#INRAE #OLARésumé
Climate change impacts forest functioning and dynamics, and large uncertainties remain regarding the interactions between species composition, demographic processes and environmental drivers. There are few robust tools available to link these processes, which precludes accurate projections and recommendations for long-term forest management. Forest gap models present a balance between complexity and generality and are widely used in predictive forest ecology. However, their relevance to tackle questions about the links between species composition, climate and forest functioning is unclear. In this regard, demonstrating the ability of gap models to predict the growth of forest stands at the annual parameterization scale resolution—representing a sensitive and integrated signal of tree functioning and mortality risk—appears as a fundamental step. In this study, we aimed at assessing the ability of a gap model to accurately predict forest growth in the short term and potential community composition in the long term, across a wide range of species and environmental conditions. To do so, we present the gap model ForCEEPS, calibrated using an original parameterization procedure for the main tree species in France. ForCEEPS was shown to satisfactorily predict forest annual growth (averaged over a few years) at the plot level from mountain to Mediterranean climates, regardless of the species. Such an accuracy was not gained at the cost of losing precision for long-term predictions, as the model showed a strong ability to predict potential community compositions. The mechanistic relevance of ForCEEPS parameterization was explored by showing the congruence between the values of key model parameter and species functional traits. We further showed that accounting for the spatial configuration of crowns within forest stands, the effects of climatic constraints and the variability of shade tolerances in the species community are all crucial to better predict short-term productivity with gap models. Synthesis. The dual ability of predicting short-term functioning and long-term community composition, as well as the balance between generality and realism (i.e. predicting accuracy) of the new generation of gap models may open great perspectives for the exploration of the biodiversity–ecosystem functioning relationships, species coexistence mechanisms and the impacts of climate change on forest ecosystems. A free Plain Language Summary can be found within the Supporting Information of this article.
Auteurs, date et publication :
Auteurs Xavier Morin , Harald Bugmann , François de Coligny , Nicolas Martin-StPaul , Maxime Cailleret , Jean-Marc Limousin , Jean-Marc Ourcival , Bernard Prevosto , Guillaume Simioni , Maude Toigo , Michel Vennetier , Eugénie Catteau , Joannès Guillemot
Publication : Functional Ecology
Date : 2025
Volume : 35
Issue : 4
Pages : 955-975
Catégorie(s)
#CNRS #FORET FontBlanche #FORET Puechabon #INRAEAuteurs, date et publication :
Auteurs Luis Portillo Lemus , Michel Bozec , Marilyne Harang , Julie Coudreuse , Jacques Haury , Solenn Stoeckel , Dominique Barloy
Publication : Plant-Environment Interactions
Date : 2025
Volume : 2
Issue : 2
Pages : 74
Catégorie(s)
#INRAE #PEARLRésumé
Temperate grassland soils store significant amounts of carbon (C). Estimating how much livestock grazing and manuring can influence grassland soil organic carbon (SOC) is key to improve greenhouse gas grassland budgets. The Rothamsted Carbon (RothC) model, although originally developed and parameterized to model the turnover of organic C in arable topsoil, has been widely used, with varied success, to estimate SOC changes in grassland under different climates, soils, and management conditions. In this paper, we hypothesise that RothC-based SOC predictions in managed grasslands under temperate moist climatic conditions can be improved by incorporating small modifications to the model based on existing field data from diverse experimental locations in Europe. For this, we described and evaluated changes at the level of: (1) the soil water function of RothC, (2) entry pools accounting for the degradability of the exogenous organic matter (EOM) applied (e.g., ruminant excreta), (3) the month-on-month change in the quality of C inputs coming from plant residues (i.e above-, below-ground plant residue and rhizodeposits), and (4) the livestock trampling effect (i.e., poaching damage) as a common problem in areas with higher annual precipitation. In order to evaluate the potential utility of these changes, we performed a simple sensitivity analysis and tested the model predictions against averaged data from four grassland experiments in Europe. Our evaluation showed that the default model's performance was 78% and whereas some of the modifications seemed to improve RothC SOC predictions (model performance of 95% and 86% for soil water function and plant residues, respectively), others did not lead to any/or almost any improvement (model performance of 80 and 46% for the change in the C input quality and livestock trampling, respectively). We concluded that, whereas adding more complexity to the RothC model by adding the livestock trampling would actually not improve the model, adding the modified soil water function and plant residue components, and at a lesser extent residues quality, could improve predictability of the RothC in managed grasslands under temperate moist climatic conditions.
Auteurs, date et publication :
Auteurs Asma Jebari , Jorge Alvaro-Fuentes , Guillermo Pardo , Maria Almagro , Agustin del Prado
Publication : PLOS ONE
Date : 2025
Volume : 16
Issue : 8
Catégorie(s)
#ACBB Laqueuille #ANR-Citation #INRAEAuteurs, date et publication :
Auteurs Nathalie Cheviron , Issifou Amadou , Virginie Grondin , Christelle Marrauld , Christian Mougin , Thierry Morvan
Publication : Data in Brief
Date : 2025
Volume : 36
Pages : 106959
Catégorie(s)
#ANR-Citation #BiochemEnv #INRAE #PRORésumé
Mixed forests are usually associated with higher aboveground carbon storage compared to the corresponding monocultures but information on the impact of tree species mixing on soil organic carbon (SOC) is still limited. Yet, maximizing SOC storage is crucial for ecosystem C sequestration and many other ecosystem services. This study used a triplet approach (ie. two-species mixed stand and respective pure stands at the same site) to assess the impact of tree species identity and mixing on SOC storage in eight pine-oak, eight pine-beech and five beechoak triplets in Europe. We sampled the forest floor (FF) and 0–40 cm in the mineral soil per 10 cm interval. For each triplet type, we fitted basal area (BA) proportion of one component species (for species identity) and a BAbased plot-level True Shannon Diversity index (for species mixing) as explanatory variables for SOC stocks in linear mixed effects models, which included stone content and plot BA as covariates, and site as a random intercept. Considering the total soil depth (FF + 0–40 cm), species identity effect on SOC stocks was only sig nificant for pine-beech and pine-oak triplets but explained more variability in SOC stocks than species mixing across triplet types. Species mixing effect was not significant for any triplet type in the total soil depth. While species identity consistently drove SOC storage in the topsoil layers across triplet types, species mixing explained more variability in SOC stocks in the deeper soil layers except for pine-oak triplets. The results showed that species identity is a stronger driver of SOC storage than species mixing. While tree species identity effect was strongly related to a conifers vs broadleaves signature, the drivers behind mixing effects remained elusive. The results suggest that targeted selection of tree species could better enhance SOC storage in European forests than a mere increase in species richness.
Auteurs, date et publication :
Auteurs Richard Osei , Hugues Titeux , Kamil Bielak , Felipe Bravo , Catherine Collet , Corentin Cools , Jean-Thomas Cornelis , Michael Heym , Nathalie Korboulewsky , Magnus Löf , Bart Muys , Yasmina Najib , Arne Nothdurft , Maciej Pach , Hans Pretzsch , Miren del Rio , Ricardo Ruiz-Peinado , Quentin Ponette
Publication : Forest Ecology and Management
Date : 2025
Volume : 481
Pages : 118752