Résumé
Soil microorganisms are essential to agroecosystem functioning and services. Yet, we still lack information on which farming practices can effectively shape the soil microbial communities. The aim of this study was to identify the farming practices, which are most effective at positively or negatively modifying bacterial and fungal diversity while considering the soil environmental variation at a landscape scale. A long-term research study catchment (12 km2) representative of intensive mixed farming (livestock and crop) in Western Europe was investigated using a regular grid for soil sampling (n = 186). Farming systems on this landscape scale were described in terms of crop rotation, use of fertilizer, soil tillage, pesticides treatments, and liming. Molecular microbial biomass was estimated by soil DNA recovery. Bacterial and fungal communities were analyzed by 16S and 18S rRNA gene pyrosequencing. Microbial biomass was significantly stimulated by the presence of pasture during the crop rotation since temporary and permanent pastures, as compared to annual crops, increased the soil microbial biomass by +23% and +93% respectively. While soil properties (mainly pH) explained much of the variation in bacterial diversity, soil tillage seemed to be the most influential among the farming practices. A 2.4% increase in bacterial richness was observed along our gradient of soil tillage intensity. In contrast, farming practices were the predominant drivers of fungal diversity, which was mainly determined by the presence of pastures during the crop rotation. Compared to annual crops, temporary and permanent pastures increased soil fungal richness by +10% and +14.5%, respectively. Altogether, our landscape-scale investigation allows the identification of farming practices that can effectively shape the soil microbial abundance and diversity, with the goal to improve agricultural soil management and soil ecological integrity.
Auteurs, date et publication :
Auteurs Cédric Le Guillou , Nicolas Chemidlin Prévost‐Bouré , Battle Karimi , Nouraya Akkal‐Corfini , Samuel Dequiedt , Virginie Nowak , Sébastien Terrat , Safya Menasseri‐Aubry , Valérie Viaud , Pierre-Alain Maron , Lionel Ranjard
Publication : MicrobiologyOpen
Date : 2025
Pages : e00676
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs Emeline Chesneau , Gabrielle Thiébaut , Jacques Haury
Date : 2025
Catégorie(s)
#INRAE #PEARLRésumé
The data were collected from experimental freshwater fishpond systems (extensive, semi-intensive and semi-intensive coupled with lagoon). The dataset presented is composed of:
- Individual Fish parameters (live weight, length at fork) at stocking and harvest for the three species reared: common carp (Cyprinus carpio), roach (Rutilus rutilus) and tench (Tinca tinca).
- Physical indicators of the water quality in pond, monthly measured :temperature, pH, conductivity, dissolved oxygen, oxygen saturation and water transparency
- Physical indicators of the water quality in pond, measured every 5 minutes on 24h in September 2014: temperature, pH, oxydo-reduction potential, conductivity, dissolved oxygen and oxygen saturation.
- Concentration in pond water of chemical compounds , monthly sampled :total nitrogen (TN), ammonium, nitrite, nitrate, orthophosphate and total phosphorus(TP)
- Concentration in pond water of chemical compounds, sampled 5 minutes on 24h in September 2014: TN, ammonium, nitrate, orthophosphate, TP
- Concentration of chlorophyll in pond water monthly sampled: chlorophyll-a from March to June and total chlorophyll, blue chlorophyll, green chlorophyll and brown chlorophyll from July to November.
- Concentration in TN and TP in the sediment of each pond at fish stocking and harvest.
Auteurs, date et publication :
Auteurs Christophe Jaeger , Joël Aubin
Date : 2025
Catégorie(s)
#INRAE #PEARLRésumé
Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 165 ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 165 rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism.
Auteurs, date et publication :
Auteurs Battle Karimi , Sebastien Terrat , Samuel Dequiedt , Nicolas P. A. Saby , Walid Horriguel , Melanie Lelievre , Virginie Nowak , Claudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Antonio Bispo , Pierre-Alain Maron , Nicolas Chemidlin Prevost-Boure , Lionel Ranjard
Publication : Science Advances
Date : 2025
Volume : 4
Issue : 7
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Simulation models are extensively used to predict agricultural productivity and greenhouse gas emissions. However, the uncertainties of (reduced) model ensemble simulations have not been assessed systematically for variables affecting food security and climate change mitigation, within multi-species agricultural contexts. We report an international model comparison and benchmarking exercise, showing the potential of multi-model ensembles to predict productivity and nitrous oxide (N2O) emissions for wheat, maize, rice and temperate grasslands. Using a multi-stage modelling protocol, from blind simulations (stage 1) to partial (stages 2–4) and full calibration (stage 5), 24 process-based biogeochemical models were assessed individually or as an ensemble against long-term experimental data from four temperate grassland and five arable crop rotation sites spanning four continents. Comparisons were performed by reference to the experimental uncertainties of observed yields and N2O emissions. Results showed that across sites and crop/ grassland types, 23%–40% of the uncalibrated individual models were within two standard deviations (SD) of observed yields, while 42 (rice) to 96% (grasslands) of the models were within 1 SD of observed N2O emissions. At stage 1, ensembles formed by the three lowest prediction model errors predicted both yields and N2O emissions within experimental uncertainties for 44% and 33% of the crop and grassland growth cycles, respectively. Partial model calibration (stages 2–4) markedly reduced prediction errors of the full model ensemble E-median for crop grain yields (from 36% at stage 1 down to 4% on average) and grassland productivity (from 44% to 27%) and to a lesser and more variable extent for N2O emissions. Yield-scaled N2O emissions (N2O emissions divided by crop yields) were ranked accurately by three-model ensembles across crop species and field sites. The potential of using process-based model ensembles to predict jointly productivity and N2O emissions at field scale is discussed.
Auteurs, date et publication :
Auteurs Fiona Ehrhardt , Jean-François Soussana , Gianni Bellocchi , Peter Grace , Russel McAuliffe , Sylvie Recous , Renáta Sándor , Pete Smith , Val Snow , Massimiliano de Antoni Migliorati , Bruno Basso , Arti Bhatia , Lorenzo Brilli , Jordi Doltra , Christopher D. Dorich , Luca Doro , Nuala Fitton , Sandro J. Giacomini , Brian Grant , Matthew T. Harrison
Publication : Global Change Biology
Date : 2025
Volume : 24
Issue : 2
Pages : e603-e616
Catégorie(s)
#ACBB #ACBB Theix #INRAERésumé
Process-based ecosystem models are used increasingly to evaluate the impacts of agricultural practices on soil organic carbon (SOC) stocks at various scales. One of the major sources of error and projection uncertainty in these models is the specification of the initial SOC pools sizes. However, few studies have examined errors and uncertainty over time and for various agricultural practices. The main purposes of our study were 1) to examine the impacts of initialization scenarios on CENTURY model V4.5 performance and 2) to quantify the initialization contribution to the total variance of error of the CENTURY model. We simulated the SOC dynamics of six wellcharacterized long-term experiments (LTEs) with 25 treatments across France, testing various agricultural practices (i.e., inorganic and organic fertilization, various crop rotations and straw and residues removed) using the CENTURY model while keeping the standard parameters unchanged. We applied nine initialization scenarios, each characterized by a unique combination of crop management and relaxation procedures. These relaxation procedures consisted of shifting simulated SOC and nitrogen levels at the end of the initialization period until they matched the stocks at the beginning of the experiment. At the end of the initialization period, the distribution pattern of SOC pools was similar in all scenarios for all LTEs. The slow pool represented the largest proportion of total SOC stocks (average value of 61.5%), whereas the active and passive pools averaged 5.3% and 27.9%, respectively. The overall analysis of CENTURY performance indicated fair results for SOC stocks prediction (R2 values of the nine initialization scenarios ranged between 0.50 and 0.75) but weak results for SOC change prediction (R2 values of the nine initialization scenarios, ranged between 0.1 and 0.36). The root mean square error (RMSE) values were moderate compared to the total measured SOC stocks and their confidence intervals. The RMSE values ranged between 6.22 Mg ha−1 and 15.24 Mg ha−1, which corresponded to 13.1% and 32.1% of the initial average total SOC stock for all LTEs, respectively. The highest values were recorded for the no relaxation procedures. CENTURY model errors (i.e., simulated - observed SOC stocks) analysis showed a slight sensitivity to the initialization scenarios (approximately 6% of the total variance of the CENTURY error). However, the second-order interaction of scenarios and LTE contributed by 33.6%. Meanwhile, agricultural practices had the greatest impact on the variance of the CENTURY error (44.7%) compared to other factors. Our findings suggest that the contribution of the initialization to the uncertainty in projected SOC changes is negligible compared to the uncertainty related to the model itself and simulated systems characteristics.
Auteurs, date et publication :
Auteurs Bassem Dimassi , Bertrand Guenet , Nicolas P.A. Saby , Facundo Munoz , Marion Bardy , Florent Millet , Manuel P. Martin
Publication : Geoderma
Date : 2025
Volume : 311
Pages : 25-36
Catégorie(s)
#INRAE #PRO #PRO QualiAgroRésumé
Although large amounts of potassium (K) are applied in tropical crops and planted forests, little is known about the interaction between K nutrition and water supply regimes on water resources in tropical regions. This interaction is a major issue because climate change is expected to increase the length of drought periods in many tropical regions and soil water availability in deep soil layers is likely to have a major influence on tree growth during dry periods in tropical planted forests. A process-based model (MAESPA) was parameterized in a throughfall exclusion experiment in Brazil to gain insight into the combined effects of K deficiency and rainfall reduction (37% throughfall exclusion) on the water used by the trees, soil water storage and water table fluctuations over the first 4.5 years after planting Eucalyptus grandis trees. A comparison of canopy transpiration in each plot with the values predicted for the same soil with the water content maintained at field capacity, made it possible to calculate a soil-driven tree water stress index for each treatment. Compared to K-fertilized trees with undisturbed rainfall (+K+W), canopy transpiration was 40% lower for K deficiency (−K+W), 20% lower for W deficit (+K−W) and 36% lower for combined K deficiency and W deficit (−K−W) on average. Water was withdrawn in deeper soil layers for −W than for +W, particularly over dry seasons. Under contrasted K availability, water withdrawal was more superficial for −K than for +K. Mean soil water content down to 18 m below surface (mbs) was 24% higher for −K+W than for +K+W from 2 years after planting (after canopy closure), while it was 24% lower for +K−W and 12% lower for −K−W than for +K+W. The soil-driven tree water stress index was 166% higher over the first 4.5 years after planting for −W than for +W, 76% lower for −K than for +K, and 14% lower for −K−W than for +K+W. Over the study period, deep seepage was higher by 371 mm yr−1 (+122%) for −K than for +K and lower by 200 mm yr−1 (−66%) for −W than for +W. Deep seepage was lower by 44% for −K−W than for +K+W. At the end of the study period, the model predicted a higher water table for −K (10 mbs for −K+W and 16 mbs for −K−W) than for +K (16 mbs for +K+W and 18 mbs for +K−W). Our study suggests that flexible fertilization regimes could contribute to adjusting the local trade-off between wood production and demand for soil water resources in planted forests.
Auteurs, date et publication :
Auteurs M. Christina , G. le Maire , Y. Nouvellon , R. Vezy , B. Bordon , P. Battie-Laclau , J.L.M. Gonçalves , J.S. Delgado-Rojas , J.-P. Bouillet , J.-P. Laclau
Publication : Forest Ecology and Management
Date : 2025
Catégorie(s)
#CIRAD #FORET Itatinga #FORET Rubberflux #INRAEAuteurs, date et publication :
Auteurs Valentin Vasselon , Agnès Bouchez , Frédéric Rimet , Stéphan Jacquet , Rosa Trobajo , Méline Corniquel , Kálmán Tapolczai , Isabelle Domaizon , Andrew Mahon
Publication : Methods in Ecology and Evolution
Date : 2025
Volume : 9
Issue : 4
Pages : 1060-1069
Catégorie(s)
#INRAE #OLARésumé
Biochemical indicators are potent tools to assess ecosystem functioning under anthropic and global pressures. Nevertheless, additional work is needed to improve the methods used for the measurement of these indicators, and for a more relevant interpretation of the obtained results. To face these challenges, the platform Biochem-Env aims at providing innovative and standardized measurement protocols, as well as database and information system favoring result interpretation and opening. Its skills and tools are also offered for expertise, consulting, training, and standardization. In addition, the platform is a service of a French Research Infrastructure for Analysis and Experimentation on Ecosystems, for research in environmental and agricultural sciences.
Auteurs, date et publication :
Auteurs Nathalie Cheviron , Virginie Grondin , Christian Mougin
Publication : Environmental Science and Pollution Research
Date : 2025
Volume : 25
Issue : 7
Pages : 6154-6157
Catégorie(s)
#ANR-Citation #BiochemEnv #INRAERésumé
Low oxygen concentrations in lakes and reservoirs are an ongoing environmental concern, particularly in light of increasing anthropogenic activity and climate change. Oxygen depletion processes in lakes are still not completely understood and a variety of models have been proposed based on limited field observations. Here, we present field measurements of oxygen depletion processes in a deep lake, Lake Geneva (Switzerland). The aim of this study was to quantify three basic processes controlling hypolimnetic oxygen depletion and their relative contribution to the total oxygen depletion (TOD) rate. Sediment oxygen uptake (SOU) and the flux of reduced substances were estimated based on oxygen microprofile measurements and sediment core data of reduced substances. Acoustic Doppler current profiler measurements and hydrodynamic modeling were used to ensure that SOU was measured under typical hydrodynamic conditions. Comparison with longterm monitoring data allowed for an estimate of the relative importance of SOU and water column mineralization (WCM). Results show a decrease in both SOU and WCM down to mid-depth which could not be explained by changes in hydrodynamic conditions or temperature. Below mid-depth, TOD increased due to an enhanced sediment area to water volume ratio (a). This vertical pattern of oxygen depletion is driven by (1) lake morphometry paired with increasing a, and (2) decreasing organic matter mineralization in the water column with depth. The findings are explained by a model which separates the oxygen depletion into an exponentially decreasing component, representing the fast-decaying fraction of the organic matter, and a constant background component.
Auteurs, date et publication :
Auteurs Robert Schwefel , Thomas Steinsberger , Damien Bouffard , Lee D. Bryant , Beat Müller , Alfred Wüest
Publication : Limnology and Oceanography
Date : 2025
Volume : 63
Issue : S1
Pages : S54-S67