Résumé

The European River lamprey Lampetra fluviatilis and the brook lamprey L. planeri are two closely related species that are also considered as partially reproductively isolated ecotypes. At the larval stage, they cannot be distinguished morphologically or genetically by mitochondrial DNA. We aimed at developing a molecular tool to identify early life stages of L. fluviatilis and L. planeri.

Auteurs, date et publication :

Auteurs Ahmed Souissi , Anne-Laure Besnard , Guillaume Evanno

Publication : Molecular Biology Reports

Date : 2022

Volume : 49

Issue : 10

Pages : 10115-10119

Catégorie(s)

#INRAE #PEARL

Résumé

Changes in soil organic carbon (SOC) stocks are a major source of uncertainty for the evolution of atmospheric CO2 concentration during the 21st century. They are usually simulated by models dividing SOC into conceptual pools with contrasted turnover times. The lack of reliable methods to initialize these models, by correctly distributing soil carbon amongst their kinetic pools, strongly limits the accuracy of their simulations. Here, we demonstrate that PARTYSOC, a machine-learning model based on Rock-Eval® thermal analysis, optimally partitions the active- and stable-SOC pools of AMG, a simple and well-validated SOC dynamics model, accounting for effects of soil management history. Furthermore, we found that initializing the SOC pool sizes of AMG using machine learning strongly improves its accuracy when reproducing the observed SOC dynamics in nine independent French long-term agricultural experiments. Our results indicate that multi-compartmental models of SOC dynamics combined with a robust initialization can simulate observed SOC stock changes with excellent precision. We recommend exploring their potential before a new generation of models of greater complexity becomes operational. The approach proposed here can be easily implemented on soil monitoring networks, paving the way towards precise predictions of SOC stock changes over the next decades.

Auteurs, date et publication :

Auteurs Eva Kanari , Lauric Cécillon , François Baudin , Hugues Clivot , Fabien Ferchaud , Sabine Houot , Florent Levavasseur , Bruno Mary , Laure Soucémarianadin , Claire Chenu , Pierre Barré

Publication : Biogeosciences

Date : 2022

Volume : 19

Issue : 2

Pages : 375-387

Catégorie(s)

#INRAE #PRO #PRO QualiAgro

Résumé

Background: Grasslands provide a wide range of ecosystem services (ESs). However, there is currently no method for easily diagnosing the level of ESs produced. Our aim was to develop ES indicators based on botanical surveys, which are readily available data and integrative of grassland spatiotemporal variability.
Methods: Based on academic knowledge and expertise, we identified several simple vegetation criteria that we aggregated using a multicriteria analysis tool to construct indicators of the level of ESs provided by grasslands. In this study, the indicators were calculated from over 2000 botanical surveys spread over a wide biogeographical gradient.
Results: Analyses of correlation between the various indicators show that “forage supply” and “diversity conservation” were not correlated. “Forage availability” and “nitrogen availability for the vegetation” were positively linked together and negatively linked to the robustness of the plant community to extreme events. A temporal approach highlights that the “biodiversity conservation” score decreased from 1970 to 2010 and that “nitrogen availability for the vegetation” was lower in 1970 and 1980 than in 2000 and 2010.
Conclusions: These results show that our aggregation method based on a large data set of botanical surveys could be appropriate for studying temporal dynamics of ESs.

Auteurs, date et publication :

Auteurs Simon Taugourdeau , Frédérique Louault , Alice Michelot‐Antalik , Samir Messad , François Munoz , Denis Bastianelli , Pascal Carrère , Sylvain Plantureux

Publication : Grassland Research

Date : 2025

Volume : 3

Issue : 1

Pages : 43-56

Catégorie(s)

#ACBB Laqueuille #ACBB Theix #INRAE

Résumé

Lakes and reservoirs are a significant source of atmospheric methane (CH4), with emissions comparable to the largest global CH4 emitters. Understanding the processes leading to such significant emissions from aquatic systems is therefore of primary importance for producing accurate projections of emissions in a changing climate. In this work, we present the first deployment of a novel membrane inlet laser spectrometer (MILS) for fast simultaneous detection of dissolved CH4, ethane (C2H6) and the stable carbon isotope of methane (δ 13CH4). During a 1-day field campaign, we performed 2D mapping of surface water of Lake Aiguebelette (France). Average dissolved CH4 concentrations and δ 13CH4 were 391.9 ± 156.3 nmol L −1 and −67.3 ± 3.4‰ in the littoral area and 169.8 ± 26.6 nmol L −1 and −61.5 ± 3.6‰ in the pelagic area. The dissolved CH4 concentration in the pelagic zone was 50 times larger than the concentration expected at equilibrium with the atmosphere, confirming an oversaturation of dissolved CH4 in surface waters over shallow and deep areas. The results suggest the presence of CH4 sources less enriched in  13C in the littoral zone (presumably the littoral sediments). The CH4 pool became more enriched in  13C with distance from shore, suggesting that oxidation prevailed over epilimnetic CH4 production and it was further confirmed by an isotopic mass balance technique with the high-resolution data. This new in situ fast response sensor allows one to obtain unique high-resolution and high-spatial coverage data sets within a limited amount of survey time. This tool will be useful in the future for studying processes governing CH4 dynamics in aquatic systems.

Auteurs, date et publication :

Auteurs R. Grilli , T. DelSontro , J. Garnier , F. Jacob , J. Némery

Publication : Journal of Geophysical Research: Biogeosciences

Date : 2025

Volume : 128

Issue : 12

Pages : e2022JG007200

Catégorie(s)

#INRAE #OLA

Résumé

Climate change is increasing the intensity and frequency of hydrological events in freshwater. Summer droughts and drying events drastically reduce the favourable habitat for aquatic organisms shaping interactions among species. Macroinvertebrates are usually less abundant during severe summer low flows, reducing prey availability for carnivorous fish, such as brown trout (Salmo trutta). To quantify the consequences of a surface water drying event on fish performance, we conducted an experiment in 6 experimental channels naturally fed by water and macroinvertebrates. After a colonisation period for macroinvertebrates, the water level was dropped to the benthic surface for two weeks in 3 channels, while it remained constant in the 3 other channels. After water level restoration, juvenile brown trout were reared for three weeks in the control and dry channels. The drying event did not reduce the abundance of macroinvertebrates. Survival and growth of juvenile trout were unaffected by drying. Our experiment provided circumstantial evidence that the hyporheic zone could potentially serve as an effective refuge for macroinvertebrates, mitigating the effects of drying events on food webs, although this mitigation would strongly depend on sediment characteristics, habitat quality and the composition of the macroinvertebrate community.

Auteurs, date et publication :

Auteurs Elorri Arevalo , Agnès Bardonnet , Stéphane Glise , François Gueraud , Emmanuel Huchet , Frédéric Lange , Jacques Rives , Aitor Larrañaga

Publication : Knowledge & Management of Aquatic Ecosystems

Date : 2025

Issue : 425

Pages : 15

Catégorie(s)

#ECP #INRAE

Résumé

There is an urgent need to evaluate the effects of anthropogenic pressures and climatic change on fish pop­ ulations’ dynamics. When monitored in lakes, fish spawning is generally assessed using traditional, mostly destructive or damaging, methods as gillnetting and collection of fertilized eggs. Over the last decade, envi­ ronmental DNA (eDNA) based methods have been widely developed and now offer a non-invasive alternative method to these traditional biomonitoring tools. In particular, the emergence of new methods as the droplet digital PCR (ddPCR) offers the possibility to quantify an absolute eDNA signal in a very sensitive way and at a low cost. Here, we developed and implemented a quantitative eDNA approach to monitor the spawning activity in a lentic environment for two non-migratory fish species, European perch and whitefish. The ddPCR protocols were formalized based on existing and newly designed COI primers, and were applied during four spawning periods in Lake Geneva. The results demonstrate the effectiveness of weekly eDNA sampling coupled with ddPCR to identify the timing and duration of the spawning periods, as well as the peak of the spawning activity for the target species. In addition, we highlight that the use of a control species (i.e., quantification of the eDNA signal of a fish that does not reproduce during the monitoring period) helps to clearly discriminate the eDNA signal associated to the spawning activity. The filtration of 2 L of subsurface water was shown to be effective for the monitoring of spawning activity; however, using discrete sampling strategy we observed a spatial variability in the eDNA signal. For future implementation, we recommend (i) using an integrative sampling strategy to smooth the local variability of the eDNA signal, and (ii) to cover a sampling period long enough to clearly distinguish the spawning signal from the basal signal of the target species. These results show that we reached an operational level to use these non-invasive eDNA approaches to monitor the spawning periods of these two fish species in large lakes.

Auteurs, date et publication :

Auteurs Marine Vautier , Cécile Chardon , Chloé Goulon , Jean Guillard , Isabelle Domaizon

Publication : Fisheries Research

Date : 2025

Volume : 264

Pages : 106708

Catégorie(s)

#INRAE #OLA

Résumé

Peri-alpine lakes are vulnerable to climate warming. Water temperature in these lakes has increased and will likely continue in the coming decades, questioning the fate of inhabiting aquatic populations. Understanding how coregonine fishes respond to these changes is of great importance as these are economically and ecologically valuable populations. Considering the diversity of European whitefish from the Coregonus genus in peri-alpine lakes, we can assume that their response to rising temperatures could be diverse. We conducted an experiment to explore how embryos from four European whitefish populations from three lakes Bourget, Geneva, and Constance responded to contrasting incubation temperatures (7.0 °C vs. 9.0 °C) in terms of incubation duration and survival. In Constance, both pelagic and littoral populations were considered separately. Survival from the eyed-egg stage to hatching at 7.0 °C in all populations was high, ranging from 89% to 98%. At 9.0 °C, increased mortality compared to the 7.0 °C treatment was the lowest in Bourget (33%) and the highest in the Constance littoral (62%) population. Mortality was intermediate for the Constance pelagic (44%) and Geneva (45%) populations. The impact of warmer incubation temperature on hatching dynamics also contrasted among populations, as both Constance populations hatched more precociously in the warm treatment relative to the cold treatment (–4.6 and 2.7% Accumulated Degree Days for littoral and pelagic populations, respectively), suggesting they are more stressed than populations from Geneva and Bourget (–1.2 and þ1.1%, respectively). These data indicate populations may possess the ability to respond differently to warming temperatures.

Auteurs, date et publication :

Auteurs Taylor R. Stewart , Charles Brun , Chloé Goulon , Jan Baer , Juha Karjalainen , Jean Guillard , Emilien Lasne , Orlane Anneville , Chloé Goulon , Juha Karjalainen , Jean Guillard , Jared T. Myers , Jason Stockwell

Publication : International Journal of Limnology

Date : 2025

Volume : 60

Pages : 19

Catégorie(s)

#INRAE #OLA

Auteurs, date et publication :

Auteurs Arnaud Giusti , Alpar Barsi , Maël Dugué , Marc Collinet , Jean-Pierre Thomé , Célia Joaquim-Justo , Benoit Roig , Laurent Lagadic , Virginie Ducrot

Publication : Environmental Toxicology and Chemistry

Date : 2013

Pages : n/a-n/a

Catégorie(s)

#INRAE #PEARL

Résumé

Multi-model ensembles are becoming increasingly accepted for the estimation of agricultural carbon-nitrogen fluxes, productivity and sustainability. There is mounting evidence that with some site-specific observations available for model calibration (with vegetation data as a minimum requirement), median outputs assimilated from biogeochemical models (multi-model medians) provide more accurate simulations than individual models. Here, we evaluate potential deficiencies in how model ensembles represent (in relation to climatic factors) the processes underlying biogeochemical outputs in complex agricultural systems such as grassland and crop rotations including fallow periods. We do that by exploring the correlation of model residuals. We restricted the distinction between partial and full calibration to the two most relevant calibration stages, i.e. with plant data only (partial) and with a combination of plant, soil physical and biogeochemical data (full). It introduces and evaluates the trade-off between (1) what is practical to apply for model users and beneficiaries, and (2) what constitutes best modelling practice. The lower correlations obtained overall with fully calibrated models high-light the centrality of the full calibration scenario for identifying areas of model structures that require further development.

Auteurs, date et publication :

Auteurs Renata Sandor , Fiona Ehrhardt , Peter Grace , Sylvie Recous , Pete Smith , Val Snow , Jean-Francois Soussana , Bruno Basso , Arti Bhatia , Lorenzo Brilli , Jordi Doltra , Christopher D. Dorich , Luca Doro , Nuala Fitton , Brian Grant , Matthew Tom Harrison , Ute Skiba , Miko U. F. Kirschbaum , Katja Klumpp , Patricia Laville

Publication : ENVIRONMENTAL MODELLING & SOFTWARE

Date : 2023

Volume : 161

Catégorie(s)

#ACBB Mons #ACBB Theix #ANR-Citation #INRAE

Auteurs, date et publication :

Auteurs Vincent Nouchi , Tiit Kutser , Alfred Wüest , Beat Müller , Daniel Odermatt , Theo Baracchini , Damien Bouffard

Publication : Aquatic Sciences

Date : 2025

Volume : 81

Issue : 2

Pages : 27

Catégorie(s)

#INRAE #OLA