Auteurs, date et publication :
Auteurs Yannick Bayona , Marc Roucaute , Kevin Cailleaud , Laurent Lagadic , Anne Bassères , Thierry Caquet
Publication : Science of The Total Environment
Date : 2014
Volume : 484
Pages : 102-113
Catégorie(s)
#INRAE #PEARLAuteurs, date et publication :
Auteurs Daniel Mika-Nsimbi Poultney , Mathias Christina , Antoine Versini
Publication : Plant and Soil
Date : 2025
Volume : 453
Issue : 1-2
Pages : 597-613
Catégorie(s)
#CIRAD #INRAE #PRO #PRO ReunionRésumé
Electrofishing is widely used to survey fish communities in freshwater, but uncertainties remain about electrotaxis (i.e. swimming toward the electrode) and the efficiency with which it catches decapod species. This three-part study was performed to define effective electrofishing settings for mixed communities of freshwater decapods and fish species. First, we studied the behaviour of five species of swimming decapods (Caridae) when exposed to four waveforms (direct current (DC) or pulsed direct current (PDC) at 2, 5 or 40 Hz) and two power density settings (low (30 µW.cm−3) or high (80 µW.cm−3)) in the laboratory. DC at low power density and PDC-2 Hz at high power density induced significantly more electrotaxis than the other settings. We then tested three electrofishing settings (low power DC (DClp), high power DC (DChp) and high power 40 Hz PDC (PDC40hp)) under natural conditions using the depletion method (with three passes) in enclosed sections of a shallow stream, followed by complete removal of bottom substrate and aquatic vegetation to catch the remaining individuals. DClp consistently detected all shrimp (nine species) and fish (seven species) after two electrofishing passes, but the two other settings did not. DC performed better than PDC for estimating the abundance of shrimp (80% vs. 70% of individuals caught, respectively) and fish (90% vs. 70%, respectively) after three electrofishing passes. Using depletion models, DClp gave the most accurate estimates of abundance for shrimp and fish species. Finally, we assessed the ability of three-pass DClp electrofishing to estimate abundances in nine shallow and coarse-substrate Caribbean streams. More than 10,000 shrimp from 10 species and 1600 fish from 8 species were caught and examined. We observed a correlation between estimated and total abundances after complete removal of bottom substrate and aquatic vegetation in the enclosed stream sections, except for small (≤ 20 mm long) shrimp. The fish mortality rate due to electrofishing was 0.22%, and only one species (Eleotris perniger) showed evidence of spinal damage (4.4% of individuals) based on ultrasound analysis of the spinal column. Thus, we recommend using DClp (30 µW.cm−3) to survey sympatric communities of shrimp and fish species in shallow, coarse-substrate tropical streams.
Auteurs, date et publication :
Auteurs Gaétan Pottier , Nicolas Bargier , Yoann Bennevault , Régis Vigouroux , Didier Azam , Frédéric Marchand , Marie Nevoux , Jean-Marc Roussel
Publication : Fisheries Research
Date : 2022
Volume : 256
Pages : 106457
Catégorie(s)
#INRAE #PEARLRésumé
Accounting for the interannual climatic variations is a well-known issue for simulation-based studies of environmental systems. It often requires intensive sampling (e.g., averaging the simulation outputs over many climatic series), which hinders many sequential processes, in particular optimization algorithms. We propose here an approach based on a subset selection in a large basis of climatic series, using an ad-hoc similarity function and clustering. A non-parametric reconstruction technique is introduced to estimate accurately the distribution of the output of interest using only the subset sampling. The proposed strategy is non-intrusive and generic (i.e. transposable to most models with climatic data inputs), and can be combined to most “off-the-shelf” optimization solvers. We apply our approach to sunflower ideotype design using the crop model SUNFLO. The underlying optimization problem is formulated as a multi-objective one to account for risk-aversion. Our approach achieves good performances even for limited computational budgets, outperforming significantly standard strategies.
Auteurs, date et publication :
Auteurs Victor Picheny , Ronan Trépos , Pierre Casadebaig
Publication : Plos One
Date : 2017
Volume : 12
Issue : 5
Pages : e0176815
Catégorie(s)
#INRAE #RecordAuteurs, date et publication :
Auteurs Marie Eden , Horst H. Gerke , Sabine Houot
Publication : Agronomy for Sustainable Development
Date : 2025
Volume : 37
Issue : 2
Catégorie(s)
#INRAE #PRO #PRO QualiAgroAuteurs, date et publication :
Auteurs Walter S Andriuzzi , Phuong-Thi Ngo , Stefan Geisen , Aidan M Keith , Kenneth Dumack , Thomas Bolger , Michael Bonkowski , Lijbert Brussaard , Jack H Faber , Abad Chabbi , others
Publication : Biology and Fertility of Soils
Date : 2025
Volume : 52
Issue : 1
Pages : 91–100
Catégorie(s)
#ACBB #ACBB Lusignan #INRAERésumé
The flux of reduced substances, such as methane and ammonium, from the sediment to the bottom water (Fred) is one of the major factors contributing to the consumption of oxygen in the hypolimnia of lakes and thus crucial for lake oxygen management. This study presents fluxes based on sediment porewater measurements from different water depths of five deep lakes of differing trophic states. In mesoto eutrophic lakes Fred was directly proportional to the total organic carbon mass accumulation rate (TOC-MAR) of the sediments. TOC-MAR and thus Fred in eutrophic lakes decreased systematically with increasing mean hypolimnion depth (zH), suggesting that high oxygen concentrations in the deep waters of lakes were essential for the extent of organic matter mineralization leaving a smaller fraction for anaerobic degradation and thus formation of reduced compounds. Consequently, Fred was low in the 310 m deep mesoeutrophic Lake Geneva, with high O2 concentrations in the hypolimnion. By contrast, seasonal anoxic conditions enhanced Fred in the deep basin of oligotrophic Lake Aegeri. As TOC-MAR and zH are based on more readily available data, these relationships allow estimating the areal O2 consumption rate by reduced compounds from the sediments where no direct flux measurements are available.
Auteurs, date et publication :
Auteurs Thomas Steinsberger , Martin Schmid , Alfred Wüest , Robert Schwefel , Bernhard Wehrli , Beat Müller
Publication : Biogeosciences
Date : 2017
Volume : 14
Issue : 13
Pages : 3275-3285
Catégorie(s)
#INRAE #OLARésumé
We investigated whether perennial soil organic amendments of pig slurry (PS) and methanized pig slurry (MPS) affect active bacterial communities and change the diversity and the C-flux of Volatile Organic Compounds (VOCs) emitted by soils compared to control plots without any fertilization (C). The long term effects of the fertilization history of the amendments and the short term impact of the organic inputs were both investigated by measuring VOCs emissions using a Proton Transfer Reaction-Mass Spectrometer (PTR-MS) and by analyzing active bacterial diversity by MiSeq Illumina sequencing just before and up to 64 days following the inputs. Soil VOCs emissions (diversity and fluxes) naturally varied with temperature and rainfall variations, irrespective of manure inputs. No effect of the 5-yr fertilization history was observed on bacterial communities’ composition and on soil VOCs emissions. However, both manure inputs (PS and MPS) were associated with an inoculation of γ-Proteobacteria (Pseudomonas sp. and/or Marinospirillum sp.) to the soil on top of which PS inputs activated native soil Bacillus sp. (Firmicutes). VOCs spectra was mainly dominated by methanol and acetonitrile, the acetonitrile emissions not depending on the organic practices. C-VOCs fluxes from the soil to the atmosphere varied from 12 to 76 μg of C-VOCs h−1 m−2 in the control plots. Pig slurry and methanized pig slurry differentially impacted soil VOCs emissions: PS inputs doubled the C-VOC fluxes due to high emission of methanol while MPS inputs reduced VOCs fluxes even less than the control unamended plots, which is of great interest in the context of mitigating greenhouse gases in agriculture. Our results suggest that soil fluxes could, under certain conditions, not be marginal compared to plant fluxes and be potentially driven by new land-uses in agriculture.
Auteurs, date et publication :
Auteurs Kevin Potard , Cécile Monard , Jean-Luc Le Garrec , Jean-Pierre Caudal , Nathalie Le Bris , Françoise Binet
Publication : Agriculture, Ecosystems & Environment
Date : 2025
Volume : 250
Pages : 25-36
Catégorie(s)
#INRAE #PRO #PRO EFELEAuteurs, date et publication :
Auteurs Sandrine Charles , Virginie Ducrot , Didier Azam , Rachel Benstead , Denise Brettschneider , Karel De Schamphelaere , Sandra Filipe Goncalves , John W. Green , Henrik Holbech , Thomas H. Hutchinson , Daniel Faber , Filipe Laranjeiro , Peter Matthiessen , Leif Norrgren , Jörg Oehlmann , Evelyn Reategui-Zirena , Anne Seeland-Fremer , Matthias Teigeler , Jean-Pierre Thome , Marysia Tobor Kaplon
Publication : Regulatory Toxicology and Pharmacology
Date : 2016
Volume : 81
Pages : 47-56
Catégorie(s)
#INRAE #PEARLRésumé
Abstract
Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate these bioindicators in paleoenvironmental reconstructions. In this study, we used the top–bottom paleolimnological approach and metabarcoding techniques applied to sed-DNA to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient. Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes, which are more strongly exposed to local human pressures. Analyses of the functional groups indicate important restructuration of the food web, including the recent increase in mixotrophs. Moreover, changes in the benthic ciliates were consistent with the widespread increase in deep water anoxia. Our results provided evidence that sed-DNA can uncover information about past ciliate communities on a wide variety of lakes. Overall, our study demonstrates the potential of using ciliates as new paleoindicators, integrating information from the pelagic to the benthic zones, and providing valuable insights into ecosystem functioning through a trait-based functional community approach. As paleoindicator, they thus offer a more holistic view on the long-term changes of aquatic ecosystems.
Auteurs, date et publication :
Auteurs Cécilia Barouillet , Valentin Vasselon , François Keck , Laurent Millet , David Etienne , Didier Galop , Damien Rius , Isabelle Domaizon
Publication : Scientific Reports
Date : 2022
Volume : 12
Issue : 1
Pages : 7899