Résumé
Bdellovibrio and like organisms (BALOs) are obligate bacterial predators of other Gramnegative bacteria. Here, we used quantitative PCR (qPCR) and recently developed specific primers which target the 16S rRNA gene to explore the abundance and distribution of three families of BALO belonging to the Oligoflexia class (i.e., Bdellovibrionaceae, Peredibacteraceae and Bacteriovoracaceae) over one year in the epilimnion and hypolimnion of Lakes Annecy and Geneva. Peredibacteraceae was the dominant group at all sampling points except at the bottom of Lake Geneva, where Bdellovibrionaceae was found in higher number. In addition, the abundance of BALOs increased significantly during the warmer months. Using high-throughput sequencing (Illumina Miseq), hundreds of OTUs were identified for Bdellovibrionaceae and Peredibacteraceae. Phylogenetic analysis suggests that Bdellovibrionaceae are more diverse than Peredibacteraceae and that some OTUs belong to new species of Bdellovibrionaceae. We also found that dominant OTUs were present simultaneously in the two lakes, while some others were specific to each lake, suggesting an adaptive pattern. Finally, both abundance and diversity of BALOs were poorly associated with abiotic factors except temperature, suggesting the importance of studying biotic relationships, assumed to play a greater role than physico-chemical variables in BALOs’ dynamics and distribution.
Auteurs, date et publication :
Auteurs Jade A. Ezzedine , Mathilde Scheifler , Yves Desdevises , Stéphan Jacquet
Publication : Microorganisms
Date : 2022
Volume : 10
Issue : 10
Pages : 1960
Catégorie(s)
#INRAE #OLARésumé
The purpose of this methodological study was to test whether similar soil hydraulic and solute transport properties could be estimated from field plots and lysimeter measurements. The transport of water and bromide (as an inert conservative solute tracer) in three bare field plots and in six bare soil lysimeters were compared. Daily readings of matric head and volumetric water content in the lysimeters showed a profile that was increasingly humid with depth. The hydrodynamic parameters optimized with HYDRUS-1D provided an accurate description of the experimental data for both the field plots and the lysimeters. However, bromide transport in the lysimeters was influenced by preferential transport, which required the use of the mobile/immobile water (MIM) model to suitably describe the experimental data. Water and solute transport observed in the field plots was not accurately described when using parameters optimized with lysimeter data (cross-simulation), and vice versa. The soil's return to atmospheric pressure at the bottom of the lysimeter and differences in tillage practices between the two set-ups had a strong impact on soil water dynamics. The preferential flow of bromide observed in the lysimeters prevented an accurate simulation of solute transport in field plots using the mean optimized parameters on lysimeters and vice versa.
Auteurs, date et publication :
Auteurs Arnaud Isch , Denis Montenach , Frederic Hammel , Philippe Ackerer , Yves Coquet
Publication : WATER
Date : 2019
Volume : 11
Issue : 6
Catégorie(s)
#ANR-Citation #INRAE #PRO #PRO ColmarRésumé
Fish communities are now studied non-invasively using environmental DNA (eDNA) recovered from water samples. The objective of this study is to evaluate the possibility of surveying these communities using fish eDNA passively “captured” by aquatic biofilms. To this end, biofilm samples developing on natural and artificial substrates were collected every 2 weeks for a year and a half in a large lake (Lake Geneva). DNA was extracted from biofilms and fish communities were targeted using a standard 12S barcode with a metabarcoding approach. The fish eDNA signal recovered from biofilms revealed temporal and spatial changes in fish communities. These changes were linked to fish habitat preferences and spawning season. Peaks in the eDNA signal of some taxa fitted with their spawning period reported in the literature. We evidenced that the nature of the biofilm's substrate (natural or artificial) does not affect the image obtained of the fish community composition. Furthermore, by using biofilms grown on artificial substrates, the studied temporal window of the eDNA signal can be controlled. With biofilms acting as environmental passive samplers, our results open up the possibility to accurately monitor fish communities and their temporal and spatial changes with eDNA in a faster and less expensive way than with the classical water filtration approach.
Auteurs, date et publication :
Auteurs Sinziana F. Rivera , Valentin Vasselon , Agnès Bouchez , Frédéric Rimet
Publication : Environmental DNA
Date : 2025
Volume : 5
Issue : 3
Pages : 570-581
Catégorie(s)
#INRAE #OLAAuteurs, date et publication :
Auteurs Longobardi Elena
Date : 1970
Catégorie(s)
#⛔ No DOI found #ECP #INRAERésumé
Natural recovery of acidic soils following heavy traffic is assumed to take several decades. The aim of this study was to monitor the recovery of soil penetration resistance (PR) after soil compaction by heavy traffic at two forest sites. The sites, located in northeast France, have soils that differ slightly in pH and silt content. The impact on soil PR following heavy traffic was dependent on the soil water content (WC) at the time of measurement, and, therefore, the entire WC range and corresponding PR values were measured. For the most acidic and silty soil, no difference in PR among treatments was observed when the soils were near saturation; however, the difference in PR values was high when soils were close to wilting point. For the least acidic and silty soil, the impact of heavy traffic on PR could be detected whatever the soil moisture, with the magnitude of the effect dependent on the soil water content and depth considered. Standardized PR values with regard to WC allowed an analysis of the evolution of the effect of heavy traffic with time. Ten years after being subjected to heavy traffic, the PR values in the 0-to 40-cm layer recovered to undisturbed values at the least acidic and silty site, but not WC dynamic. The most acidic and silty soil site did not show any recovery of PR or WC dynamic ten years following traffic, although liming at this site was able to increase the regeneration of PR to undisturbed levels.
Auteurs, date et publication :
Auteurs Noémie Pousse , Pascal Bonnaud , Arnaud Legout , Frédéric Darboux , Jacques Ranger
Publication : Soil Use and Management
Date : 2025
Volume : 38
Issue : 1
Pages : 815-835
Catégorie(s)
#FORET Azerailles-Clermont #INRAEAuteurs, date et publication :
Auteurs Pauline Buysse , Benjamin Loubet , Florence Lafouge , Alain Fortineau , Jeremie Depuydt , Raluca Ciuraru , Baptiste Esnault , Celine Decuq , Pedro-Henrique Herig-Coimbra , Mathis Lozano , Vincent Michoud , Christopher Cantrell
Date : 2023
Catégorie(s)
#INRAE #PT-RMSRésumé
Using strontium (Sr) and barium (Ba) in otoliths to determine natal origins and understand patterns of fish movements is based on the fundamental assumption that otoliths record water chemistry signals without any major alterations. Although prior studies highlighted that fish physiology can modify the water signal in otoliths, studies for freshwater fish are scarce. We exposed different groups of Atlantic salmon parr Salmo salar to different scenarios of ambient-level variations in Sr/Ca and Ba/Ca ratios and then combined otolith chemical profiles with environmental data (water chemistry and temperature), Fulton’s index, and otolith growth rates to assess what factors explain/influence the elemental ratios of Sr and Ba in otoliths. Generalized additive mixed models (GAMMs) using water-based otolith composition, temperature, Fulton’s index, and “individual” as explanatory variables allow to demonstrate that water chemistry alone cannot fully explain measured ratios in otoliths, except in scenarios involving significant changes in water chemistry. Other factors (physiological effects) should be accounted for reproducing short and minimal seasonal variations in water composition, considering that inter-individual variability contributes quite significantly in most scenarios.
Auteurs, date et publication :
Auteurs G. Bareille , M. Vignon , A. Chappaz , A. Fontaine , H. Tabouret , F. Morat , J. Martin , J.C. Aymes , F. Daverat , C. Pécheyran , O. Donard
Publication : Canadian Journal of Fisheries and Aquatic Sciences
Date : 2024
Volume : 81
Issue : 2
Pages : 223-240
Catégorie(s)
#ECP #INRAERésumé
The standard Eisenia fetida chronic toxicity reproduction test is normalized and needs up to 8 weeks of exper-imentation. Many matrixes have shown toxic effects on the earthworms' survey, growth and reproduction. But the food factor may affect the organisms' responses to contaminated media in such tests. We try to evaluate the effect, or not, of the organic carbon content present in the environment, as spreadable organic wastes added in soil, on the reproduction test of Eisenia fetida. We confirm the influence of the organic matter content on earthworm reproduction. This “food” factor must be considered when studying environmental samples rich in organic matter, since that could mask potentially harmful effects. To minimize this potential “food” effect during reproduction tests, we recommend an inverse gradient of organic matter contribution by the “horse dung” food applied in all conditions according to the dose of agricultural amendments tested.
Auteurs, date et publication :
Auteurs J. -P. Bedell , O. Roques , R. Bayard
Publication : ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY
Date : 2023
Volume : 104
Catégorie(s)
#ANR-Citation #BiochemEnv #INRAERésumé
Ecological theory posits that temporal stability patterns in plant populations are associated with differences in species' ecological strategies. However, empirical evidence is lacking about which traits, or trade-offs, underlie species stability, especially across different biomes. We compiled a worldwide collection of long-term permanent vegetation records (greater than 7000 plots from 78 datasets) from a large range of habitats which we combined with existing trait databases. We tested whether the observed inter-annual variability in species abundance (coefficient of variation) was related to multiple individual traits. We found that populations with greater leaf dry matter content and seed mass were more stable over time. Despite the variability explained by these traits being low, their effect was consistent across different datasets. Other traits played a significant, albeit weaker, role in species stability, and the inclusion of multi-variate axes or phylogeny did not substantially modify nor improve predictions. These results provide empirical evidence and highlight the relevance of specific ecological trade-offs, i.e. in different resource-use and dispersal strategies, for plant populations stability across multiple biomes. Further research is, however, necessary to integrate and evaluate the role of other specific traits, often not available in databases, and intraspecific trait variability in modulating species stability.
Auteurs, date et publication :
Auteurs Luisa Conti , Enrique Valencia , Thomas Galland , Lars Götzenberger , Jan Lepš , Anna E-Vojtkó , Carlos P. Carmona , Maria Májeková , Jiří Danihelka , Jürgen Dengler , David J. Eldridge , Marc Estiarte , Ricardo García-González , Eric Garnier , Daniel Gómez , Věra Hadincová , Susan P. Harrison , Tomáš Herben , Ricardo Ibáñez , Anke Jentsch
Publication : Proceedings of the Royal Society B: Biological Sciences
Date : 2023
Volume : 290
Issue : 2001
Pages : 20230344
Catégorie(s)
#ACBB #ACBB Laqueuille #ACBB Theix #INRAERésumé
Improved understanding of the interactions between management practices and climate variability is critical for the development of sustainable grassland management and the provision of bundles of ecosystem services in a changing environment. Here we used a long-term fertilizer field trial to examine the impacts of climate variability (annual temperature, rainfall) on an upland grassland subjected to a gradient of nutrient availability. We tested for the effect of climatic indices, fertilizer regime, and their interactions, on annual biomass production, forage quality (crude protein content, digestibility) and plant diversity (species richness, equitability). During the 15-year study period we recorded significant interannual variation in both climate and grassland properties. We found that fertilizer treatments, mean annual temperature and annual precipitation all affected the grassland variables in this study, but interactions between climate and management treatment were generally limited. Contrary to expectations, interactions were driven by the PK rather than the NPK treatment. These results highlight the importance of management for projected responses to future climate change in models of grassland function.
Auteurs, date et publication :
Auteurs Frédérique Louault , Juliette M. G. Bloor
Publication : Grassland Science in Europe
Date : 2025
Volume : 27
Pages : 207