Auteurs, date et publication :
Auteurs E. V. Da Silva , J.-P. Bouillet , J. L. M. Gonçalves , C. H. Abreu Junior , P. C. O. Trivelin , P. Hinsinger , C. Jourdan , Y. Nouvellon , J. L. Stape , J. P. Laclau
Publication : Functional Ecology
Date : 2025
Volume : 25
Pages : 996-1006
Catégorie(s)
#CIRAD #FORET Itatinga #INRAERésumé
In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France). The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource availability impact the functional diversity and to a lesser extent the taxonomic diversity of the bacterial communities.
Auteurs, date et publication :
Auteurs Stephane Uroz , Panos Ioannidis , Juliette Lengelle , Aurelie Cebron , Emmanuelle Morin , Marc Buee , Francis Martin
Publication : Plos One
Date : 2013
Volume : 8
Issue : 2
Catégorie(s)
#FORET Breuil #INRAEAuteurs, date et publication :
Auteurs Cédric Grangeteau , Daniel Gerhards , Sebastien Terrat , Samuel Dequiedt , Hervé Alexandre , Michèle Guilloux-Benatier , Christian von Wallbrunn , Sandrine Rousseaux
Publication : Journal of Microbiological Methods
Date : 2025
Volume : 121
Pages : 50-58
Catégorie(s)
#Genosol #INRAERésumé
Soil fungi play a fundamental role in the cycling of nutrients and tree nutrition in forests. As mycorrhizal fungi are closely associated with their host trees and provide them essential base cations and phosphorus, we hypothesize that they actively mine soil minerals and transfer their nutritive content to their host. Therefore, mycorrhizal fungi are expected to be important colonizers of soil mineral surfaces relative to other fungal trophic guilds. To test this hypothesis, 50 μm nylon mesh bags were filled with three different mineral types (i.e. calcite, apatite and obsidian) and buried in the same soil colonized by three forest stands (i.e. beech, Corsican pine and coppice with standards). After an in situ incubation period of 29 months in the topsoil, mineral dissolution was detectable in the mesh bags, and the analysis of the fungal communities was therefore undertaken. Minerals presented a lower fungal biomass than the surrounding bulk soil and no difference between the three mineral types tested was observed. The high-throughput sequencing (HTS) approach showed that the fungal communities differed among the three forest stands, but in each case, mineral associated fungal taxa differed significantly from those in the bulk soil. To a lesser extent, fungal communities further varied between the three mineral types. Overall, trophic inference analyses suggested that two groups of plant-associated fungi, namely the ectomycorrhizal and endophytic fungi, were the major fungal mineral colonizers. Saprophytes also appeared significantly enriched on minerals comparatively to the surrounding bulk soil. Together, our data reveal at local scale that the mineral-associated fungal communities are first determined by the forest plant cover and then by the type of mineral.
Auteurs, date et publication :
Auteurs Y. Colin , M. -P. Turpault , L. Fauchery , M. Buée , S. Uroz
Publication : European Journal of Soil Biology
Date : 2021
Volume : 105
Pages : 103334
Catégorie(s)
#FORET Breuil #INRAERésumé
Soil atmosphere composition results from a balance between biological activity and gas transfer, both likely to be affected by soil compaction following heavy traffic. We monitored soil atmosphere composition, temperature and moisture once a month for three years in the trafficked (by a wood-loaded forwarder) and undisturbed plots of two sites in the NE part of France. Our aim was to assess the impact of compaction on soil air composition and to test if soil restoration resulted in undisturbed levels of gas production/consumption and transfer. Soil air oxygen, O-2 and carbon dioxide, CO2 contents were the two soil gasses most sensitive to compaction and climatic variations. During at least the first year following compaction at 30 cm depth, heavy traffic resulted in an increase in soil atmosphere CO2 concentration ([CO2]) whatever the air-filled pore space. Following the first soil drought experienced at both sites, this initial impact disappeared toward an effect alternating between an increase in [CO2] when water filled pore space and a decrease when the soil was dry. The same interchanging impact was observed for soil air O-2 content but with opposite trends. We assumed that soil cracks formed in the trafficked treatment due to lower resistance to stresses when the soil dried out drastically during summer droughts, resulting in an increase in soil gas diffusion while considering same soil temperature and air-filled porosity. However, three to four years following heavy traffic, soil air-filled porosity was still significantly decreased and gas production/consumption seemed to be still affected by compaction. (c) 2012 Elsevier B.V. All rights reserved.
Auteurs, date et publication :
Auteurs N. Goutal , P. Renault , J. Ranger
Publication : Geoderma
Date : 2013
Volume : 193
Pages : 29-40
Catégorie(s)
#FORET Azerailles-Clermont #INRAERésumé
Fluctuations in the number and size of spawning perch (Perca fluviatilis) in Lake Geneva were evaluated and compared each year from 1984 to 2011 in two locations. This evaluation was based on: (1) each mature female lays only one egg strand per year and (2) the number and size of mature females are well correlated with those of their egg strands. Egg strands were counted and measured at two locations in France and in Switzerland. The collection of egg strands from either artificial substrates (France) or by direct sampling of the natural lake bottom by a diver (Switzerland) did not seem to affect the results. In most years the number and mean width of egg strands fluctuated in the same way in both locations. In addition, yearly perch catches were correlated with the number of egg strands at both locations. However, more small egg strands were found in France than in Switzerland, whereas the reverse was true of large egg strands. Fishing pressure concentrated to a greater extent on small perch in France than in Switzerland could explain this difference.
Auteurs, date et publication :
Auteurs C. Gillet , C. Lang , J. P. Dubois
Publication : Fisheries Management and Ecology
Date : 2025
Volume : 20
Issue : 6
Pages : 484-493
Catégorie(s)
#INRAE #OLARésumé
Climate forcing, in combination with local anthropogenic pressures, has drastically modified the physical and chemical properties of lakes worldwide, affecting the abundance and diversity of fish populations. In the context of these combined changes, understanding the interactions between global and local forcing has become a major challenge for developing sustainable fisheries. We analyzed commercial landing statistics of Lake Geneva to describe the long-term changes in the abundance of exploited fish species and to identify mechanisms responsible for fish population changes. We showed a significant relationship between the decrease in phosphorus concentrations and structural changes in the composition of the fish community. Local management of reducing phosphorus loadings played a major role in the recovery of whitefish (Coregonus lavaretus) spawning areas and slowed the process toward more climate-induced percid and cyprinid communities. In addition, rising spring water temperatures have increased whitefish larval growth rates and improved whitefish recruitment. Unexpectedly, climate change and phosphorus reduction can have synergistic effects, and our results highlight the need to consider interactions between global and local anthropogenic forcing to fully understand and predict lake fish population variability in a warming world.
Auteurs, date et publication :
Auteurs Orlane Anneville , Camille Vogel , Jérémy Lobry , Jean Guillard
Publication : Inland Waters
Date : 2017
Volume : 7
Issue : 1
Pages : 65-76
Catégorie(s)
#INRAE #OLARésumé
Fish eDNA metabarcoding is usually performed from filtered water samples. The volume of filtered water depends on the study scope and can rapidly become time consuming according to the number of samples that have to be processed. To avoid time allocated to filtration, passive DNA samplers have been used to recover fish eDNA from marine environments faster. In freshwater ecosystems, aquatic biofilms were used to catch eDNA from macroinvertebrates. Here, we test the capacity of aquatic biofilms to entrap fish eDNA in a large lake and, therefore, the possibility to perform fish eDNA metabarcoding from this matrix compared to the traditional fish eDNA approach from filtered water samples. Methodological aspects of the use of aquatic biofilms for fish eDNA metabarcoding (e.g. PCR replicates, biological replicates, bioinformatics pipeline, reference database and taxonomic assignment) were validated against a mock community. When using biofilms from habitats sheltered from wind and waves, biofilm and water approach provided similar inventories. Richness and diversity were comparable between both approaches. Approaches differed only for rare taxa. Our results illustrate the capacity of aquatic biofilms to act as passive eDNA samplers of fish eDNA and, therefore, the possibility to use biofilms to monitor fish communities efficiently from biofilms. Furthermore, our results open up avenues of research to study a diversity of biological groups (among which bioindicators as diatoms, macroinvertebrates and fish) from eDNA isolated from a single environmental matrix reducing sampling efforts, analysis time and costs.
Auteurs, date et publication :
Auteurs Sinziana F. Rivera , Frédéric Rimet , Valentin Vasselon , Marine Vautier , Isabelle Domaizon , Agnès Bouchez
Publication : Molecular Ecology Resources
Date : 2025
Volume : 22
Issue : 4
Pages : 1440-1453
Catégorie(s)
#INRAE #OLARésumé
Hydroacoustic methods are routinely used for fish population assessment and monitoring in lakes and reservoirs around the world and are particularly embedded in European and North American lake management. However, the comparability of hydroacoustic results can be difficult to assess due to the large number of variables (sound frequency, sound pulse duration, system manufacturer, analysis method, etc.) that can influence acoustic estimates. This study investigates the effect of variations in analysis method and hydroacoustic system on commonly produced outputs. Volume backscattering strength (Sv), mean target strength (TS), fish abundance, and biomass were estimated using two analysis methods (echo integration and track-counting) using data recorded from a large, deep lake (Windermere, UK) by four vertically oriented split-beam systems operating at three sound frequencies (120 kHz, 200 kHz, and 400 kHz). The two analysis methods used produced similar estimates of fish abundance and fish biomass. We therefore concluded that echo integration and trackcounting can be robustly used and outputs justifiably compared under the conditions of the Windermere surveys. In addition, we compared mean Sv, mean TS, fish abundance, and biomass estimates across the four hydroacoustic systems. The only significant result was for abundance estimates, however, the system made a small contribution to the overall variability. All four systems provided similar results for the other metrics, demonstrating that independent hydroacoustic surveys operating within the European Standard can make a major contribution to the assessment and monitoring of fish populations in deep lakes and reservoirs.
Auteurs, date et publication :
Auteurs Vladislav Draštík , Malgorzata Godlewska , Helge Balk , Peter Clabburn , Jan Kubečka , Emma Morrissey , Jon Hateley , Ian J. Winfield , Tomáš Mrkvička , Jean Guillard
Publication : Limnology and Oceanography: Methods
Date : 2025
Volume : 15
Issue : 10
Pages : 836-846
Catégorie(s)
#INRAE #OLAAuteurs, date et publication :
Auteurs Tiina Nõges , Orlane Anneville , Jean Guillard , Juta Haberman , Ain Järvalt , Marina Manca , Giuseppe Morabito , Michela Rogora , Stephen J. Thackeray , Pietro Volta , Ian J. Winfield , Peeter Nõges
Publication : Journal of Limnology
Date : 2017