Résumé
Increases in phytoplankton biomass have been widely observed over the past decades, even in lakes experiencing nutrient reduction. However, the mechanisms giving rise to this trend remain unclear. Here, we unveil the potential mechanisms through quantifying the relative contribution of bottom–up versus top–down control in determining biomasses of phytoplankton assemblages in Lake Geneva. Specifically, we apply nonlinear time series analysis, convergent cross mapping (CCM), to decipher the degree of bottom–up versus top–down control among phytoplankton assemblages via quantifying 1) causal links between environmental factors and various phytoplankton assemblages and 2) the relative importance of bottom–up, top–down, and environmental effects. We show that the recent increase in total phytoplankton biomass, albeit with phosphorus reduction, was mainly caused by a particular phytoplankton assemblage which was better adapted to the re‐oligotrophicated environment characterized by relatively low phosphorus concentrations and warm water temperature, and poorly controlled by zooplankton grazing. Our findings suggest that zooplankton act as a critical driver of phytoplankton biomass and strongly impact the dynamics of recovery from eutrophication. Therefore, our phytoplankton assemblage approach in combination with causal identification of top–down versus bottom–up controls provides insights into the reason why phytoplankton biomass may increase in lakes undergoing phosphorus reduction.
Auteurs, date et publication :
Auteurs Orlane Anneville , Chun-Wei Chang , Gael Dur , Sami Souissi , Frédéric Rimet , Chih-hao Hsieh
Publication : Oikos
Date : 2025
Catégorie(s)
#INRAE #OLAAuteurs, date et publication :
Auteurs T. Masset , V. Frossard , M.E. Perga , N. Cottin , C. Piot , S. Cachera , E. Naffrechoux
Publication : Science of The Total Environment
Date : 2025
Volume : 674
Pages : 472-481
Catégorie(s)
#INRAE #OLARésumé
To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.
Auteurs, date et publication :
Auteurs Pierre Plassart , Nicolas Chemidlin Prevost-Boure , Stephane Uroz , Samuel Dequiedt , Dorothy Stone , Rachel Creamer , Robert I. Griffiths , Mark J. Bailey , Lionel Ranjard , Philippe Lemanceau
Publication : Scientific Reports
Date : 2019
Volume : 9
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Recycling organic residues in agrosystems presents several benefits but faces the question of contaminants, among them a few trace metals which eventually accumulate in soils following regular applications of organic waste products (OWP) and represent an ecological risk. The increase of total trace metal contents in amended topsoils can be predicted by a mass balance approach, but the evolution of their available fractions is a more intricate issue. We aimed at modelling this evolution by using the dataset of a long-term field experiment of OWP applications (manure and three urban waste composts). Two operationally-defined fractions of 6 trace metals have been quantified in the OWP and amended topsoils between 2002 and 2015: the soluble and potentially available metals, extracted in 0.01 M CaCl2 and 0.05 M EDTA solutions, respectively. The potentially available metals have progressively increased in amended topsoils, at rates depending on elements and types of OWP. For Zn, these increases corresponded in average to inputs of potentially available Zn from OWP. But the soil stocks of potentially available Cu increased faster than from the inputs of EDTA-extractable Cu, showing linear regression slopes between 1.4 and 2.5, depending on OWP type. The influence of OWP has been provisionally interpreted in the light of their efficiency to increase soil organic matter and their inputs of reactive oxides. Soluble copper has increased with repeated amendments. But soluble cadmium, nickel and zinc have generally decreased, as they are influenced by changing soil variables such as pH and organic matter. Statistic models were used to unravel the relationships between soluble and EDTA-extractable metals and other soil variables. For Cu, the most satisfactory models just relate soluble and potentially available Cu. Developing such models could contribute to predict the long-term effects of a precise scenario of agricultural OWP recycling upon available trace metals in soils. (C) 2018 Elsevier B.V. All rights reserved.
Auteurs, date et publication :
Auteurs Philippe Cambier , Aurelia Michaud , Remigio Paradelo , Myriam Germain , Vincent Mercier , Annie Guerin-Lebourg , Agathe Revallier , Sabine Houot
Publication : Science of the Total Environment
Date : 2019
Volume : 651
Issue : 2
Pages : 2961-2974
Catégorie(s)
#ANR-Citation #INRAE #PRO #PRO QualiAgroRésumé
OLA Information system (©SOERE OLA-IS, AnaEE-France, INRA Thonon-les-Bains, developed by Eco-Informatics ORE INRA Team) has been developed to meet data management needs of lake environmental research observatories in order to make data available for scientific communities. Software architecture of this IS is structured around (i) a shared central component dedicated to generic functions and (ii) modular components specific to lake thematics. The creation of the IS is done by inheriting the core component and using the appropriate modular components. SI is developed with the Java language (version 8). The components are Java projects that follow the structuring of a "multi-module" Maven project. The web interfaces are developed by using the framework JSF with Primefaces user interface component library. Spring and Hibernate frameworks complete the development tools. PostgreSQL is the relational database management system used. (2019-01-18). This information system makes it possible to store and make available physico-chemical data, biodiversity data (phytoplankton, zooplankton, fishes), data from multiparameter probes, chlorophyll, primary production, etc.
Auteurs, date et publication :
Auteurs Antoine Schellenberger , Ghislaine Monet , Denis Barbet , Damien Maurice , Guillaume Enrico , Amélie Fiocca
Date : 2019
Catégorie(s)
#Ecoinfo #INRAERésumé
Information systems have been developed to meet data management needs of environmental research observatories in order to make data available for scientific communities. Software architecture of these IS is structured around (i) a central component dedicated to generic functions shared by all IS and (ii) modular components specific to the environmental themes studied by the observatories. The creation of the IS is done by inheriting the core component and using the appropriate modular components. SI are developed with the Java language (version 8). The components are Java projects that follow the structuring of a "multi-module" Maven project. The web interfaces are developed by using the framework JSF with Primefaces user interface component library. Spring and Hibernate frameworks complete the development tools. PostgreSQL is the relational database management system used. Information system are developed by Eco-Informatics ORE INRA Team, AnaEE-France,
Auteurs, date et publication :
Auteurs Antoine Schellenberger , Philippe Tcherniatinsky , Vivianne-Judith Yayende-Guedoka , Rachid Yahiaoui , Damien Maurice , Ghislaine Monet
Date : 2019
Catégorie(s)
#Ecoinfo #INRAERésumé
Key messageWe compared two methods for detailed individual tree measurements: single image photogrammetry (SIP), a simplified, low-cost method, and the state-of-the-art terrestrial laser scanning (TLS). Our results provide evidence that SIP can be successfully applied to obtain accurate tree architectural traits in mature forests.ContextTree crown variables are necessary in forest modelling; however, they are time consuming to measure directly, and they are measured in many different ways. We compare two methods to obtain crown variables: laser-based and image-based. TLS is an advanced technology for three-dimensional data acquisition; SIP is a simplified, low-cost method.AimsTo elucidate differences between the methods, and validate SIP accuracy and usefulness for forest research, we investigated if (1) SIP and TLS measurements are in agreement in terms of the most widely used tree characteristics; (2) differences between the SIP traits and their TLS counterparts are constant throughout tree density and species composition; (3) tree architectural traits obtained with SIP explain differences in laser-based crown projection area (CPA), under different forest densities and stand compositions; and (4) CPA modelled with SIP variables is more accurate than CPA obtained with stem diameter-based allometric models. We also examined the correspondence between local tree densities extracted from images and from field measurements.MethodsWe compared TLS and SIP in a temperate pure sessile oak and mixed with Scots pine stands, in the Orleans Forest, France. Standard major axis regression was used to establish relations between laser-based and image-based tree height and diameter at breast height. Four SIP-derived traits were compared between the levels of stand density and species composition with a t test, in terms of deviations and biases to their TLS counterparts. We created a set of linear and linear mixed models (LMMs) of CPA(TLS), with SIP variables. Both laser-based and image-based stem diameters were used to estimate CPA with the published allometric equations; the results were then compared with the best predictive LMM, in terms of similarity with CPA(TLS) measurement. Local tree density extracted from images was compared with field measurements in terms of basic statistics and correlation.ResultsTree height and diameter at breast height were reliably represented by SIP (Pearson correlation coefficients r=0.92 and 0.97, respectively). SIP measurements were affected by the stand composition factor; tree height attained higher mean absolute deviation (1.09m) in mixed stands, compared to TLS, than in pure stands (0.66m); crown width was more negatively biased in mixed stands (-0.79m), than in pure stands (-0.05m); and diameter at breast height and crown asymmetry were found unaffected. Crown width and mean branch angle were key SIP explanatory variables to predict CPA(TLS). The model was approximately 2-fold more accurate than the CPA allometric estimations with both laser-based and image-based stem diameters. SIP-derived local tree density was similar to the field-measured density in terms of mean and standard deviation (9.6 (3.5) and 9.4 (3.6) trees per plot, respectively); the correlation between both density measures was significantly positive (r=0.76). ConclusionSIP-derived variables, such as crown width, mean branch angle, branch thickness, and crown asymmetry, were useful to explain tree architectural differences under different densities and stand compositions and may be implemented in many forest research applications. SIP may also provide a coarse measure of local competition, in terms of number of neighbouring trees. Our study provides the first test in mature forest stands, for SIP compared with TLS.
Auteurs, date et publication :
Auteurs Kamil Kedra , Ignacio Barbeito , Mathieu Dassot , Patrick Vallet , Anna Gazda
Publication : ANNALS OF FOREST SCIENCE
Date : 2019
Volume : 76
Issue : 1
Catégorie(s)
#ANR-Citation #FORET OPTMix #INRAERésumé
The temporal dynamics of rhizosphere and root microbiota composition was compared between healthy and infected Chinese cabbage plants by the pathogen Plasmodiophora brassicae. When inoculated with P. brassicae, disease was measured at five sampling dates from early root hair infection to late gall development. The first symptoms of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root from healthy and inoculated plants was characterized through high-throughput DNA sequencing of bacterial (16S) and fungal (18S) molecular markers and compared at each sampling date. In healthy plants, Proteobacteria and Bacteroidetes bacterial phyla dominated the rhizosphere and root microbiota of Chinese cabbage. Rhizosphere bacterial communities contained higher abundances of Actinobacteria and Firmicutes compared to the roots. Moreover, a drastic shift of fungal communities of healthy plants occurred between the two last sampling dates, especially in plant roots, where most of Ascomycota fungi dominated until they were replaced by a fungus assigned to the Chytridiomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly at a late step during the root secondary cortical infection stage of clubroot disease. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytridiomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.
Auteurs, date et publication :
Auteurs Lionel Lebreton , Anne-Yvonne Guillerm-Erckelboudt , Kevin Gazengel , Juliette Linglin , Morgane Ourry , Pascal Glory , Alain Sarniguet , Stephanie Daval , Maria J. Manzanares-Dauleux , Christophe Mougel
Publication : PLOS ONE
Date : 2019
Volume : 14
Issue : 2
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Although land use drives soil bacterial diversity and community structure, little information about the bacterial interaction networks is available. Here, we investigated bacterial co-occurrence networks in soils under different types of land use (forests, grasslands, crops and vineyards) by sampling 1798 sites in the French Soil Quality Monitoring Network covering all of France. An increase in bacterial richness was observed from forests to vineyards, whereas network complexity respectively decreased from 16,430 links to 2,046. However, the ratio of positive to negative links within the bacterial networks ranged from 2.9 in forests to 5.5 in vineyards. Networks structure was centered on the most connected genera (called hub), which belonged to Bacteroidetes in forest and grassland soils, but to Actinobacteria in vineyard soils. Overall, our study revealed that soil perturbation due to intensive cropping reduces strongly the complexity of bacterial network although the richness is increased. Moreover, the hub genera within the bacterial community shifted from copiotrophic taxa in forest soils to more oligotrophic taxa in agricultural soils.
Auteurs, date et publication :
Auteurs Battle Karimi , Samuel Dequiedt , Sebastien Terrat , Cloudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Antonio Bispo , Nicolas Chemidlin Prevost-Boure , Lionel Ranjard
Publication : SCIENTIFIC REPORTS
Date : 2019
Volume : 9
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Recycling composted organic residues in agriculture can reduce the need for mineral fertilizers and improve the physicochemical and biological properties of cultivated soils. However, more studies dealing with soil physical properties after compost amendment are still needed. The objective of this study was to investigate the impact of long-term compost amendment on soil physical properties in a silt loam Luvisol under a maize-wheat rotation in the Paris Basin. Since 1998, three composts and one manure were applied every second year after wheat harvest, at a rate of ca. 4 Mg C ha(-1). Bulk density, organic carbon concentration on a mass basis, water holding capacity, gas transport properties and Atterberg limits were measured on topsoil samples taken 15 years after the beginning of the experiment. Soil moisture was monitored in the field down to a depth of 160 cm during two years with different climatic conditions: a year with a dry summer (2010) and a year with a wet summer (2012). Compost and manure amendments reduced bulk density and increased organic carbon concentrations, which improved apparent air permeability and gas diffusivity, but only one of the amendments (a green waste-sewage sludge compost) increased water-holding capacity. The amendments also increased the water contents at the Atterberg limits and overall produced better soil conditions for tillage and other agricultural operations, in particular in wet years. However, field moisture measurements showed that in general, soil water contents were not higher in the amended soils than in the control at any of the periods considered.
Auteurs, date et publication :
Auteurs Remigio Paradelo , Marie Eden , Ingrid Martinez , Thomas Keller , Sabine Houot
Publication : SOIL & TILLAGE RESEARCH
Date : 2019
Volume : 191
Pages : 207-215