Résumé
Using organic waste products (OWP) in agriculture has been reported to impact both the activity and composition of soil microbial communities. However, little information is available on how the response of a soil microbial community to a given OWP may depend on the physicochemical and microbial properties of the soil receiving the input. Here, we performed a microcosm experiment to compare the effect of 2 different OWPs (GWS: co-compost of Green Wastes and Sewage sludge or FYM: FarmYard Manure), each applied to 5 different soils, on the activity, abundance and diversity of the soil microbial communities. Soils were selected to represent a range of physicochemical and climatic characteristics. CO2 and N2O emissions, microbial biomass and taxonomic diversity were monitored for 28 days following OWP input. The five soils presented different prokaryotic and fungal communities structures before OWP application. During the 28 days of incubation, those control soils (without OWP) harboring the highest organic matter contents released the greatest CO2 and N2O emissions, and had the highest soil microbial biomass. The impact of organic amendments on soil activity and microbial diversity differed with the nature of the OWP. FYM application increased CO2 emissions 2-fold and delayed N2O emissions compared to GWS. Major changes in prokaryotic genetic structures were also observed when GWS was applied. The effect of OWPs was dependent on soil type and the five soils exhibited distinct patterns of CO2 and N2O emission after a given input. This accorded with the fact that the structure and composition of the microbial communities harbored by each soil type responded differently to a given OWP application. To conclude, our results show that different soil types, harboring distinct microbial community structures, responded differently to OWP application, leading to different patterns and rates of greenhouse gas emissions. This response was also OWP-dependent.
Auteurs, date et publication :
Auteurs Sophie Sadet-Bourgeteau , Sabine Houot , Battle Karimi , Olivier Mathieu , Vincent Mercier , Denis Montenach , Thierry Morvan , Valerie Sappin-Didier , Francoise Watteau , Virginie Nowak , Samuel Dequiedt , Pierre-Alain Moron
Publication : APPLIED SOIL ECOLOGY
Date : 2019
Volume : 143
Pages : 70-79
Catégorie(s)
#ANR-Citation #INRAE #PRO #PRO ColmarRésumé
Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.
Auteurs, date et publication :
Auteurs Anne-Laure Vivant , Dominique Garmyn , Pierre-Alain Maron , Virginie Nowak , Pascal Piveteau
Publication : Plos One
Date : 2013
Volume : 8
Issue : 10
Pages : e76991
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs François Maillard , Valentin Leduc , Cyrille Bach , José Leonardo de Moraes Gonçalves , Fernando Dini Androte , Laurent Saint-André , Jean-Paul Laclau , Marc Buée , Agnès Robin
Publication : Microbial ecology
Date : 2025
Pages : 1-6
Catégorie(s)
#CIRAD #FORET Itatinga #INRAERésumé
Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2x10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica) and spruce (Picea abies) forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60%) and metazoans while protists represented less than 12% of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52% from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39% and 31.5% of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides), sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin) and glycoside hydrolases represented 0.5% (beech soil)-0.8% (spruce soil) of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases) were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter.
Auteurs, date et publication :
Auteurs Coralie Damon , Frederic Lehembre , Christine Oger-Desfeux , Patricia Luis , Jacques Ranger , Laurence Fraissinet-Tachet , Roland Marmeisse
Publication : Plos One
Date : 2012
Volume : 7
Issue : 1
Catégorie(s)
#FORET Breuil #INRAEAuteurs, date et publication :
Auteurs Theo Baracchini , Alfred Wüest , Damien Bouffard
Publication : Water Research
Date : 2025
Volume : 172
Pages : 115529
Catégorie(s)
#INRAE #OLARésumé
Ixodes ricinus ticks (Acari: Ixodidae) are the most important vector for Lyme borreliosis in Europe. As climate change might affect their distributions and activities, this study aimed to determine the effects of environmental factors, i.e., meteorological, bioclimatic, and habitat characteristics on host-seeking (questing) activity of I. ricinus nymphs, an important stage in disease transmissions, across diverse climatic types in France over 8 years. Questing activity was observed using a repeated removal sampling with a cloth-dragging technique in 11 sampling sites from 7 tick observatories from 2014 to 2021 at approximately 1-month intervals, involving 631 sampling campaigns. Three phenological patterns were observed, potentially following a climatic gradient. The mixed-effects negative binomial regression revealed that observed nymph counts were driven by different interval-average meteorological variables, including 1-month moving average temperature, previous 3-to-6-month moving average temperature, and 6-month moving average minimum relative humidity. The interaction effects indicated that the phenology in colder climates peaked differently from that of warmer climates. Also, land cover characteristics that support the highest baseline abundance were moderate forest fragmentation with transition borders with agricultural areas. Finally, our model could potentially be used to predict seasonal human-tick exposure risks in France that could contribute to mitigating Lyme borreliosis risk.
Auteurs, date et publication :
Auteurs Phrutsamon Wongnak , Séverine Bord , Maude Jacquot , Albert Agoulon , Frédéric Beugnet , Laure Bournez , Nicolas Cèbe , Adélie Chevalier , Jean-François Cosson , Naïma Dambrine , Thierry Hoch , Frédéric Huard , Nathalie Korboulewsky , Isabelle Lebert , Aurélien Madouasse , Anders Mårell , Sara Moutailler , Olivier Plantard , Thomas Pollet , Valérie Poux
Publication : Scientific Reports
Date : 2022
Volume : 12
Issue : 1
Pages : 7833
Catégorie(s)
#FORET OPTMix #INRAERésumé
The sustainability of forest ecosystems may be at stake especially in forests on base-poor soils due to reduced nutrient deposition and intensified silvicultural practices. Understanding nutrient availability and cycling is therefore essential to manage forest soil fertility. This study aims to assess in a beech plot Mg and Ca vertical transfer in soil and root uptake using an isotopic tracing experiment. A simulated rainfall containing a small amount (960 g Mg.ha(-1); 530 g Ca.ha(-1)) of highly enriched Mg-26 and Ca-44 was sprayed on the forest floor of a 35-yr-old beech plot. The isotopic composition of fine roots and of the soil exchangeable Mg and Ca pool was monitored during 1 year. A pool and flux model (IsoMod) was developed to predict the labeling of the soil and vertical transfer of tracers. Tracers (Ca-44 and Mg-26) were immediately retained in the thin litter layer. During the following year, Mg and to a lesser extent Ca were progressively released. After 1 year, the exchangeable Mg and Ca pools of the upper mineral layer (0-5 cm) were strongly labeled (similar to 660 aEuro degrees, representing similar to 55 % of the tracer input and similar to 370 aEuro degrees, similar to 41 % of the tracer input respectively). A significant proportion (similar to 8 % Mg-26, similar to 2 % Ca-44) of tracer was leached through the soil, below 10 cm. This amount was much larger than what was predicted using a simple mixing model. The Ca and Mg isotopic composition of fine roots at all depths was close or lower than that of exchangeable Ca and Mg respectively. An in situ ecosystem-scale Mg-26 and Ca-44 isotopic tracing experiment was successfully carried out. Tracers were at first strongly retained in the litter layer, then progressively transferred to soil horizons below. Nutrient cycling of Mg and Ca were proven to be very different. Mg had a higher mobility in the soil than Ca, and nutrient uptake sources were proven to be different.
Auteurs, date et publication :
Auteurs Gregory van der Heijden , Arnaud Legout , Andrew J. Midwood , Carol-Ann Craig , Benoit Pollier , Jacques Ranger , Etienne Dambrine
Publication : Plant and Soil
Date : 2013
Volume : 369
Issue : 1-2
Pages : 33-45
Catégorie(s)
#FORET Breuil #INRAERésumé
Many forest stands grow on acid and nutrient poor soils. To better understand how they cope with very low mineral resources, we investigated (1) Mg and Ca uptake in relation to depth, and (2) the allocation of these elements from the roots to the canopy, using a multi-isotopic (Mg-26, Ca-44) tracing experiment in a beech stand on a very poor soil. The distribution of the tracers in the soil was taken from van der Heijden et al. (Plant Soil 369:33-45, 2013a, Geoderma 195-196:12-22, 2013b, For Ecol Manag 293:65-78, 2013c). A model simulating Mg, Ca, Mg-26 and Ca-44 uptake was developed and applied to estimate the vertical distribution of Mg and Ca uptake in the soil profile. The vertical distribution of tracers in aboveground biomass was measured from four felled trees 2 years after the application of the tracers. The modeled distribution of root uptake in relation to depth shows differences between Mg and Ca: the main source of Mg uptake is the litter layer (circa. 43 % of total uptake) and the top mineral soil (0-5 cm) for Ca (circa. 42 %). The deeper soil layers (15-60 cm) also contribute to uptake. The study does not show clear evidence that uptake occurs in the very deep soil layers (> 70 cm). The distribution of tracers in the aboveground biomass shows a vertical gradient from the stump to the canopy with no or very small amounts of tracers being observed in the foliage during the 2 years after the application of tracers. This suggests that Mg and Ca transport from roots to leaves along the xylem sap flow is quite slow. As Ca and Mg supply to the trees from deep soil horizons is not evidenced, and tracer transport from roots to the leaves is slow, we suggest that the tree internal pool of Ca and Mg may be more active than previously thought. This pool may act as a buffer when nutrient availability is in shortage.
Auteurs, date et publication :
Auteurs Gregory van der Heijden , Etienne Dambrine , Benoit Pollier , Bernhard Zeller , Jacques Ranger , Arnaud Legout
Publication : Biogeochemistry
Date : 2015
Volume : 122
Issue : 2-3
Pages : 375-393
Catégorie(s)
#FORET Breuil #INRAERésumé
Many forest soils are acidic and have very low plant-available pools of magnesium. Past and present sylvicultural, nutritional and/or climatic pressures endured by forest ecosystems can result in net losses of nutrients and ecosystem function losses. Liming with a carbonate product is an alternative to counteract these degradations but the effects of liming on the biogeochemical cycling of nutrients over time and the dynamics of Mg released from liming products are still unclear. We studied the Mg isotopes composition in four paired-treatment experimental beech forest ecosystems in northern France. At the sites where dolomitic lime was applied, the variation in exchangeable and foliar δ26Mg demonstrated the direct contribution of dolomite-derived Mg to the replenishment of topsoil exchangeable pools and to tree nutrition improvement: dolomite-derived Mg was incorporated into the biological cycling which allows its retention on the mid to long term in the soil–plant system. At the sites limed with calcium carbonate, the changes in exchangeable and foliar Mg contents and δ26Mg observed on the long term suggest that the applied product contained a small amount of Mg and/or that Mg cycling changed after liming, to cope in particular with the low Mg availability. Lastly, our results highlight the high δ26Mg of the organic layer (humus): fractionation processes occurring within this layer (mineralization/ageing of organic matter, preferential retention of 26 Mg) could explain these singular signatures that could greatly influence the topsoil Mg exchangeable pools.
Auteurs, date et publication :
Auteurs Mélanie Court , Gregory Van Der Heijden , Pascale Louvat , Emile Bolou-Bi , Guillaume Caro , Julien Bouchez , Benoit Pollier , Serge Didier , Claude Nys , Laurent Saint-André , Arnaud Legout
Publication : Biogeochemistry
Date : 2021
Volume : 153
Issue : 2
Pages : 115-134
Catégorie(s)
#FORET Breuil #INRAEAuteurs, date et publication :
Auteurs Ana de Santiago-Martın , Natalie Cheviron , Jose R Quintana , Concepcion Gonzalez , Antonio L Lafuente , Christian Mougin
Publication : Arch Environ Contam Toxicol
Date : 2025
Pages : 11