Résumé
Soil enzymes are major contributors the decomposition of soil organic matter. They are believed to reflect microbial nutrient and energy acquisition strategies and limitations. Whilst enzyme activities in surface soil layers have been widely studied, activities down the soil profile have received far less attention. Here, we present the results of a meta-analysis of hydrolase and oxidoreductase activities involved in the C, N and P cycles as a function of soil depth. The aim of the analysis was to understand how the relationship between microbial communities and their nutritional environment changes with depth. We assembled a database of 210 soil profiles published in 40 studies from diverse locations, soil types, land uses and climates. In order to compare activity profiles, we used Gaussian process regression, followed by hierarchical clustering. Our results show that, when expressed per soil mass, the majority of hydrolase activities decrease with increasing soil depth. However, this is not the case for a majority of oxidoreductase activities, possibly indicative of changes in microbial community resource acquisition strategies with depth. Microbial biomass specific enzyme activities tended to increase with soil depth, suggesting an increase in microbial allocation to resource acquisition in response to decreased resource (C, N and P) availability and/or an increased enzyme stabilization on mineral and organic surfaces.
Auteurs, date et publication :
Auteurs Fatima El Mekdad , Naoise Nunan , Samuel Abiven , Xavier Raynaud
Date : 2022
Catégorie(s)
#CNRS #Ecotron IleDeFranceRésumé
Background: The drivers of species co-existence in local communities are especially enigmatic for assemblages of morphologically cryptic species. Here we characterize the colonization dynamics and abundance of nine species of Caenorhabditis nematodes in neotropical French Guiana, the most speciose known assemblage of this genus, with resource use overlap and notoriously similar external morphology despite deep genomic divergence.
Methods: To characterize the dynamics and specificity of colonization and exploitation of ephemeral resource patches, we conducted manipulative field experiments and the largest sampling effort to date for Caenorhabditis outside of Europe. This effort provides the first in-depth quantitative analysis of substrate specificity for Caenorhabditis in natural, unperturbed habitats.
Results: We amassed a total of 626 strain isolates from nine species of Caenorhabditis among 2865 substrate samples. With the two new species described here (C. astrocarya and C. dolens), we estimate that our sampling procedures will discover few additional species of these microbivorous animals in this tropical rainforest system. We demonstrate experimentally that the two most prevalent species (C. nouraguensis and C. tropicalis) rapidly colonize fresh resource patches, whereas at least one rarer species shows specialist micro-habitat fidelity.
Conclusion: Despite the potential to colonize rapidly, these ephemeral patchy resources of rotting fruits and flowers are likely to often remain uncolonized by Caenorhabditis prior to their complete decay, implying dispersal-limited resource exploitation. We hypothesize that a combination of rapid colonization, high ephemerality of resource patches, and species heterogeneity in degree of specialization on micro-habitats and life histories enables a dynamic co-existence of so many morphologically cryptic species of Caenorhabditis.
Auteurs, date et publication :
Auteurs Céline Ferrari , Romain Salle , Nicolas Callemeyn-Torre , Richard Jovelin , Asher D. Cutter , Christian Braendle
Publication : BMC Ecology
Date : 2025
Volume : 17
Issue : 1
Catégorie(s)
#CNRS #FORET NouraguesRésumé
Earthworms in interaction with soil microorganisms play a key role in litter decomposition. Moreover, as soil engineers, earthworms modify microbial communities and their enzymatic activities. Most studies focusing on earthworms and soil enzymatic activities compare distinct ecological categories of earthworms whereas their contributions and interactions within a given ecological category remain largely unknown. In this context, the aims of the present study were to determine and compare the contribution of (1) three strict-anecic earthworm species, (2) three epi-anecic earthworm species and (3) the pairwise interactions between these different species on Lolium perenne leaf litter decomposition and soil microbial activity. After 30 days of incubation, the surface litter mass loss and five soil enzymatic activities (FDAse, β-D-glucosidase, cellobiohydrolase, leucine amino-peptidase and acid phosphatase) were measured in both earthworm burrows and middens. In mono-specific assemblages, leaf litter mass loss and enzymatic activities were significantly higher in the presence of epi-anecic compared to strict-anecic species, whatever the species identity. These differences were higher for the β-D-glucosidase, leucine amino-peptidase and FDAse (+78%, +57% and +34%, respectively). Earthworm species interactions at both intra- and inter-ecological sub-categories did not enhance either leaf litter mass loss or enzymatic activities. Interestingly, FDAse activity was higher in earthworm burrows whereas acid phosphatase activity was higher in earthworm middens. These results indicate that the two anecic ecological sub-categories have different impacts on soil functioning and each of them regroups earthworm species with similar behaviour. This functional distinction highlights the key role of epi-anecic earthworms in fresh surface litter burial and decomposition, featuring their importance on nutrient cycling in soil and for microbial activities stimulation through resource availability.
Auteurs, date et publication :
Auteurs Kevin Hoeffner , Mathieu Santonja , Daniel Cluzeau , Cécile Monard
Publication : Soil Biology and Biochemistry
Date : 2019
Volume : 132
Pages : 93-100
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β-diversity) along ecological gradients. Here, we characterize soil microbial β-diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β-diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β-diversities with respect to plant β-diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β-diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β-diversities were mostly related to plant β-diversity, while bacterial β-diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β-diversities with plant β-diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β-diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early-evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.
Auteurs, date et publication :
Auteurs Loïc Chalmandrier , Johan Pansu , Lucie Zinger , Frederic Boyer , Eric Coissac , Alexandre Génin , Ludovic Gielly , Sébastien Lavergne , Nicolas Legay , Vincent Schilling , Pierre Taberlet , Tamara Münkemüller , Wilfried Thuiller
Publication : Ecography
Date : 2025
Volume : 42
Issue : 12
Pages : 2144-2156
Catégorie(s)
#CNRS #eDNARésumé
We aimed to evaluate the importance of modulations of within-tree carbon (C) allocation by water and low-temperature stress for the prediction of annual forest growth with a process-based model.
Auteurs, date et publication :
Auteurs Joannès Guillemot , Christophe Francois , Gabriel Hmimina , Eric Dufrêne , Nicolas K. Martin-StPaul , Kamel Soudani , Guillaume Marie , Jean-Marc Ourcival , Nicolas Delpierre
Publication : New Phytologist
Date : 2025
Volume : 214
Issue : 1
Pages : 180-193
Catégorie(s)
#CNRS #FORET PuechabonAuteurs, date et publication :
Auteurs Mélanie Fichaux , Jason Vleminckx , Elodie A Courtois , Jacques HC Delabie , Jordan Galli , Shengli Tao , Nicolas Labrière , Jérôme Chave , Christopher Baraloto , Jérôme Orivel
Publication : Biotropica
Date : 2025
Volume : 53
Issue : 1
Pages : 97-109
Catégorie(s)
#CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs Olivier Dézerald , Stanislas Talaga , Céline Leroy , Jean-François Carrias , Bruno Corbara , Alain Dejean , Régis Céréghino
Publication : Hydrobiologia
Date : 2025
Volume : 723
Issue : 1
Pages : 77-86
Catégorie(s)
#CNRS #FORET NouraguesRésumé
An excessive supply of sediment is observed in numerous rivers across the world where it leads to deleterious impacts. Information on the sources delivering this material to waterbodies is required to design effective management measures, and sediment tracing or fingerprinting techniques are increasingly used to quantify the amount of sediment derived from different sources. However, the current methods used to identify the land use contributions to sediment have a limited discrimination power. Here, we investigated the potential of environmental DNA (eDNA) to provide more detailed information on the plant species found in sediment source areas as a next generation fingerprint. To this end, flood sediment deposits (n = 12) were collected in 2017 in two catchments impacted by the Fukushima radioactive fallout along differing river sections draining forests, cropland or a mix of both land uses. Conventional fingerprints (i.e. fallout radionuclides and organic matter properties) were also measured in these samples. The conventional fingerprint model results showed that most sediment samples contained a dominant proportion of subsoil material. Nevertheless, the eDNA information effectively discriminated the three above-mentioned groups of sediment, with the dominance of tree, shrub and fern species in sediment sampled in rivers draining forests versus a majority of grass, algae and cultivated plant species in sediment collected in rivers draining cropland. Based on these encouraging results, future research should examine the potential of eDNA in mixed land use catchments where the contribution of topsoil to sediment dominates and where the cultivation of land has not been abandoned in order to better characterize the memory effect of eDNA in soils and sediment.
Auteurs, date et publication :
Auteurs Olivier Evrard , J Patrick Laceby , Gentile Francesco Ficetola , Ludovic Gielly , Sylvain Huon , Irène Lefèvre , Yuichi Onda , Jérôme Poulenard
Publication : Science of The Total Environment
Date : 2025
Volume : 665
Pages : 873–881
Catégorie(s)
#CNRS #eDNARésumé
Dispersal, defined as any movements potentially leading to gene flow, is a major process driving a species’ capacity to cope with human-induced environmental modifications. However, the dispersal process is multi-causal, which currently hinders predictions regarding a species’ resilience to global change. We used a multifaceted approach to disentangle the relative importance of a suite of dispersal-related factors in the butterfly Lycaena tityrus, including condition- (morphology and behavior) and context- (environmental) dependent factors. Experiments were conducted at an experimental platform dedicated to study dispersal, the Metatron, to record emigration propensity in two-patch experimental metapopulations under different environmental conditions. The butterflies’ individual condition was subsequently assessed in the laboratory. Individual condition did not generally influence emigration propensity. We detected a significant sex bias in emigration propensity, being generally higher in females than in males, but in a context-dependent manner. The environmental context affected emigration propensity, which was higher when habitat quality was poor. Our results show that emigration is not random in L. tityrus, but is rather an active process triggered by sex and habitat quality. Our main finding was that individual condition, and particularly flight ability measured by a performance test, was not related to emigration propensity in experimental metapopulations. Our results may have important implications for forecasting future species distributions, as deteriorating environmental contexts are likely to increase emigration whatever the individual condition is.
Auteurs, date et publication :
Auteurs Elisabeth Reim , Michel Baguette , Franziska Günter , Klaus Fischer
Publication : Ecosphere
Date : 2025
Volume : 9
Issue : 11
Pages : e02502
Catégorie(s)
#CNRS #Metatron terrestreRésumé
Type III epithelial–mesenchymal transition (EMT) has been previously associated with increased cell migration, invasion, metastasis, and therefore cancer aggressiveness. This reversible process is associated with an important gene expression reprogramming mainly due to epigenetic plasticity. Nevertheless, most of the studies describing the central role of epigenetic modifications during EMT were performed in a single-cell model and using only one mode of EMT induction. In our study, we studied the overall modulations of gene expression and epigenetic modifications in four different EMT-induced cell models issued from different tissues and using different inducers of EMT. Pangenomic analysis (transcriptome and ChIP–sequencing) validated our hypothesis that gene expression reprogramming during EMT is largely regulated by epigenetic modifications of a wide range of genes. Indeed, our results confirmed that each EMT model is unique and can be associated with a specific transcriptome profile and epigenetic program. However, we could select some genes or pathways that are similarly regulated in the different models and that could therefore be used as a common signature of all EMT models and become new biomarkers of the EMT phenotype. As an example, we can cite the regulation of gene-coding proteins involved in the degradation of the extracellular matrix (ECM), which are highly induced in all EMT models. Based on our investigations and results, we identified ADAM19 as a new biomarker of in vitro and in vivo EMT and we validated this biological new marker in a cohort of non-small lung carcinomas.
Auteurs, date et publication :
Auteurs Paul Peixoto , Amandine Etcheverry , Marc Aubry , Anaïs Missey , Camille Lachat , Jérôme Perrard , Elodie Hendrick , Régis Delage-Mourroux , Jean Mosser , Christophe Borg , Jean-Paul Feugeas , Michaël Herfs , Michaël Boyer-Guittaut , Eric Hervouet
Publication : Cell Death & Disease
Date : 2019
Volume : 10
Issue : 3
Pages : 1-17