Résumé
Spatial scaling and determinism of the wide-scale distribution of macroorganism diversity has been largely demonstrated over a century. For microorganisms, and especially for soil bacteria, this fundamental question requires more thorough investigation, as little information has been reported to date. Here by applying the taxa–area relationship to the largest spatially explicit soil sampling available in France (2,085 soils, area covered ~5.3 × 105 km2) and developing an innovative evaluation of the habitat–area relationship, we show that the turnover rate of bacterial diversity in soils on a wide scale is highly significant and strongly correlated with the turnover rate of soil habitat. As the diversity of micro- and macroorganisms appears to be driven by similar processes (dispersal and selection), maintaining diverse and spatially structured habitats is essential for soil biological patrimony and the resulting ecosystem services.
Auteurs, date et publication :
Auteurs L. Ranjard , S. Dequiedt , N. Chemidlin Prévost-Bouré , J. Thioulouse , N. P. A. Saby , M. Lelievre , P. A. Maron , F. E. R. Morin , A. Bispo , C. Jolivet , D. Arrouays , P. Lemanceau
Publication : Nature Communications
Date : 2013
Volume : 4
Pages : 1434
Catégorie(s)
#Genosol #INRAERésumé
In this study, we evaluated the driving forces exerted by a large set of environmental and biological parameters on the spatial and temporal dynamics of archaeal community structure in two neighbouring peri-alpine lakes that differ in terms of trophic status. We analysed monthly data from a 2-year sampling period at two depths corresponding to the epi- and hypolimnetic layers. The archaeal communities seemed to be mainly composed of ammonia-oxidizing archaea belonging to the thaumarchaeotal phylum. The spatio-temporal dynamics of these communities were very similar in the two lakes and were characterized by (1) disparities in archaeal community structure in both time and space and (2) no seasonal reproducibility between years. The archaeal communities were regulated by a complex combination of abiotic factors, including temperature, nutrients, chlorophyll a and dissolved oxygen, and biotic factors such as heterotrophic nanoflagellates and ciliates. However, in most cases, these factors explained < 52% of the variance in archaeal community structure, while we showed in a previous study that these factors explained 70–90% of the temporal variance for bacteria. This suggests that Bacteria and Archaea may be influenced by different factors and could occupy different ecological niches despite similar spatio-temporal dynamics.
Auteurs, date et publication :
Auteurs Lyria Berdjeb , Thomas Pollet , Cécile Chardon , Stéphan Jacquet
Publication : FEMS Microbiology Ecology
Date : 2025
Volume : 86
Issue : 2
Pages : 215-230
Catégorie(s)
#INRAE #OLARésumé
We conducted a 1-year survey of the surface waters of two deep peri-alpine lakes, and investigated the abundances and community structure of picocyanobacteria and co-occurring cyanomyophages. Picocyanobacterial abundances ranged between 4.5 9 104 and 1.6 9 105 cells mLÀ1 in Lake Annecy vs. 2.2 9 103 and 1.6 9 105 cells mLÀ1 in Lake Bourget. Cyanomyoviruses ranged between 2.8 9 103 and 3.7 9 105 copies of g20 mLÀ1 in Lake Annecy vs. between 9.4 9 103 and 9.4 9 105 copies of g20 mLÀ1 in Lake Bourget. The structures of picocyanobacteria and cyanomyoviruses differed in the two lakes, and a more pronounced dynamic pattern with greater seasonality was observed in Lake Bourget. At the annual scale, there was no relationship between cyanomyovirus and picocyanobacterial abundances or structures, but we could observe that abundances of the two communities covaried in spring in Lake Bourget. We showed that (i) the changes of picocyanobacteria and cyanomyoviruses were caused by the combined effect of several environmental and biological factors the importance of which differed over time and between the lakes, and (ii) the viral control of the picocyanobacterial community was probably relatively weak at the scale of the investigation.
Auteurs, date et publication :
Auteurs Xu Zhong , Lyria Berdjeb , Stéphan Jacquet
Publication : FEMS Microbiology Ecology
Date : 2025
Volume : 86
Issue : 2
Pages : 312-326
Catégorie(s)
#INRAE #OLARésumé
• ContextThe effects of leaf inclination on plant light capture, growth, and water balance of monospecific canopies are well documented, but we still lack information on such effects in the case of multispecific canopies.• AimsWe investigated the effects of leaf inclination on the absorption of photosynthetically active radiation (PAR) of a mixed forest.• MethodsWe ran a 3D mechanistic radiation transfer model for a Mediterranean forest where Pinus halepensis makes the upper strata while Quercus ilex occupies the lower strata. As factors, we included (1) the distributions of leaf inclinations that ranged from vertical to horizontal (including the actual inclinations), (2) the fraction of diffuse light, sun position, and leaf area index (LAI), and (3) the Pinus/Quercus LAI ratio.• ResultsSimulated PAR absorption was more than twice as sensitive to leaf inclination in oaks than in pines because oaks depended on PAR transmitted below the pine layer. The extent of the effect depended on season, fraction of diffuse light, LAI, and vegetation spatial structure. None of the observed inclinations maximized PAR absorption, suggesting a trade-off with water economy.• ConclusionErroneous assumptions about leaf inclination lead to larger errors when modelling heterogeneous, mixed canopies. This also highlights potential caveats when using models that do not account for the spatial structure of canopies.
Auteurs, date et publication :
Auteurs Guillaume Simioni , Marion Durand-Gillmann , Roland Huc
Publication : Annals of Forest Science
Date : 2013
Volume : 70
Issue : 2
Pages : 123-131
Catégorie(s)
#FORET FontBlanche #INRAERésumé
Accurate nutrient budgets in forest ecosystems are needed in order to plan sustainable forest management on poor soils. Such budgets require precise measurements of water and nutrient leaching through the soil. This study aims to characterize the hydrological processes and compute hydrological budgets occurring in a very poor and acidic soil under a 30-year-old beech stand in the Morvan Mountains (France). A forest plot was set up with rain collectors, lysimeters and TDR probes, and we used a deuterated water tracing experiment and two hydrological models (BILJOU and HYDRUS-1D) to estimate the proportion of preferential and slow convective water flow, and to compute the influence of preferential flow paths on nutrient leaching. Preferential flow paths were evidenced by the deuterium tracing experiment. Tracer dynamic through the soil and soil water content variations were successively modeled. This approach enabled us to define the main condition leading to preferential flow generation (rainfall above 3.5 mm/h) and quantify the proportion of preferential flow (54%). Finally, the computed nutrient leaching fluxes of major elements Ca, Mg, NO3 and Al were strongly increased when considering preferential flow paths. The experimental and modeling approach proved to be complementary and we recommend the use of tracing experiments for better model calibration, especially when their outputs are used to compute nutrient leaching fluxes. (c) 2012 Elsevier B.V. All rights reserved.
Auteurs, date et publication :
Auteurs Gregory van der Heijden , Arnaud Legout , Benoit Pollier , Claude Brechet , Jacques Ranger , Etienne Dambrine
Publication : Geoderma
Date : 2013
Volume : 195
Pages : 12-22
Catégorie(s)
#FORET Breuil #INRAERésumé
Models for predictions of soil compaction following forest traffic represent important decision tools for forest managers in order to choose the best management practices for preserving soil physical quality. In agricultural soil compaction research, analytical models are widely used for this purpose. Our objective was to assess the ability of an analytical model to predict forest soil compaction under forwarder traffic. We used the results from two experimental sites set up in north-eastern France in 2007 and 2008 to compare simulations using the SoilFlex model with observed bulk density following forwarder traffic. The best model-based predictions were found when considering the mean initial soil conditions and an increased rebound parameter in the upper soil layers (0-10 cm) in comparison to the deeper layers (10-50 cm). The need to increase the rebound parameter in the soil surface layer to improve model accuracy was attributed to a large soil organic matter content in the uppermost layers of forest soils. For the site where initial soil mechanical parameters were measured as a function of soil bulk density and water content, the model performance was good, with a root mean square error (RMSE) of 0.06. The model performed poorer (RMSE of 0.11), especially for the surface soil layer, for the second site that was wetter at the time of traffic and where soil mechanical properties were not measured but estimated by means of pedo-transfer functions. SoilFlex was found to yield satisfactory predictions and could help forest managers estimate the risk of compaction and to select the most appropriate machinery for given soil conditions in order to preserve the soil from physical degradation during traffic in forest ecosystems. However, our results emphasise the need for research on soil mechanical properties of forest soils, in particular on the role of soil organic matter and roots on soil compressive properties.
Auteurs, date et publication :
Auteurs N. Goutal , T. Keller , P. Defossez , J. Ranger
Publication : Annals of Forest Science
Date : 2013
Volume : 70
Issue : 5
Pages : 545-556
Catégorie(s)
#FORET Azerailles-Clermont #INRAEAuteurs, date et publication :
Auteurs Lise Thouvenot , Jacques Haury , Gabrielle Thiébaut
Publication : Flora - Morphology, Distribution, Functional Ecology of Plants
Date : 2013
Volume : 208
Issue : 7
Pages : 430-437
Catégorie(s)
#INRAE #PEARLAuteurs, date et publication :
Auteurs Arnaud Giusti , Virginie Ducrot , Célia Joaquim-Justo , Laurent Lagadic
Publication : Environmental Toxicology and Chemistry
Date : 2013
Volume : 32
Issue : 8
Pages : 1740-1745
Catégorie(s)
#INRAE #PEARLRésumé
The turnover of organic matter in soil depends on the activity of microbial decomposers. However, little is known about how modifications of the diversity of soil microbial communities induced by fresh organic matter (FOM) inputs can regulate carbon cycling. Here, we investigated the decomposition of two 13C labeled crop residues (wheat and alfalfa) and the dynamics of the genetic structure and taxonomic composition of the soil bacterial communities decomposing 13C labeled FOM and native unlabeled soil organic matter (SOM), respectively. It was achieved by combining the stable isotope probing method with molecular tools (DNA genotyping and pyrosequencing of 16S rDNA). Although a priming effect (PE) was always induced by residue addition, its intensity increased with the degradability of the plant residue. The input of both wheat and alfalfa residues induced a rapid dynamics of FOM-degrading communities, corresponding to the stimulation of bacterial phyla which have been previously described as copiotrophic organisms. However, the dynamics and the identity of the bacterial groups stimulated depended on the residue added, with Firmicutes dominating in the wheat treatment and Proteobacteria dominating in the alfalfa treatment after 3 days of incubation. In both treatments, SOM-degrading communities were dominated by Acidobacteria, Verrucomicrobia, and Gemmatimonadetes phyla which have been previously described as oligotrophic organisms. An early stimulation of SOM-degrading populations mainly belonging to Firmicutes and Bacteroidetes groups was observed in the alfalfa treatment whereas no change occurred in the wheat treatment. Our findings support the hypothesis that the succession of bacterial taxonomic groups occurring in SOM- and FOM-degrading communities during the degradation process may be an important driver of the PE, and consequently of carbon dynamics in soil.
Auteurs, date et publication :
Auteurs Noémie Pascault , Lionel Ranjard , Aurore Kaisermann , Dipankar Bachar , Richard Christen , Sébastien Terrat , Olivier Mathieu , Jean Lévêque , Christophe Mougel , Catherine Henault , Philippe Lemanceau , Michel Péan , Séverine Boiry , Sébastien Fontaine , Pierre-Alain Maron
Publication : Ecosystems
Date : 2013
Volume : 16
Issue : 5
Pages : 810-822
Catégorie(s)
#Genosol #INRAEAuteurs, date et publication :
Auteurs Vincent Berthon , Aldo Marchetto , Frédéric Rimet , Emmanuelle Dormia , Jean-Philippe Jenny , Cécile Pignol , Marie-Elodie Perga
Publication : Journal of Limnology
Date : 2013
Volume : 72
Issue : 3
Pages : 34