Résumé
Wastewater can be recycled in agricultural soil as fertilizer to increase crop yields. However, adding wastewater induces sometimes ecotoxicological issues such as pollution by toxic compounds, which may lead to the loss of arable land. Bioenergy crops such as Miscanthus x giganteus have been tested to rehabilitate polluted soils, but the impact of Miscanthus on soil microbes is unknown. Here, we evaluated the effects of Miscanthus cropping on bacterial and fungal taxonomic composition in a wastewater-contaminated soil using synchronic and diachronic evaluation strategies. A 3-year field experiment close to Paris was set up on an agricultural site irrigated by raw wastewater for more than one century, thus resulting in strong metal and organic contamination. Soil microbial taxonomic composition was characterized by direct analysis of soil DNA using metagenomic tools such as 454 pyrosequencing of ribosomal genes. Our results demonstrate that Miscanthus cropping stimulates specific populations of bacteria such as Rhizobiales, increased by 1.4 in relative abundance, Nistrospira (x1.5), Azospira (x2), and Gemmatimonas (x2), and fungi: Glomeromycota (x3) and Mortierella (x1.5) for fungi. Noteworthy, these microbial genera are known to be strongly involved in plant symbiosis, organic matter mineralization, and nutrient cycling. Overall our findings show that Miscanthus cropping enhances regeneration of soil microbiological functions and services in polluted soil by stimulating populations beneficial for soil fertility and crop production.
Auteurs, date et publication :
Auteurs Emilie Bourgeois , Samuel Dequiedt , Melanie Lelievre , Folkert van Oort , Isabelle Lamy , Lionel Ranjard , Pierre Alain Maron
Publication : Environmental Chemistry Letters
Date : 2025
Volume : 13
Issue : 4
Pages : 503-511
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs C. Chenu , S. Abiven , M. Annabi , S. Barray , M. Bertrand , F. Bureau , D.J. Cosentino , F. Darboux , O. Duval , L. Fourrié , C. Francou , S. Houot , C. Jolivet , K. Laval , Y. Le Bissonnais , L. Lemée , S. Menasseri , J.P. Petraud , B. Verbèque
Publication : Etude et Gestion des Sols
Date : 2025
Volume : 18
Issue : 3
Pages : 161-174
Catégorie(s)
#INRAE #PRO #PRO QualiAgroAuteurs, date et publication :
Auteurs Sabine Allou , Anne Tréguier , Nicolas Houdouin , Jean-Pierre Destouches , Laurent Beaulaton , Frédéric Marchand , Didier Azam
Date : 2025
Pages : 41
Catégorie(s)
#INRAE #PEARLAuteurs, date et publication :
Auteurs Anne Tréguier , Nicolas Houdouin , Jean-Pierre Destouches , Laurent Beaulaton , Frédéric Marchand , Didier Azam
Date : 2025
Pages : 113
Catégorie(s)
#INRAE #PEARLAuteurs, date et publication :
Auteurs F. Watteau , M.F. Dignac , A. Bouchard , A. Revallier , S. Houot
Publication : Frontiers in Sustainable Food Systems
Date : 2025
Volume : 2
Issue : Article no 81
Pages : 14 p.
Catégorie(s)
#INRAE #PRO #PRO QualiAgroRésumé
Soil microbes play major agricultural functions such as the transformation of soil organic matter into plant fertilizers. The effects of agricultural practices on soil microbes at the scale of plots, from meters to hectare, are well documented. However, the impact at soil microscale, from micrometers to millimeters, is much less known. Therefore, we studied bacterial community density and diversity at microscale in crop soil under grassland, tillage, and no tillage. We fractionated macroaggregates, from 2,000 to 250 μm and from 250 to 63 μm; microaggregates, from 63–20 μm and 20–2 μm; and clay particles, lower than 2 μm. We measured the bacterial density and diversity by real-time PCR and 454-pyrosequencing of 16S rRNA genes of soil DNA, respectively. Results show that bacterial density and diversity were heterogeneous among size aggregates. Tillage decreased bacterial density from 22 to 74 %, and diversity from 4 to 11 %, and changed taxonomic groups in micro- and macroaggregates. This change led to the homogenization of bacterial communities and is explained by a higher protection of microaggregates. As a consequence, microaggregates contained similar bacterial communities whatever the land management is, whereas strong differences were observed between communities inhabiting macroaggregates. These findings demonstrate that bacterial diversity in microaggregates was mainly controlled by historical contingency, whereas bacterial communities in macroaggregates are shaped by contemporary perturbations. Our findings thus revealed unprecedented insights of the effect of agriculture on soil microbes. Potential applications include using crop management options that preserve macroaggregate structure to promote soil heterogeneity and therefore microbial diversity.
Auteurs, date et publication :
Auteurs Florentin Constancias , Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Simon Aussems , Virginie Nowak , Jean-Philippe Guillemin , Aline Bonnotte , Luc Biju-Duval , Aline Navel , Jean MF Martins , Pierre-Alain Maron , Lionel Ranjard
Publication : Agronomy for Sustainable Development
Date : 2014
Volume : 34
Issue : 4
Pages : 831-840
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs M.N. Bravin , A. Versini , F. Feder , L. Le Mézo
Publication : Cahier technique CaroCanne no 45
Date : 2025
Pages : 8 p.
Catégorie(s)
#INRAE #PRORésumé
Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site.
Auteurs, date et publication :
Auteurs L. C. Kelly , Y. Colin , M.-P. Turpault , S. Uroz
Publication : Microbial Ecology
Date : 2016
Volume : 72
Issue : 2
Pages : 428-442
Catégorie(s)
#FORET Breuil #INRAERésumé
Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.
Auteurs, date et publication :
Auteurs Y. Colin , O. Nicolitch , M.-P. Turpault , S. Uroz
Publication : Applied and environmental microbiology
Date : 2017
Volume : 83
Issue : 5
Catégorie(s)
#FORET Breuil #INRAERésumé
Minerals constitute an ecological niche poorly investigated in the soil, in spite of their important role in biogeochemical cycles and plant nutrition. To evaluate the impact of minerals on the structure of the soil bacterial communities, we compared the bacterial diversity on mineral surfaces and in the surrounding soil. Three pure and calibrated minerals (apatite, plagioclase and a mix of phlogopite-quartz) were buried into the organo-mineral layer of a forest soil. After a 4-year incubation in soil conditions, mineral weathering and microbial colonization were evaluated. Apatite and plagioclase were the only two significantly weathered minerals. The analysis of the 16S rRNA gene sequences generated by the cloning-sequencing procedure revealed that bacterial diversity was higher in the surrounding soil and on the unweathered phlogopite-quartz samples compared with the other minerals. Moreover, a multivariate analysis based on the relative abundance of the main taxonomic groups in each compartments of origin demonstrated that the bacterial communities from the bulk soil differed from that colonizing the minerals. A significant correlation was obtained between the dissolution rate of the minerals and the relative abundance of Beta-proteobacteria detected. Notably, many sequences coming from bacteria colonizing the mineral surfaces, whatever the mineral, harbored high similarity with efficient mineral weathering bacteria belonging to Burkholderia and Collimonas genera, previously isolated on the same experimental site. Taken together, the present results provide new highlights concerning the bacterial communities colonizing minerals surfaces in the soil and suggests that the minerals create true ecological niches: the mineralosphere.
Auteurs, date et publication :
Auteurs S. Uroz , M. P. Turpault , C. Delaruelle , L. Mareschal , J. -C. Pierrat , P. Frey-Klett
Publication : Geomicrobiology Journal
Date : 2025
Volume : 29
Issue : 1
Pages : 88-98