Auteurs, date et publication :
Auteurs Cintia Blanco Nouche , Carine Cochet , Marie-Pierre Turpault , Stéphane Uroz
Publication : npj Materials Degradation
Date : 2024
Volume : 8
Issue : 1
Pages : 129
Catégorie(s)
#FORET Breuil #INRAERésumé
While mineral weathering (MWe) plays a key role in plant growth promotion and soil fertility, the molecular mechanisms and the genes used by bacteria to weather minerals remain poorly characterized. Acidification-based dissolution is considered the primary mechanism used by bacteria. This mechanism is historically associated with the conversion of glucose to protons and gluconic acid through the action of particu lar glucose dehydrogenases (GDH) dependent on the pyrroquinoline quinone (PQQ) cofactor. Recently, bacteria lacking the GDH-PQQ system have been shown to perform the same enzymatic conversion with a glucose/methanol/choline (GMC) FAD-dependent oxidoreductase. Determining whether this particular enzyme is specific or widespread is especially important in terms of ecology and evolution. Genome analysis of the effective MWe strain Caballeronia mineralivorans PML1(12) revealed the presence of both systems (i.e., GDH-PQQ and several GMC oxidoreductases). The combination of mutagenesis, functional assays, and geochemical analyses demonstrated the key role of one of these GMC oxidoreductases in the mineral weathering ability of strain PML1(12) and the importance of the carbon source metabolized. Mass spectrometry confirmed the conversion of glucose to gluconic acid. Phylogenetic analyses highlighted a good relatedness of this new GMC oxidoreductase with GMC oxidoreductases presenting a GDH activity in Burkholderia cepacia and Collimonas pratensis and conferring its mineral weathering ability to the last one. Together, our analyses expand the number of bacteria capable of weathering minerals using GMC oxidoreductases, showing that such enzymes are not restricted to Collimonas.
Auteurs, date et publication :
Auteurs Cintia Blanco Nouche , Laura Picard , Carine Cochet , Cedric Paris , Philippe Oger , Marie-Pierre Turpault , Stéphane Uroz , Arpita Bose
Publication : Applied and Environmental Microbiology
Date : 2024
Volume : 90
Issue : 12
Pages : e01221-24
Catégorie(s)
#FORET Breuil #INRAERésumé
Calcium dissolved deposition shows an unusual spatial structure in France, probably due to the contribution of southern air masses from Mediterranean Sea and Saharan desert. These masses are often loaded with terrigenous particles that contain carbonates. However, no precise relationship has been quantified between dissolved Ca and mineral dust deposition (MDD). The database of the French network RENECOFOR, gathering atmospheric deposition <0.45 mu m in 27 sites near forests during 18 years, was used to determine the non-sea-salt atmospheric deposition over France. This study (1) explores the relationship between dissolved components to decipher their origin in atmospheric deposition nearby forests and (2) tests the use of dissolved Ca and Mg as proxies for MDD. In the RENECOFOR database, non-sea-salt Ca (nssCa) preferentially deposited between May and August. MDD observed in RENECOFOR was synchronic with high nssCa deposition, particularly in June 2008, when air mass highly loaded with Saharan dust covered France. The dissolution of this mineral dust likely contributed to the nssCa deposition of this period and suggested a relationship between the depositions of nssCa and MDD. Then, MDD was specifically sampled with dissolved deposition in four sampling sites. Encouraging relationships were found between MDD and the depositions of nssMg and nssCa, suggesting that the latter could be used as a proxy for MDD in regions where it is not monitored, and in a retrospective approach in order to calculate nutrient fluxes.
Auteurs, date et publication :
Auteurs Emeline Lequy , Manuel Nicolas , Sebastien Conil , Marie-Pierre Turpault
Publication : Water, air and soil pollution
Date : 2013
Volume : 224
Issue : 9
Catégorie(s)
#FORET Breuil #INRAERésumé
We compared the properties of the clay mineral fraction and the composition of soil solutions in a Fagus sylvatica coppice (native forest) and four adjacent plantations of Pseudotsuga menziesii, Pinus nigra, Picea abies and Quercus sessiliflora planted in 1976. The results revealed changes of clay fraction properties due to tree species effect. Clay samples from Douglas fir and pine stands differ when compared to other species. Twenty-eight years after planting, we observed the following changes: a more pronounced swelling after citrate extraction and ethylene glycol solvation, a higher CEC and a smaller poorly crystallised aluminium content. All these changes affecting the clay fraction agreed well with soil solution analyses which revealed high NO3 (-), H+ and Al concentrations under Douglas fir and pine. These changes were explained by a strong net nitrification under Douglas fir and pine stands when compared with other tree species. The higher NO3 (-) concentrations in soil solutions should be linked to the presence, type and activity of ammonia-oxiding bacteria which are likely influenced by tree species. The production of NO3 (-) in excess of biological demand leads to a net production of hydrogen ion and enhances the dissolution of poorly crystallised Al-minerals. Secondary Al-bearing minerals constituted the principal acid-consuming system in these soils. As a consequence, the depletion of interlayer spaces of hydroxyinterlayered minerals increases the number of sites for exchangeable cation fixation and increases CEC of the clay fraction. The dissolution of Al oxy-hydroxides explain the increase in Al concentrations of soil solutions under Douglas fir and pine stands when compared to other species. Nitrate and dissolved aluminium were conjointly leached in the soil solutions. A change in environmental conditions, like an introduction of tree species, enough modifies soil processes to induce significant changes in the soil mineralogical composition even over a period of time as short as some tens of years. Generally, mineral weathering has been considered to be very slow and unlikely to change over tens of years, resulting in few studies capable of detecting changes in mineralogy. This study appears to have detected changes in clay mineralogy during a period of 28 years after the planting of forest species. Our study represents a single location with a limited block design, but causes us to conclude that the observed changes could be widely representative. Where available, archived samples should be utilized and long-term experiments set up so that similar changes can be tested for and detected using more robust designs. The plausible hypothesis we present to explain apparent changes in clay mineralogy has strong relevance to the sustainable management of land.
Auteurs, date et publication :
Auteurs Louis Mareschal , Marie-Pierre Turpault , Pascal Bonnaud , Jacques Ranger
Publication : Biogeochemistry
Date : 2013
Volume : 112
Issue : 1-3
Pages : 293-309
Catégorie(s)
#FORET Breuil #INRAEAuteurs, date et publication :
Auteurs Yves Thiry , Taku Tanaka , Maïté Bueno , Paulina Pisarek , Marine Roulier , Hervé Gallard , Arnaud Legout , Manuel Nicolas
Publication : Science of The Total Environment
Date : 2025
Volume : 831
Pages : 154901
Catégorie(s)
#FORET Breuil #INRAERésumé
We developed a process-oriented model called NutsFor that simulates nutrient cycling of major cations (Ca, Mg, K, Al, NH4, Na) and anions (NO3, SO4, Cl) and the stable isotope tracers for each of the respective elements at the scale of an ecosystem (isotopic fractionation are not simulated). We tested the ability of NutsFor to reproduce major element and stable isotope tracer (Mg-26 and Ca-44) cycling with the data from 35-yr old beech stand in France. NutsFor correctly reproduced the measured trends in soil solution chemistry for most major elements. The high similarity between modeled and measured distribution of Mg-26 and Ca-44 tracers in the ecosystem provided a unique and robust way to evaluate the hypotheses grounding the model and study the efficiency of Mg and Ca cycling at this very nutrient-poor site. (C) 2017 Elsevier Ltd. All rights reserved.
Auteurs, date et publication :
Auteurs G. van der Heijden , S. Belyazid , E. Dambrine , Jacques Ranger , A. Legout
Publication : Environmental Modelling & Software
Date : 2017
Volume : 95
Pages : 365-380
Catégorie(s)
#FORET Breuil #INRAERésumé
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
Catégorie(s)
#FORET Breuil #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