Evaluation de l'impact de la culture de plantes d'intérêt agronomique (blé, maîs, colza et soja) sur la biodégradation de produits phytosanitaires (atrazine, diclofop-méthyl, bentazone, diuron, isoproturon et pendiméthaline) dans le sol (analyse phénoménologique et moléculaire de la stimulation de la biodégradation de l'atrazine dans la rhizosphère du maïs)

L'utilisation intensive de produits phytosanitaires en agriculture a engendré une contamination importante du sol et des eaux superficielles et profondes. Parmi les solutions biologiques (biostimulation et bioaugmentation) envisagées pour diminuer ces contaminations, la rhizostimulation consiste à tirer profit du fait que la plante modifie considérablement les conditions notamment biologiques du sol sous l'influence de son système racinaire en favorisant l'installation et le développement de populations de micro-organismes. Celles-ci peuvent, le cas échéant, assurer la biodégradation des molécules xénobiotiques. Le travail a mis en évidence l'effet bénéfique produit par la culture d'une plante d'intérêt agronomique sur le maintien de la capacité de minéralisation de la microflore du sol vis à vis de certains herbicides (bentazone, diuron, isoproturoH et pendiméthaline) dégradés par co-métabolisme. Outre cet effet, nous avons montré que la culture pouvait favoriser l'apparition et la mise en place de la dégradation accélérée pour l'atrazine et le diclofop-méthyl. L'approche phénoménologique et moléculaire conduite pour appréhender l'effet biostimulant du maïs sur la biodégradation de l'atrazine a montré que la communauté bactérienne possédant le gène de dégradation atz C était fortement augmentée dans le sol rhizosphérique comparé au sol nu. Par contre, la technique RISA n'a pas permis de mettre en évidence de changement majeur dans la structure des communautés bactériennes du sol. Enfin, l'isolement de souches dégradantes a surtout révélé les limites des techniques traditionnelles et le fait que l'image de la diversité des communautés bactériennes obtenue n'est certainement pas un reflet réel de l'ensemble des communautés dégradantes présentes et du polymorphisme des gènes impliqués. Elle a toutefois permis l'isolement d'une souche dégradant l'atrazine (Nocardioides sp.) et d'une souche dégradant le diclofop-méthyl (Sinorhizobium BKIO).NANCY/VANDOEUVRE-INPL (545472102) / SudocSudocFranceF

Caractérisation de la communauté bactérienne impliquée dans la minéralisation du soufre organique dans les rhizosphères de colza et d'orge

Depuis une trentaine d années, l élément soufre (S) est devenu un des éléments les plus limitants pour la croissance des cultures du fait de nombreux facteurs, comme les nouvelles pratiques de gestion des sols et la limitation des pollutions anthropiques. Ainsi, des carences en S apparaissent au sein des cultures et particulièrement en Europe de l Ouest. Nos objectifs ont été d appréhender la communauté bactérienne fonctionnelle du sol qui, de par son activité arylsulfatase, permet la minéralisation de la forme majoritaire du S en sulfate (forme de S assimilée par les plantes). D après nos résultats, la densité de cette communauté bactérienne fonctionnelle est plus importante dans les environnements où le S est potentiellement plus limitant (rhizosphère de colza vs orge). De plus, cette communauté fonctionnelle apparaît diversifiée et est notamment composée de divers genres bactériens affiliés à de nombreuses classes taxonomiques (Actinobactéries, Firmicutes, a-, ß-, d-, ?-protéobactéries et aux Planctomycètes). De plus, au sein de la rhizosphère du colza, des variations temporelles de structure et de diversité de cette communauté fonctionnelle ont également été mises en évidence. En conclusion, l ensemble des expérimentations semble mettre en évidence, que la communauté bactérienne fonctionnelle minéralisant les esters de sulfate apparaît stimulée sous colza comparée à celle présente sous orge. Ces résultats laissent présager le rôle potentiel de cette communauté fonctionnelle dans le turn-over du S dans les sols agricoles et la mise en place d approches d écologie fonctionnelle supplémentaires permettrait de mieux cerner son implication dans la nutrition soufrée des culturesOver the past thirty years, Sulfur (S) has become one of the most limiting element for crop growth due to many factors, such as new soil management practices and depletion of the anthropogenic pollution. Thus, S deficiencies increase in crops, particularly in Western Europe. Our objectives were to apprehend the soil functional bacterial community which, by its arylsulfatase activity, allows the mineralization of the majority form of S to sulfate (form of S assimilated by plants). Based on our results, the density of the functional bacterial community are higher in environments where S is potentially limiting (rapeseed rhizosphere vs. barley rhizosphere). Moreover, this functional community appeared diverse and belonging to several taxonomic classes (Actinobacteria, firmicutes, a-, ß-, d-, ?-proteobacteria and Planctomycetea). In addition, in the rapeseed rhizosphere, temporal variations of the structure and diversity of this functional community have also been highlighted. In conclusion, our experiments appear to demonstrate that this functional bacterial community mineralizing sulphate esters appeared stimulated in rapeseed rhizosphere compared to that present in barley rhizosphere. However, the establishment of new approaches to allow additional functional ecology bases for this community should be made to allow a better understanding of its potential involvement in sulfur nutrition of cropsNANCY-INPL-Bib. électronique (545479901) / SudocSudocFranceF

Spatial distribution of the abundance and activity of the sulfate ester-hydrolyzing microbial community in a rape field

International audienceSulfur (S) plays a vital role in plant metabolism, and the detrimental impact of S deficiency in several field crops has increased over the last 30 years. The bio-availability of organic S to plant depends on arylsulfatase (ARS), a key enzyme for S mineralization in soil. In this study, we characterized the spatial variability of ARS activity in an agricultural soil cropped with the rape plant (Brassica napus). Because rape requires relatively large amounts of S per yield unit compared to most grain crops, it is very sensitive to S deprivation similarly to the other plants of the Brassicaceae family, with consequences for seed quality and yield.The spatial variability of (a) ARS activity, (b) the abundance of culturable bacteria possessing the ARS, and (c) soil properties (temperature, soil pH, SO (4) (2-) -S (sulfate-S) content, labile carbon (C) and nitrogen (N), soil microbial biomass carbon SMB-C, and nitrogen SMB-N) was estimated at 40 sites within a rape field, using a 4 x 5-m sampling grid. Geostatistics were used to model the spatial distribution of the measured variables, and relationships between variables were tested using linear statistical analyses.The total ARS activity showed a low variability ranging between 69.0 and 153.1 mu g p-nitrophenol g(-1) dry soil h(-1) while the abundance of the culturable ARS community ranged within one order of magnitude. The distribution of both the abundance and activity of the ARS community exhibited spatial dependence in 800 m(2) agricultural field.The spatial pattern of ARS activity in the field was correlated with several soil properties, and results suggest that soil pH, labile C and N, and SBM-C/SBM-N ratio were the main parameters linked to the ARS activity rather than the abundance of the culturable ARS bacterial community or the SO (4) (2-) -S concentratio

Soil Microbial Communities Involved in Proteolysis and Sulfate-Ester Hydrolysis Are More Influenced by Interannual Variability than by Crop Sequence

Proteases, catalysing protein hydrolysis, and arylsulfatases, catalysing sulfate-ester hydrolysis, are key microbial enzymes for N and S mineralization in soil. However, knowledge gaps remain regarding the effect of crop successions and seasonal and interannual meteorological variations on microbial communities responsible for those activities. Here, we compared the effect of six cropping sequences on the abundance and activity of microbial communities involved in proteolysis and sulfate-ester hydrolysis in northern France over four years, with two sampling dates per year. Crop sequences impacted soil microbial communities involved in proteolysis but not those involved in sulfate-ester hydrolysis. Oilseed rape following wheat presented a higher abundance of fungal 18S rDNA, culturable bacteria and alkaline metalloprotease genes and higher protease activity than other crop sequences (wheat following oilseed rape or pea, barley following wheat and pea following barley). Net N and S mineralization was not impacted by the cropping sequence. However, interannual variability of microbial parameters was large, and largely overcame the effect of crop sequences. Precipitation variability between years was the likely cause of this effect. In conclusion, the interaction between current crop, previous crops and yearly meteorology can strongly impact the soil microbial communities in agroecosystems

Fertilité des sols en systèmes bovins laitiers : recherche d’indicateurs microbiologiques et évaluation de l’effet des pratiques agricoles

International audienc

Growth dynamics of fast-growing tree species in mixed forestry and agroforestry plantations

International audienceIn recent years, plantations of fast-growing tree species have emerged as a possible way to meet the increasing demand for biomass for renewable energy in Europe. Agroforestry plantations including fast-growing tree species could be an attractive option because they reduce land competition for biomass and food production while providing forest benefits. Today, the species interactions that determine whether a given mixture will be more productive than the corresponding monocultures are still poorly understood. Our objective was to assess the performance of fast-growing trees, i.e. poplar (Populus nigra × P. deltoides) and alder (Alnus glutinosa), in association with herbaceous species either N 2-fixing species (succession alfalfa (Medicago sativa) and clover (Trifolium pratense)) or graminoids (succession of wheat (Triticum aestivum)-triticale (Triticosecale)-temporary grassland consisting of mixtures of perennial ryegrass (Lolium perenne) and fescue (Festuca ovina)), respectively, and in association together. We compared tree growth in mixed stands to growth in the respective tree monocultures. An experimental plantation composed of three blocks including the different treatments was set up in 2014 in northeastern France. In the forest mixture, poplar and alder were planted in alternating rows, and in the agro-forestry plots, every second line of trees was replaced by the crops. No fertilizers (of any kind) were used during the experiments. During six growing seasons, tree growth (height and diameter at breast height) was monitored monthly in the agroforestry stands, the forest mixture stand and the two tree monocultures. By the end of 2019, poplar stem height in association with N 2-fixing crops (alfalfa, then clover) was higher than in the forest mixture and the monoculture. During the warmest growing season with a marked dry period in June-July (2018), poplar height growth rate in the agroforestry treatment was between three and five times higher than for the poplars in the monoculture and the forest mixture. A facilitation process in the agroforestry plantations could explain this result due to a significant enrichment of the soil in nitrogen by the N 2-fixing crops. This result only appeared several years after tree planting, and management actions were necessary in order to control the strong competition between crops and trees during the early stages. In the forest mixture, poplars associated with alders were smaller than in their monoculture, in spite of a stratification of the canopies of the two species. For alders, tree growth did not appear to be affected by either an association with graminoids or with poplar

Additions of maize root mucilage to soil changed the structure of the bacterial community

International audienceThe organic compounds released from roots (rhizodeposits) stimulate the growth of the rhizosphere microbial community. They may be responsible for the differences in the structure of the microbial communities commonly observed between the rhizosphere and the bulk soil. Rhizodeposits consists of a broad range of compounds including root mucilage. The aim of this study was to investigate if additions of maize root mucilage, at a rate of 70 μg C g−1 day−1 for 15 days, to an agricultural soil could affect the structure of the bacterial community. Mucilage additions moderately increased microbial C (+23% increase relative to control), which suggests that the turnover rate of microorganisms consuming this substrate was high. Consistent with this, the number of cultivable bacteria was enhanced by +450%. Catabolic (Biolog® GN2) and 16S–23S intergenic spacer fingerprints exhibited significant differences between control and mucilage treatments. These data indicate that mucilage can affect both the metabolic and genetic structure of the bacterial community as shown by a greater catabolic potential for carbohydrates. We concluded that mucilage is likely to significantly contribute to differences in the structure of the bacterial communities present in the rhizosphere compared to the bulk soil

Effects of glucose on sulphur dynamics in calcareous arable and fallow soils

The magnitude of microbial sulphur (S) immobilization as well as the synthesis of inducible enzymes such as arylsulphatase (ARS) are basically controlled by carbon (C) additions. In order to assess soil fertility after a period of fallow a better knowledge of S dynamics including S immobilization and ARS activities of a natural fallow soil (3.9% organic C) in comparison with an arable soil (2.3% organic C) is required. Thus, the objectives of this work were to (i) examine the effects of glucose-C additions, a representative labile organic C in the rhizosphere, on the intensities of S immobilization in relation with ARS activities and (ii) distinguish extra- and intra-cellular ARS activities induced by glucose-C applied to the two soils. The amounts of glucose-C were added at six rates (0, 125, 250, 500, 750 and 1000 mg kg-1 soil) to the studied soils after a 1-week soil pre-incubation at 25°C and then incubated one week more (to promote microbial S immobilization over S remineralization) with a Na235S04 solution (518 kBq kg-1 dry soil and 20 mg S kg-1 soil) prior to analysis. All soils received the same amount of 80 mg N kg soil as NaN03. Soil S042 -S content was extracted with 0.009 M Ca (H2P04)2. The use of 35S makes it possible to calculate the amount of fertilizer S immobilized. The ARS method used determines the total ARS which corresponds to the ARS located either outside the cells (extra-cellular ARS) or inside the cells (intra-cellular ARS). Recovery tests using 0.009 M Ca(H2P04)2 showed a 100% recovery of S042- -35S introduced in the sample and extracted immediately after addition. Therefore, physical immobilization (adsorption of S042- -35S onto soil particles) was excluded and the 35S immobilized corresponded exclusively to microbial immobilization. Glucose-C additions increased both microbial S immobilization and ARS activities. Related to the rate 0 (control), largest increase in immobilized-S was observed in the arable soil (300.7%) compared with the fallow soil (153.1%). In contrast, the ARS activity increased by 16.4% in the arable soil versus 32.1% in the fallow soil. These results indicate that glucose proportionately affected more the intensities of immobilized-S than those of ARS. We found positive and significant correlation coefficients of ARS activities with immobilized-S in the arable soil (r = 0.86, P < 0.05) and in the fallow soil (r = 0.83, P < 0.05). Accordingly, by extrapolating to zero immobilized-S (or microbial biomass-S), the results showed a presence of extra-cellular ARS activity of 38.7 mg jc-nitrophenol kg-1 soil h-1 in the arable soil and of 63.5 mg jc-nitrophenol kg-1 soil h-1 in the fallow soil. Without glucose-C (rate 0), values of 3.7 and 20.0 mg jc-nitrophenol kg-1 soil h-1 of intra-cellular ARS activity (difference between total ARS and extra-cellular ARS activity) were found in the arable and fallow soil, respectively. It was concluded that fallowing generated greater ARS activities. Fallow regime re-established soil fertility through increasing soil organic matter content and thereby enhancing the activities of extra- and intra-cellular ARS enzyme compared with the arable soil that is regularly disturbed by tillage, pesticide treatment and fertilization

La nature du sol et la composition floristique comme facteurs de modulation de la diversité et de la fonctionnalité des communautés microbiennes en prairie permanente

National audienceLa composition floristique, le mode d’exploitation (fauche, pâturage), l’intensité d’exploitation (chargement, fréquence des coupes, fertilisation) et la pérennité de la couverture végétale sont connus comme étant des facteurs déterminants du fonctionnement des prairies permanentes (Gaujour et al. 2012). Ces pratiques de gestion peuvent modifier les stocks de C directement en modulant les entrées de matières organiques (MO) (litière et/ou effluents d’élevage) et indirectement en orientant la composition et le fonctionnement des communautés végétales ce qui pourrait agir sur le temps de résidence et la localisation de la MO (Hassink et Neeteson 1991). Ce projet a pour objectif de caractériser les pools de C organique du sol et les communautés bactériennes sous des prairies permanentes différant selon leur composition floristique et la nature de l’antécédent en termes de couverture de sol (3 habitats : culture, forêt, prairie). L’hypothèse de ce travail est que ces facteurs en modifiant la nature des pools de C du sol (labile vs récalcitrant) ont sélectionné des communautés bactériennes différentes tant du point de vue de la diversité génétique que de leurs traits fonctionnels en lien avec la minéralisation des MO. Pour valider cette hypothèse, des échantillons de sol ont été prélevés en mai 2017 sur 12 parcelles de prairies (4 parcelles par habitat) sur lesquelles des relevés de composition floristique ont été effectués. Les résultats montrent que la composition floristique des 12 parcelles de prairies permanentes échantillonnées se différencie selon la nature de l’antécédent. Des différences de pH et de teneurs en C entre les sols de 3 types de prairies étudiées. Les activités enzymatiques (en lien avec les cycles biogéochimiques) mettent en évidence des différences selon l’antécédent de couverture du sol suggérant des fonctionnalités différentielles liées d’une part au temps de résidence des pools de C et d’autre part à des différences de diversité des communautés microbiennes du sol