Éditeur(s) : HAL CCSD Elsevier
Résumé : Extracting and purifying a representative fraction of bacteria from soil is necessary for the application of many techniques of microbial ecology. Here the influence of different soil types on the quantitative and qualitative recovery of bacteria by soil grinding and Nycodenz density gradient centrifugation was investigated. Three soils presenting contrasted physicochemical characteristics were used for this study. For each soil, the total (AODC: acridine orange direct count) and culturable (cfu: colony-forming units) bacterial densities were measured in three distinct fractions: (i) the primary soil, (ii) the soil pellet (soil remaining after centrifugation), and (iii) the extracted cells. The automated-ribosomal intergenic spacer analysis (A-RISA) was used to characterize the community structure directly from the DNA extracted from each fraction. The physicochemical characteristics of soils were found to influence both the efficiency of bacterial cell recovery and the representativeness of the extracted cells in term of community structures between the different fractions. Surprisingly, the most representative extracted cells were obtained from the soil exhibiting the lowest efficiency of cell recovery. Our results demonstrated that quantitative and qualitative cell recovery using Nycodenz density gradient centrifugation are not necessarily related and could be differentially biased according to soil type.
ISSN: 1164-5563

hal-01031904
https://hal.archives-ouvertes.fr/hal-01031904
DOI : 10.1016/j.ejsobi.2005.08.003

Éditeur(s) : HAL CCSD Elsevier
Résumé : Understanding the pattern in spatial distribution of soil microbial processes is critical to understand the environmental factors that regulate them as well as to scale up these processes to ecosystem. Soil samples from a I ha tropical rainforest plot (Paracou, French Guiana) were analyzed according a nested sampling approach using different separation distances ranging from 0.4 to 40 m. The variability of substrate induced respiration (SIR) and of denitrification enzyme activity (DEA) was characterized in relation to various soil properties (total C and N contents, NIRS related index of soil organic matter quality, SOMQ and index of tree influence potential, IP). The variability of SIR and DEA was higher than that of environmental properties. The patterns of accumulated variance as a function of distance varied among the soil properties. The variability of SIR and DEA mainly occurred at small (1 m) scale (and at the 10-40 m-scales for SIR), probably reflecting the quality of litter input that results of the influence of local assemblage of different tree species, though changes in the soil N and C contents. Indeed, total soil C and N contents explained the microbial properties at every scale. Coefficients of codispersion showed that neither SOMQ nor IP did correlate with SIR and DEA, and confirmed that total C and N contents explained microbial properties in a scale dependent and complex manner. Such spatial dependency underlines the importance of soil heterogeneity in this tropical forest with implications for sampling strategies when studying the microbial processes and their response to disturbances. (C) 2012 Elsevier B.V. All rights reserved.
ISSN: 0016-7061

hal-01032409
https://hal.archives-ouvertes.fr/hal-01032409
DOI : 10.1016/j.geoderma.2012.12.009

Éditeur(s) : HAL CCSD
Résumé :   Diplôme : Master Recherche
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
Notre étude porte sur la caractérisation à l'échelle de l'hectare de la variabilité spatiale (1) du fonctionnement microbien du sol et (2) de sa stabilité (i.e. de sa réponse à un stress). Elle a été menée sur une forêt tropicale humide (forêt primaire) proche de Kourou en Guyane (site de Paracou). Les indicateurs fonctionnels utilisés sont les potentiels d'activités respiratoires (RP) et dénitrifiantes (OP). La variabilité spatiale du fonctionnement microbien du sol a fait l'objet d'un nombre important d'études mais très peu d'entre elles ont concerné ce type d'écosystème. Un autre aspect novateur réside dans la recherche de la variabilité spatiale de la stabilité du fonctionnement. A notre connaissance, il s'agit de la première étude de ce type en milieu tropical comme en milieu tempéré. Les principales conclusions sont les suivantes : (1) à l'échelle 10m (grille principale) les coefficients de variation (CV) des potentiels de fonction sont similaires pour les 2 processus et élevés (RP : 53% ; OP : 54%) au regard des valeurs de la littérature sur des milieux tempérés, mais RP et OP présentent des variabilités spatiales différentes à des échelles inférieures ; (2) l'utilisation d'un indice de densité locale (ID) des arbres n'a pas permis de mettre en évidence une corrélation entre les répartitions spatiales de la végétation et du fonctionnement microbien du sol. De même, aucun déterminisme clair de l'intensitè des potentiels microbiens n'a pu être dégagé par la prise en compte de la variabilité des caractéristiques physico-chimiques du sol; (3) un stress thermique génère à très court terme (résistance) un accroissement de la spatialisation du potentiel de respiration. A plus long terme, la variabilité inter-échantillons s'atténue pour retrouver ses valeurs initiales et, (4) l'activité originelle (avant stress) n'est pas corrélée avec la résistance et est négativement corrélée aux valeurs observées 15 et 30 jours après le stress. Outre son intérêt intrinsèque, cette étude vise à se doter de données de « cadrage » sur la forêt primaire (non perturbée) qui nous permettront d'accéder à de meilleures évaluations et compréhensions des mécanismes impliqués dans la réponse des écosystèmes tropicaux à l'anthropisation lors de projets en cours. Un exemple de ce type d'application est brièvement décrit.
https://hal.archives-ouvertes.fr/hal-01189259

hal-01189259
https://hal.archives-ouvertes.fr/hal-01189259
PRODINRA : 20250

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
Previous studies in lowland tropical rainforests of French Guiana showed that, among non-N2-fixing trees, two groups of late successional species contrasting in their leaf 15N natural abundance coexist, suggesting two different main ways of nitrogen acquisition. Two abundant late-successional species typically co-occurring in rainforests in French Guiana, namely Eperua falcata and Dicorynia guianensis, were chosen as representative of each group. Stable isotope techniques and measurements of potentials of microbial N transformation were performed to assess to what extent leaf 15N natural abundance of these species could be related to (i) d15N signatures of soil mineral N sources and (ii) the capacity of soil to express nitrification and denitrification (both processes being directly involved in the balance between NH4 + and NO3 - ). Soil d15N-NH4 + was roughly similar to leaf d15N of D. guianensis (around 3.5%), suggesting a preferential use of NH4 +, whereas in E. falcata, leaf d15N values were closer to root d15N-NO3 _ values (0.2 and _2.0%, respectively), suggesting a preferential use of NO3 _. These differences in N source utilization were not accompanied by differences in availability in soil NO3 _ or in intensity of microbial functions responsible for soil N mineral evolution. However, (i) under both tree species, these functions showed clear spatial partitioning, with denitrification occurring potentially in soil and nitrification in the litter layer, and (ii) E. falcata fine roots colonized the litter layer much more strongly than D. guianensis fine roots. This strongly suggests that (i) the contrasted leaf d15N values found in the two late-successional species reveal distinct N acquisition strategies and (ii) the ability of roots to predominantly exploit the litter layer (E. falcata) or the soil (D. guianensis) may constitute an important explanation of the observed differences. A complementarity between tree species, based on mineral N resource partitioning (itself resulting from a spatially structured location of the microbial functions responsible for the balance between NH4 + and NO3 - ), can thus be supposed.
ISSN: 0038-0717

hal-01032035
https://hal.archives-ouvertes.fr/hal-01032035
DOI : 10.1016/j.soilbio.2007.09.011

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Understanding the ability of ecosystem processes to resist to and to recover from disturbances is critical to sustainable land use. However, the spatial variability of the stability has rarely been addressed. Here, we investigated the functional stability of a soil microbial process for 24 soils collected from adjacent locations from a 0.3 ha tropical rainforest plot in Paracou, French Guiana. The 24 locations were characterized regarding soil chemical and biological (microbial diversity) parameters and forest structure. The corresponding soils were submitted to an experimental transient heat disturbance during a microcosm experiment. The response of the respiration process was followed using substrate-induced respiration (SIR). The response of soil SIR to heat disturbance varied widely between samples. The variability of the SIR response increased just after the disturbance, and a global rather homogeneous decrease in SIR rates was observed 15 and 30 days after. The stability of SIR in response to heat disturbance could not be related to either the genetic or the metabolic diversity of the microbial community. The initial level of SIR before the disturbance was the soil variable that best correlated with the impact of the disturbance: the soil locations with the highest initial SIR rates were the most affected 15 and 30 days after the heat disturbance. Such a heterogeneous response suggests that the response of soil processes to a disturbance will be difficult to assess from only local-scale analyses and highlights the need for spatial explicitness in understanding biogeochemical processes.
ISSN: 1439-0108

hal-01204209
https://hal.archives-ouvertes.fr/hal-01204209
DOI : 10.1007/s11368-012-0528-7
PRODINRA : 214444

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
Microbial-based indicators, such as C and N contents or microbial functions involved in C and N cycles, are currently used to describe the status of soils in disturbed areas. Microbial functions are more accurate indicators but their measurement for studies at the ecosystem level remains problematical because of the huge spatial variability of these processes and, consequently, of the large number of soil samples which must be analyzed. Our goal was to test the capacity of near-infrared reflectance spectroscopy (NIRS) to predict respiration and denitrification but also carbon and nitrogen contents of soils submitted to various procedures of restoration. To achieve this objective, we took advantage of an experiment conducted on a reforestation system established after open-cast gold mining in French Guiana. In this experimental station, plantations of various ages and various soil textures were at our disposal. Our results showed that both plantations and soil texture had a strong impact on the recovery of soil functioning: carbon and nitrogen contents, respiration and denitrification increased with age of plantation and clay content. Calibrations were performed between spectral data and microbial-based indicators using partial least squares regression (PLS). The results showed that C and N contents were accurately predicted. Microbial functions were less precisely predicted with results more accurate on clayey soils than on sandy soils. In clayey soils, perturbed or restored soils and the year of plantation were discriminated very efficiently through principal component analyses of spectral signatures (over 80% of variance explained on the first two axes). Near-infrared spectroscopy may thus be extended to the prediction of functional soil parameters, but the capacity of this method must be strengthened by expending the databases with other soils in other contexts. The possibility of using NIRS provides many opportunities for understanding both the temporal dynamics and the spatial variability of the recovery of key microbial functions during soil restoration.
ISSN: 0929-1393

hal-01032188
https://hal.archives-ouvertes.fr/hal-01032188
DOI : 10.1016/j.apsoil.2007.07.001