Les phénols de la lignine et le 13C, traceurs de l'origine des matières organiques du sol

Abstract In spodosols of Gascony (France), conversion of maritime pine stands into maize cropping leads to an incorporation of maize organic matter, which changed the isotopic (δ13C) and phenolic signature in A and L horizons of soil. Hydrolysis of phenol lignin in forests and cultivated soils showed the predominance of vanillic units under forest and the early but moderate incorporation of cinnamic acids. Incorporation of syringic units appeared higher, related to a large maize production of stable syringic phenols. Syringic units represented a long-term marker of maize inputs in soils, whereas vanillic units revealed the degradation of forest organic matter.

THE FRENCH NATIONAL SOIL QUALITY MONITORING NETWORK (RMQS) AS A SUPPORT FOR MONITORING SOIL BIODIVERSITY: past, present and future programs

Soil biodiversity would represent about 25% of the species on Earth. It is threatened, and although it is essential for human activities, it remains largely unknown. The French National Soil Quality Monitoring Network (RMQS) has a significant impact in removing the grey areas through its programs on soil microorganisms, soil meso and macrofauna, meadow flora, truffles and more recently enzymatic activities. The first distribution maps of bacterial phyla on a national scale and of soil fauna on a regional scale (in Brittany) have been developed. For the white truffle, three new areas of presence have been identified in France. The habitats of the bacteria were also described for the first ti…

A soil biodiversity survey coupled with the national soil quality monitoring network?

International audience; Despite its importance for human activities, soil biodiversity remains largely unknown and threatened. Aware of the need for large-scale monitoring, we studied the feasibility to add a soil biodiversity survey (RMBS-Biodiversity) to the already existing French soil quality monitoring network (RMQS). We worked with soil biodiversity experts to couple RMBS-Biodiversity with RMQS i.e. to choose soil taxons and functions, the methodologies and the sampling design. According to the experts, the sampling design of RMQS fits with a soil biodiversitysurvey. We propose sampling protocols for i) bacteria and fungi, ii) protists, iii) nematodes, iv) mesofauna (particularly spri…

Biotic and abiotic soil properties influence survival of Listeria monocytogenes in soil

International audience; Listeria monocytogenes is a food-borne pathogen responsible for the potentially fatal disease listeriosis and terrestrial ecosystems have been hypothesized to be its natural reservoir. Therefore, identifying the key edaphic factors that influence its survival in soil is critical. We measured the survival of L. monocytogenes in a set of 100 soil samples belonging to the French Soil Quality Monitoring Network. This soil collection is meant to be representative of the pedology and land use of the whole French territory. The population of L. monocytogenes in inoculated microcosms was enumerated by plate count after 7, 14 and 84 days of incubation. Analysis of survival pr…

Diversité des communautés microbiennes telluriques à l'échelle du territoire national

Communication orale - résumé Session 5 : sols, biodiversité, écologie fontionnelleCommunication orale - résumé Session 5 : sols, biodiversité, écologie fontionnelle; absent

Caractérisation et dynamique du carbone organique du sol

Rapport final des recherches engagées dans le cadre du GIP ECOFOR "Fonctionnement de l'écosystème forestier landais"*INRA Orléans, Documentation de centre, Ardon 45166 Olivet Diffusion du document : INRA Orléans, Documentation de centre, Ardon 45166 Olivet; National audience

Adding a soil biodiversity monitoring to the French National Soil Quality Monitoring Network :the RMQS-Biodiversity

International audience

Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management

Aim The spatial organization of soil microbial communities on large scales and the identification of environmental factors structuring their distribution have been little investigated. The overall objective of this study was to determine the spatial patterning of microbial biomass in soils over a wide extent and to rank the environmental filters most influencing this distribution.

Bacterial social networks across the French National territory

EA SPE BIOME GENOSOL UB Agrosup EA SPE BIOME GENOSOL UB AgrosupEASPEBIOMEGENOSOL UB Agrosup; New generation sequencing evidenced that soil houses a huge microbial biodiversity. Based on these observations, it is now possible to better describe the spatial distribution of soil microbial communities, to study the ecological processes involved (environmental selection, dispersal limitations), and to compute the data to define the ecological attributes of soil microbial taxa. These huge datasets also offer the opportunity to study how soil microbial populations are interrelated. With this study, we revealed the first soil bacterial "social" network across French national territory based on 2,20…

Mise en place d'outils et de bio-indicateurs pertinents de la qualité des sols

International audience

How to add a biodiversity survey to an already existing national pedologic survey? Case study of the french soil quality monitoring network

International audience; Despite its importance for human activities, soil biodiversity remains largely unknown. This gap of knowledge is a strong limit for studies including it such as in the agricultural field. Particularly, in France, no large-scale monitoring of soil biodiversity exist for the moment except for microorganisms (bacteria and fungi). Aware to this need, with the support of OFB, we studied the feasibility to add a soil biodiversity survey (RMQS-Biodiversity) to the already existing French soil quality monitoring network (RMQS). It is a systemic monitoring based on a 16*16 km grid where the sampling is done on a plot at the center of the mesh, which could belong to different …

Mise en place d’outils et bio-indicateurs pertinents de qualité des sols

EABIOME; National audience; Depuis plus de quinze ans, l’intérêt pour la composante biologique des sols est croissant, que ce soit pour des questions liées à la connaissance et la protection de cette biodiversité encore méconnue ou pour être en mesure de piloter les organismes du sol dans le cadre de pratiques agroécologiques (e.g., biocontrôle des ravageurs, nutrition des plantes). Plusieurs projets européens et nationaux ont été financés afin de développer et de valider des méthodes d’accès à cette information biologique. Cela a permis d’une part de développer de nouvelles approches d’identification moléculaire basées sur l’ADN extrait des sols et, d’autre part, de former de jeunes spécia…

Biogeographical patterns of soil molecular microbial biomass

Affiche - résumé. Session GC: Microbes in the Changing Environmenl: Global Climate Change and Soif under Human Impact; International audience; The spatial organization of soil microbial communities over large areas and the identification of environmental factors structuring their distribution have been liUle investigated. The overall objective of this study was to determine the spatial paUerning of microbial biomass in soils on wide extent and to rank the environmental fiUers most influencing this distribution, by using the French Soil Quality Monitoring Network. This network covers ail the French terrilory and soils were sampled at2,150 sites along a systematic grid sampling. The soil DNA …

Spatial processes driving soil microbial community assembly on a wide scale

International audience; Soil houses a huge biodiversity involved in ecological services through microbial community assembly. However, processes driving soil microbial community assembly are still scarcely understood, particularly the relative importance of environmental heterogeneity regarding to dispersal limitations. This can be achieved through studying the determinism of taxa-area relationship (TAR, how community composition change with geographic distance), a fundamental relationship in ecology. Here, a biogeographical approach was applied on a wide scale to evaluate TAR for soil bacterial and fungal communities and to partition their spatial variations into environmental heterogeneit…

Détection de sources animales et environnementales de souches d’E. coli productrices de betalactamases à spectre élargi (BLSE) à l’échelle d’une région française (Bourgogne)

National audience

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant differenc…

Clear-cutting effects on soil organic matter content and quality in a temperate maritime pine forest a spatial and temporal assessment

International audience

Impact d'une coupe rase sur les teneurs en carbone organique et leur dynamique dans les sols des Landes de Gascogne

National audience

Distribution de bactéries pathogènes dans les sols évaluée par PCR quantitative en temps réel

National audience

Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen (R) method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affec…

Organic carbon dynamics in soil particle-size separates of sandy Spodosols when forest is cleared for maize cropping

Summary In southwest France, much of the forest lands on sandy Spodosols has been converted to continuous maize cropping in the last few decades. To evaluate the impacts of such change on the content and properties of the soil organic matter, we compared the amount of organic carbon and 13C natural abundance in soil and particle-size separates at three locations, selected on the basis of different contents of 0–50 μm particles (clay + silt). After three decades of cultivation, the amount of carbon from the forest pools (Cf) decreased by about 60%, attributable mainly to easily degradable material in sand-sized fractions (−70%). However, a recalcitrant residue remained in soil at a constant …

Biogeographical design of soil microbial habitats

International audience; Since the beginning of 21th century, soil microbial diversity is intensively studied gathering ahuge knowledge at local and global scales. Nevertheless, the microbial habitats have beenpoorly investigated, limiting our ability to link biodiversity description and regulation. In our study,we used a pyrosequencing approach targeting 16S rRNA genes directly amplified from soil DNAto have a comprehensive view of soil bacterial and archaeal community composition across thelargest spatially explicit soil sampling available in France (2173 soils, area covered = 5.5x105km2). Based on the multivariate regression tree (MRT) method, we designed 16 distinctterrestrial microbial …

Bacterial "social" network in french soils : a Metagenomics insight

EA SPE BIOME GENOSOL UB Agrosup EA SPE BIOME GENOSOL UB AgrosupEASPEBIOMEGENOSOL UB Agrosup; New generation sequencing evidenced that soil houses a huge microbial biodiversity. Based on these observations, it is now possible to better describe the spatial distribution of soil microbial communities, to study the ecological processes lying behind (environmental selection, dispersal limitations), and to mine the data to define the ecological attributes of soil microbial taxa. These huge datasets also offer the opportunity to study how soil microbial populations are interrelated. The objective of this study was to design the first bacterial "social" network in french soils to characterize how b…

Le projet ECOMIC-RMQS ou comment faire de la microbiogéographie à l'échelle de la France

Collectes des données de pratiques agricoles des sites du Réseau de Mesures de la Qualité des Sols

The INRAE InfoSol unit, mandated by the Gis Sol, coordinates the French Soil Monitoring Network (RMQS) set up to assess the quality and evolution of soils in France. A local trained team collects management data through a survey with farmers or operators for each site and campaign. The initial objective of collecting all soil-related management data, answering multidisciplinary uses, has faced collection difficulties and lengthy interviews. Hence, survey forms were revised before the second campaign, started in 2016. The new forms were tested and improved for two years, and the data collection strategy was tuned. In order to analyze the first responses and to suggest improvements, the study…

Mise en place d’outils et de bio-indicateurs pertinents de la qualité des sols (Chapitre 9)

Mise en place d’outils et de bio-indicateurs pertinents de la qualité des sols (Chapitre 9)

Biogeography of soil microbial communities: a review and a description of the ongoing french national initiative

International audience; Microbial biogeography is the study of the distribution of microbial diversity on large scales of space and time. This science aims at understanding biodiversity regulation and its link with ecosystem biological functioning, goods and services such as maintenance of productivity, of soil and atmospheric quality, and of soil health. Although the initial concept dates from the early 20th century (Beijerinck (1913) De infusies en de ontdekking der backterien, in: Jaarboek van de Knoniklijke Akademie van Wetenschappen, Muller, Amsterdam), only recently have an increasing number of studies have investigated the biogeographical patterns of soil microbial diversity. A such …

Relevance of different soil fauna and microflora groups in the monitoring of soil biodiversity: RMQS-Biodiv, a French pilot area experience.

PosterFR2116Poster

Distribution des bactéries pathogènes dans les sols évaluée par PCR quantitative en temps réel

National audience

Is soil an island for bacteria ? Contribution of the soil bacterial taxa area relationship unsing new generation sequencing

EA SPE BIOME GENOSOL; International audience

Water-extractable organic matter linked to soil physico-chemistry and microbiology at the regional scale

10 pages; International audience; A better understanding of the links between dissolved organic matter and biogeochemical processes in soil could help in evaluating global soil dynamics. To assess the effects of land cover and parental material on soil biogeochemistry, we studied 120 soil samples collected from various ecosystems in Burgundy, France. The potential solubility and aromaticity of dissolved organic matter was characterised by pressurised hot-water extraction of organic carbon (PH-WEOC). Soil physico-chemical characteristics (pH, texture, soil carbon and nitrogen) were measured, as was the δ13C signature both in soils and in PH-WEOC. We also determined bacterial and fungal abund…

Soil biodiversity monitoring in Europe : ongoing activities and challenges

International audience; The increasing interest in soil biodiversity and its protection includes both the biodiversity conservation issues and the mostly unknown economic and ecological values of services provided by soil biodiversity. Inventory and monitoring are necessary tools for the achievement of an adequate level of knowledge regarding soil biodiversity status and for the detection of biodiversity hot spots as well as areas where current levels of biodiversity are under threat of decline. In this paper the main tools and methodological approaches for soil biodiversity measurement are presented. Technical aspects related to the inventory and monitoring activities at a large spatial sc…

Organic carbon dynamics in soil particle-size separates of sandy spodosols when forest is cleared for maize cropping

21 ref.; International audience

Le RMQS au service de l'écologie microbienne des sols français

International audience; L'écologie microbienne des sols a longtemps été reconnue comme souffrant d'un certain manque de généricité car les études ont souvent été menées à l'échelle de parcelles voire de petits territoires et avec peu de sites investigués. Il en résulte un manque de connaissances sur les processus de distribution des populations et de la régulation de la diversité microbienne à grande échelle face à des modifications environnementales dues aux usages des terres ou au changement climatique. Dans les années 2000, le RMQS, avec 2 240 sites échantillonnés sur toute la France, a représenté une opportunité unique pour étudier les micro-organismes du sol sur de grandes échelles spa…

Microbiogéographie à l'échelle du territoire national

Evaluation de la qualité des sols sur le secteur de référence de l'observatoire pérenne de l'environnement

National audience; L’Observatoire pérenne de l’environnement (OPE) de l’Andra a mis en œuvre depuis 2007 un réseau d’inventaires et d’observations à long terme des différents milieux de l’environnement sur un territoire de 240 km2 dans les départements de Meuse et de Haute-Marne. Un réseau de suivi de la qualité des sols a ainsi été mis en place selon un maillage systématique, conduit à l’échelle du paysage sur une grille de 1,5 km x 1,5 km, en suivant le protocole national d’échantillonnage et d’analyse du Réseau de Mesures de la Qualité des Sols (RMQS). L’objectif du réseau de suivi de la qualité des sols de l’OPE est d’établir un état de référence consistant à caractériser les sols en te…

The RMQS-Biodiversity as a project of large-scale soil biodiversity monitoring in France

International audience

Occurrence of CTX-M Producing Escherichia coli in Soils, Cattle, and Farm Environment in France (Burgundy Region).

Article en open access; International audience; CTX-M [a major type of extended-spectrum beta-lactamase (ESBU] producing Escherichia coli are increasingly involved in human infections worldwide. The aim of this study was to investigate potential reservoirs for such strains: soils, cattle, and farm environment. The prevalence of bla(CTX-M) genes was determined directly from soil DNA extracts obtained from 120 sites in Burgundy (France) using real-time PCR. bla(CTX-M) targets were found in 20% of the DNA extracts tested. Samples of cattle feces (n = 271) were collected from 182 farms in Burgundy. Thirteen ESBL-producing isolates were obtained from 12 farms and further characterized for the pr…

Soil bacterial interaction networks on a wide scale

EA BIOME INRA AGROSUP UB; International audience

Atlas français des champignons du sol

Un seul gramme de sol peut contenir plusieurs millions de champignons microscopiques !Depuis un milliard d’années d’évolution et d’adaptations, le règne des champignons est un acteur incontournable de la biodiversité de notre planète. Les champignons sont souvent observés grâce à leurs sporophores qui se développent au-dessus du sol. Ces derniers représentent pourtant seulement la pointe de l’iceberg de leur diversité car les champignons sont en réalité majoritairement présents sous forme microscopique dans nos sols. Dans cet atlas, les auteurs, qui sont des chercheurs INRAE spécialistes en écologie microbienne et en sciences du sol, dévoilent une nouvelle vision des champignons. Ils ont ré…

Nation-wide study of the occurrence of Listeria monocytogenes in French soils using culture-based and molecular detection methods

Identifiant HAL : hal-01120618; International audience; Soil is a potential reservoir of human pathogens and a possible source of contamination of animals, crops and water. In order to study the distribution of Listeria monocytogenes in French soils, a real-time PCR TaqMan assay targeting the phosphoribosylpyrophosphate synthetase (prs) gene of L. monocytogenes was developed for the specific detection and quantification of this bacterium within a collection of 1315 soil DNAs originated from the French Soil Quality Monitoring Network. The prs real-time PCR TaqMan assay was specific for L. monocytogenes and could quantify accurately down to 104L. monocytogenes per gram of dry soil. Among the …

Prevalence of CTX-M producing E. coli in cattle and soil environment in the Burgundy region

National audience

Microbial-biogeography at the scale of France by the use of molecular tools applied to the French soil quality monitoring network (RMQS)

International audience

Comparaison de l'arisa et du séquençage haut débit pour l'étude des processus de diversification des communautés microbiennes du sol

EA SPE EcolDur GenoSol; National audience

Biogéographie Microbienne: mythe ou réalité ?

National audience; Bien que les microorganismes soient les organismes les plus diversifiés et les plus abondants de notre planète, le déterminisme de leur diversification et de leur distribution spatiale à petite, comme à grande échelle, est très peu documenté. Ce manque d’intégration de l’échelle spatiale en écologie microbienne limite l’application des concepts développés en biogéographie pour les macro-organismes tels que la bêta-diversité (comment la composition des communautés change à l’échelle du paysage), qui est centrale pour la compréhension de la régulation et de l’évolution de la biodiversité en fonction des paramètres du milieu. Par conséquent, il est impossible à ce jour de dé…

Biogeographical patterns of soil bacterial communities.

International audience; This study provides the first maps of variations in bacterial community structure on a broad scale based on genotyping of DNA extracts from 593 soils from four different regions of France (North, Brittany, South-East and Landes). Soils were obtained from the soil library of RMQS (Réseau de Mesures de la Qualité des Sols = French soil quality monitoring network). The relevance of a biogeographic approach for studying bacterial communities was demonstrated by the great variability in community structure and specific geographical patterns within and between the four regions. The data indicated that the distribution of bacterial community composition might be more relate…

Exploring the links between Vis NIR spectra and bacterial communities structure of soils by PLS2 regression models

International audience

Influence du type de sol et du mode d’occupation des sols sur la quantité d’ADN extraite et la densité des communautés bactériennes indigènes

National audience

Soil fungal communities ecology: a biogeographical approach

Affiche, résumé; International audience

Distribution et déterminisme de la diversité des communautés de champignons telluriques à l'échelle de trois régions françaises

aeres : C-ACTN; National audience; no abstract

Contrasting Spatial Patterns and Ecological Attributes of Soil Bacterial Taxa across French National Territory

EA SPE BIOME GENOSOL UB UB Agrosup EA SPE BIOME GENOSOL UB UB AgrosupEASPEBIOMEGENOSOLUB UB Agrosup; Even though recent studies have clarified the influence of environmental filters on bacterial community diversity, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand the ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across the French country, by using a 16x16 km systematic grid representing 1825 sites to precisely decipher th…

Carbohydrate dynamics in particle-size fractions of sandy spodosols following forest conversion to maize cropping

International audience; In southwest France, much of the forested land on sandy spodosols has been converted to continuous maize cropping in the last few decades. To evaluate the impacts of this change on soil organic matter properties, we compared total organic C and neutral and amino sugars content in whole soil and particle size separates of two forested, and five related sites that had been either clear-cut for 12 and 18 mo, or cultivated to maize for 4-22yr. Soil carbohydrates accounted for 4-7% of the total organic C across all sites. Soil organic C contents of clear-cut and cultivated sites were only 57-79% of the average value measured in forested sites. Accordingly, carbohydrate co…

Biogeographical patterns of soil bacterial diversity at the scale of France

EA SPE BIOME GENOSOLEASPEBIOMEGENOSOL; Biogeographical patterns of soil bacterial diversity at the scale of France. 16. International Symposium on Microbial Ecology - ISME16

Ecomic - RMQs : Cartographie de la diversité microbienne des sols à l'échelle de la France

aeres : C-AFF; National audience; no abstract

Soils as reservoir of opportunistic human material pathogens and impact of agricultural practices

Affiche, résumé; National audience

How build up soil bacterial co-occurrence networks from wide spatial scalesampling?

National audience; Although land use drives soil bacterial diversity and community structure, littleinformation about the bacterial interaction networks is available. Here, we investigatedbacterial co-occurrence networks in soils under different types of land use (forests, grasslands,crops and vineyards) by sampling 1798 sites in the French Soil Quality Monitoring Networkcovering all of France. An increase in bacterial richness was observed from forests tovineyards, whereas network complexity respectively decreased from 16,430 links to 2,046.However, the ratio of positive to negative links within the bacterial networks ranged from 2.9 inforests to 5.5 in vineyards. Networks structure was ce…

Patterns biogéographiques de la diversité bactérienne des sols à l'échelle du territoire national

aeres : C-COM; National audience; no abstract

Optimization criteria in sample selection step of local regression for quantitative analysis of large soil NIRS database

International audience; Large soil spectral libraries compiling thousands of NIR (Near Infrared) reflectance spectra have been created encompassing a wide diversity and heterogeneity of spectra. Among the many chemometric approaches to the calibration of chemical and physical properties from these large libraries, local calibrations have the advantage of being able to select the most similar spectra to the spectrum of a target sample. This is particularly relevant when dealing with highly heterogeneous media such as soils, where the mineral matrix has a strong influence on spectral features. A crucial step in the implementation of local calibration procedures is the construction of local ne…