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…

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 …

Les sols et la préservation de la biodiversité

Les sols et la préservation de la biodiversité. Journée Mondiale des Sols

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…

Procedures and protocol for soil biodiversity monitoring : ‘RMQS-Biodiv', a french pilot area experience.

PosterFR2116Poster

Les indicateurs de l'état biologique des sols : Guide de sélection selon le type d’application et/ou la problématique

National audience

Intérêt de la normalisation de méthodes pour la recherche publique et la société

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…

Innovative tools to diagnose the impact of land use practices on soil microbial communities

International audience; Preservation and sustainable use of soil biological communities represent major challenges in the current agroecological context. Indeed, most of soil ecosystem services results from biological functions particularly driven by taxonomic and functional assemblages of microbiological communities (i.e. nutrient cycling, soil aggregation, depollution, etc.). Consequently, soil microbial communities are logical candidates as effective indicators of soil quality and sustainability. But, good biological indicators must be associated with references that encompass an operating range of measured values that allow performing the desired diagnosis. Even if numerous studies have…

Soil bioindicators: how to select them in function of the site issues?

Soil bioindicators: how to select them in function of the site issues?. 13th International AquaConSoil Conference

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

PosterFR2116Poster

Application of soil bioindicators for risk assessment, monitoring and soil characterization in contaminated soils. Results from the French national “Bioindicators Programme”

International audience; absent

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

EA SPE BIOME GENOSOL; International audience

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…

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…

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

International audience

Mapping, understanding and predicting soil microbial diversity across France

International audience; Microorganisms are extremely abundant and diverse in soils. Their huge diversity is central in soil functioning regarding the diversity of functions it supports (mineralization, detoxification, stability of soil…) and is more and more studied, especially in a context of increasing pressure on soil resources. Conversely to macroorganisms whose distribution on a wide scale has been studied for over a century, spatial scaling and determinism distribution of soil microorganisms on nationwide scale still needs to be documented, notably to decipher the environmental filters shaping these communities. communities were investigated at the scale of France to characterize thei…

Predictive models of abundance and diversity of soil microbial communities

International audience

Soil bacterial interaction networks on a wide scale

EA BIOME INRA AGROSUP UB; International audience

Application of soil bioindicators for risk assessment, monitoring and soil characterization in contamined soils. Results from the French national "Bioindicators Programme"

EA GenoSol IPM CT?; International audience

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples"

International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …

Animation scientifique et technique sur "La microbiologie moléculaire au service du diagnostic environnemental"

INRA EA BIOmEINRAEABIOmE; Dans une société où il devient urgent de réduire l’empreinte environnementale des activités humaines, l’établissement d’un diagnostic fiable de la qualité des divers écosystèmes (terrestres, aquatiques, atmosphériques) est une priorité absolue. Les microorganismes, de par leur petite taille, leur énorme diversité taxonomique et fonctionnelle, leurs capacités d’adaptations aux perturbations et leur forte implication dans les cycles biogéochimiques sont des candidats incontournables pour élaborer ce diagnostic

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…

Agrosyst : Poursuite de la réalisation du système d’information https://agrosyst.fr/ Plan Ecophyto - Ecophyto I – Axe 2 – Action 14 - Ecophyto II – Axe 2 – Action 2- Rapport final - Mars 2018

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

Recherche de bioindicateurs d'impact du recyclage de produits résiduaires organiques en sols cultivés : lien avec la disponibilité de micropolluants organiques et métalliques

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…

Monitoring microbial diversity in European soils: ongoing projects and challenges

SPEEcolDurGenoSolCT3communication orale invitée, résumé et slides; According to the Convention of Biological Diversity (Rio de Janeiro, 1992), biodiversity is the variation in life from genes to species, communities, ecosystems, and landscapes. Soils represent a huge reservoir of biodiversity which varies in terms of taxonomic richness, relative abundance and distribution according to soil types, climatic conditions, vegetation and land uses. The key functions supporting ecosystem services as identified in the Millennium Ecosystem Assessment (MEA, 2005) largely depend upon organisms that inhabit the soil. Thus, the design and implementation of a sustainable soil management strategy requires…

Impact du travail du sol sur son fonctionnement biologique

National audience; Les impacts des différentes modalités de travail du sol (labour, semis direct) sur l’environnement et les états du sol, sur la biodiversité ou sur le climat font l’objet de débats parfois passionnés mais souvent trop peu instruits sur les plans scientifique et technique. Que nous enseignent les expérimentations les plus récentes sur ce sujet ? Quelles sont les innovations qui se dessinent à l’heure actuelle ? Cet ouvrage propose une synthèse des connaissances les plus récentes dans ce domaine.