Mapping and determinism of soil microbial community distribution across an agricultural landscape.

Article en open access; International audience; Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13km(2). Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured 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…

Membres du Comité d’Organisation

National audience; Les journées françaises de l’Ecologie du Paysage ont lieu tous les deux ans pour faire le point sur les avancées récentes dans cette discipline et offrir un lieu d’échanges entre chercheurs et gestionnaires des paysages. Dans cette édition, les sessions s’orienteront autour de l’agroécologie et des questions de recherche et de développement que pose, à l’échelle du paysage et du territoire, cette thématique émergente. En tant que discipline scientifique, l’agroécologie interroge sur les liens entre biodiversité et fonctionnements écologiques des agroécosystèmes. Les enjeux sont notamment la gestion aux échelles larges des ravageurs des cultures, des maladies, des résistan…

Global Soil Biodiversity Atlas

SPE EA Pôle BIOME The Atlas is divided in 8 chapters covering all the aspects of soil biodiversity: - Chapter I: The soil habitat - Chapter II: Diversity of soil organisms - Chapter III: Geographical and temporal distribution - Chapter IV: Ecosystem functions and services - Chapter V: Threats - Chapter VI: Interventions - Chapter VII: Policy, education and outreach - Chapter VIII: Conclusions Soil biodiversity experts from all over the world are involved in the project aiming at the creation of a reference publication not only for soil biodiversity researchers but also policy makers and general public.; International audience; The Global Soil Biodiversity Initiative (GSBI) and the Joint Res…

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…

Is there a microbial sub alpha-diversity at soil microscale ?

The distribution of the soil microbial diversity depends on a broad range of environmental filters nested in spatial scales from continent to millimeter. Although microbial biogeography studies have recently shown the influence of environmental factors (texture/pH/plant cover and land-use) on soil microbial abundance and diversity, little is still known about spatial heterogeneity at a micro-scale within soil. Our study aims at describing and understanding the distribution of abundance and diversity of soil microbial communities between different soil microenvironments. Four soils were selected on the basis of differences in physico-chemical properties and historical land-management practic…

Distribution and determinism of abundance, diversity and structure of microbial communities at different spatial scales to support agricultural development

Les propriétés des sols déterminent notre capacité à produire des biens et des services en quantité et en qualité. Dans ce contexte, la composante microbienne des sols occupe une place prépondérante de part son abondance et son extrême diversité : on estime qu’un gramme de sol contient 109 bactéries et 105 champignons, pour environ 106 espèces bactériennes et 103 à 104 espèces de champignons. Cette diversité taxonomique des microorganismes du sol supporte une extraordinaire diversité fonctionnelle qui leur confère un rôle déterminant dans le fonctionnement du sol tant qualitativement (cycles biogéochimiques, structure du sol ; dégradation des composés exogènes, régulation biologique) que qu…

Impact des pratiques agricoles sur l’état biologique des sols: Quelles recommandations et pistes de R&D en matière de pilotage biologique des sols

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…

Présentation de l’étude de l’impact de la fertilisation des prairies sur les communautés microbiennes du sol au lait

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…

Tillage intensity and pasture in rotation effectively shape soil microbial communities at a landscape scale

International audience; Soil microorganisms are essential to agroecosystem functioning and services. Yet, we still lack information on which farming practices can effectively shape the soil microbial communities. The aim of this study was to identify the farming practices, which are most effective at positively or negatively modifying bacterial and fungal diversity while considering the soil environmental variation at a landscape scale. A long-term research study catchment (12 km2 ) representative of intensive mixed farming (livestock and crop) in Western Europe was investigated using a regular grid for soil sampling (n = 186). Farming systems on this landscape scale were described in terms…

Journées Nationales de l'Innovation Agricole (JIAG 2015) 1ère édition colloque OFSV, Angers, France, 2-3 novembre 2015

Ecological networks as a promising approach to decipher the role of microbial communities in soil ecosystems

Soil ecosystem is one of major reservoirs of microbial diversity on our planet. Many biological processes and interactions take place in soil, contributing to a considerable number of ecosystem services. Recent methodological advances, e.g. high throughput sequencing, provide an extensive knowledge on soil microbial communities in terms of diversity and composition. Thanks to these technological advances, numerous studies have investigated the variation of diversity indices and taxonomic composition of microbial communities according to changes in environmental conditions. However, estimates of microbial diversity through diversity metrics calculation such as Shannon, richness, evenness ind…

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

EA SPE BIOME GENOSOL; International audience

L’usage des terres et les pratiques agricoles contrôlent la minéralisation du C par l’intermédiaire de la biomasse bactérienne et de quelques familles fongiques clés.

Studying and modelling soil microbial communities dynamics at a landscape scale in response to agricultural practices

Soil microbial communities play a major role in soil fertility and are important as bioindicators to evaluate the impacts of agricultural practices on soils. The challenge is to promote their use in order to support / accelerate innovation by proposing to farmers the tools necessary to assess the impacts of practice modifications on the soil microbial composition before implementing and validating them. The goal of this thesis is to characterize spatial and temporal dynamics of soil microbial communities at the scale of an agricultural landscape in order to create models and propose a Decision Support Instrument (DSI) for stakeholders in the agricultural communities. This will use a multi-d…

A spatially explicit model to simulate soil microbial communities’ dynamics at an agricultural landscape scale

Soil microorganisms play a major role in soil functions and are an efficient indicator to evaluate the impact of agricultural practices on soil quality. Biogeographical studies over wide scales ranging from landscape to countries have concluded that soil microbial abundance and soil prokaryotic richness is following a heterogeneous distribution in space under the dependence of soil properties (e.g. pH, soil texture, organic matter content) and agricultural practices. The goal of this study is the creation of a model that can predict dynamics of soil microbial communities depending on the agricultural management over time. For this, we focus on a monitored landscape (Fénay landscape, 1.200 h…

Caractérisation de la distribution spatiale des communautés microbiennes du sol et de ses déterminants à l’échelle du paysage

International audience; Depuis plusieurs années, des approches biogéographiques ont été développées pour mieux caractériser la distribution spatiale des communautés microbiennes du sol, comprendre les processus écologiques mis en œuvre et identifier les filtres environnementaux déterminant leur diversité et leur structure. Ces approches ont été mises en œuvre à différentes échelles spatiales allant de celle de la parcelle agricole à celle d’un territoire et d’un continent. Elles ont permis de mettre en évidence que les communautés microbiennes du sol sont distribuées suivant des patterns biogéographiques non aléatoire et que ces dernières sont soumises à des processus déterministes (sélecti…

Re-Clustering tool using an Open-Reference method that improves OTU definition

International audience; 1.Environmental microbial communities are now widely studied using metabarcoding approaches, thanks to the democratization of high‐throughput DNA sequencing technologies. The massive number of reads produced with these technologies requires bioinformatic solutions to be treated. A key step in the analysis is to cluster reads into Operational Taxonomic Units (or OTUs) and thus reduce the amount of data for downstream analyses. Due to the important impact of the clustering method on the quantity and quality of OTUs, finding an equilibrium between the reliability and time‐consuming nature of the chosen strategy is a real challenge. The present article proposes a new pos…

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…

Atlas Français des bactéries du sol

Battle Karimi est post-doctorante dans l’UMR Agroécologie à l’INRA de Dijon et s’intéresse à l’écologie des communautés microbiennes. Elle a intégré l’équipe de recherche Biocom en 2016 afin d’analyser l’ensemble des données environnementales et microbiologiques issues du RMQS (Réseau de Mesures de la Qualité des Sols) et de les valoriser sous la forme du présent ouvrage. Elle a participé à la rédaction et à la mise en forme de la majeure partie de l’atlas, et a coordonné son avancement au sein de l’équipe d’auteurs.Nicolas Chemidlin-Prévost Bouré est maître de conférences en biologie des sols à AgroSup Dijon et membre de l’UMR Agroécologie. Spécialisé en écologie des communautés microbienn…

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

Distribution spatiale et traduction fonctionnelle de la diversité microbienne des sols

Le sol, après avoir longtemps été considéré comme un support de construction et de production, est maintenant légitimé comme un des derniers remparts pour la biodiversité terrestre. Parmi les organismes indigènes du sol, les microorganismes et notamment les bactéries sont les plus abondants et diversifiés avec plusieurs milliards d’individus représentant plusieurs millions d’espèces différentes par gramme de sol. De plus, ces microorganismes ont un rôle dans les cycles biogéochimiques des éléments majeurs (C, N, P…) et donc dans les services écosystèmiques que peut rendre le sol (recyclage éléments minéraux, qualité de l’atmosphère et de l’eau, production primaire…). Par conséquent, afin d’…

Land-use and other biogeochemical constraints modulate priming effect at the landscape scale: a fingerprinting approach using analytical pyrolysis

Soil has the potential to sequester or to emit great amounts of CO2, since soil carbon stocks constitute the largest terrestrial reservoir of carbon. Land-use is among the main factors affecting the net storage or the net mineralization of soil organic carbon (SOC) and land-use policies are currently aiming to increase soil organic carbon stocks.However, adding labile sources of carbon to soil (e.g. more crop residues or manure) may alter the carbon cycle, increasing the microbial degradation of the existing SOC pools, a process called “priming effect” (PE). PE could significantly reduce the net storage of carbon and taking into account this effect into carbon storage models may alter their…

Studying and modelling the dynamics of soil microbial communities at a landscape scale in response to agricultural practices

National audience; Soil Microbial communities play a major role in soil fertility and are important as bioindicators to evaluate the impacts of agricultural practices on soils. The challenge is to promote their use in order to support / accelerate innovation by proposing to farmers the tools necessary to assess the impacts of practice modifications on the soil microbial composition before implementing and validating them. The goal of this thesis is to characterize spatial and temporal dynamics of soil microbial communities at the scale of an agricultural landscape in order to create models and propose a Decision Support Instrument (DSI) for stakeholders in the agricultural communities. This…

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

Le séquençage massif pour caractériser la diversité microbienne des sols, standardisation et applications au sein de la plateforme GenoSol

EA SPE GenoSol EcolDur; National audience; Les microorganismes (bactéries, archées et champignons) sont les organismes les plus abondants et les plus diversifiés de la matrice sol. Ils représentent un réservoir encore largement méconnu et presque infini de ressources génétiques, fortement impliqué dans le fonctionnement biologique du sol et plus largement dans la plupart des services écosystémiques fournis par ce sol. Malgré ce rôle central dans le fonctionnement des écosystèmes, nos connaissances sur la diversité génétique, taxonomique et fonctionnelle de ces microorganismes restent limitées à ce jour. Ceci s’explique essentiellement par des difficultés techniques pour accéder à ces organi…

Bilan de l’état microbiologique des sols en France

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…

Spatial patterns of microbial communities at a soil micro-scale

International audience

Increase inabovegroundfreshlitterquantityover-stimulatessoil respiration inatemperatedeciduousforest

In the context of climate change, the amount of carbon allocated to soil, particularly fresh litter, is predicted to increase with terrestrial ecosystem productivity, and may alter soil carbon storage capacities. In this study we performed a 1-year litter-manipulation experiment to examine how soil CO2 efflux was altered by the amount of fresh litter. Three treatments were applied: litter exclusion (E), control (C, natural amount: 486 g m −2 ) and litter addition (A, twice the natural amount: 972 g m −2

Soil fungal communities ecology: a biogeographical approach

Affiche, résumé; International audience

Évaluation des transferts microbiens du sol au lait en filière AOP Comté

International audience

Le projet Tandem

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

Outils de saisie pour la caractérisation des sols

Temporal dynamics of soil bacterial communities at a landscape scale: dependence to soil properties and agricultural practices.

International audience; Soil microbial communities play a major role in agricultural functions and are an efficient indicator to evaluate the impacts of agricultural practices on soils. Studies on wide scales ranging from landscape to countries demonstrated that soil microbial communities were heterogeneously distributed in space under the dependence of soil properties (e.g. pH, soil texture, Organic matter Content) and agricultural practices. However, temporal dynamics of soil microbial communities at a landscape scale still need to be documented in order to go further in evaluating the sustainability of agricultural practices. In this extensive monitoring study, we focused on landscape dy…

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…

Étude et modélisation des impacts des pratiques agricoles sur la dynamique de la distribution des communautés microbiennes des sols à l’échelle du paysage

National audience; Les micro-organismes telluriques, de par leur abondance et leur richesse, jouent un rôle centraldans le fonctionnement des écosystèmes et sont des bioindicateurs intéressants pour évaluerl’impact des pratiques agricoles sur la qualité des sols. L’enjeu est de favoriser leur utilisationpour accompagner l’innovation dans le monde agricole. Cette thèse a pour objectif de permettreune meilleure compréhension des dynamiques spatiales et temporelles des communautésmicrobiennes du sol à l’échelle du paysage. Pour cela, nous proposons de modéliser cesdynamiques et de partager les connaissances aux acteurs du monde agricole via un OAD (outild’aide à la décision). Le paysage de Fén…

Le semis direct sous couverture végétale favorise les microbes du sol

Les pratiques agricoles modifient les propriétés physiques et chimiques des sols, qui à leur tour peuvent affecter les micro-organismes qui y vivent avec des conséquences sur le fonctionnement biologique et la qualité de ces sols. Nous connaissons cependant peu de choses sur les interactions entre les pratiques agricoles, les propriétés physico-chimiques et les communautés microbiennes des sols. Peu d'études ont notamment été conduites dans les savanes herbacées des zones tropicales, fortement acides et lessivées, alors que ces espaces représentent des réservoirs importants de terres agricoles, aujourd’hui peu mis en valeur, alors qu’ils pourraient répondre, dans de bonnes conditions d’expl…

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

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…

Impact de la fertilisation des prairies sur leur biodiversité et sur les transferts microbienset chimiques du sol au lait (IFEP)

National audience

Seasonal dynamics of the bacterial community in forest soils under different quantities of leaf litter

International audience; Soil microbial communities play an important role in soil carbon functioning, particularly in forest ecosystems. Their variation in response to climate change may affect soil carbon processes, highlighting the importance of understanding how environmental factors affect microbial communities. This study aimed to determine to what extent an increase in the quantity of fresh litter may affect heterotrophic mineralization of organic carbon and bacterial community structure in soil and litter. A litter manipulation experiment was performed in situ in a temperate deciduous forest. Three treatments of fresh litter inputs were considered: litter exclusion, natural condition…

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

aeres : C-COM; National audience; no abstract

Distribution spatiale de la diversité microbienne des sols à l’échelle du territoire national

Le sol représente un exceptionnel réservoir de biodiversité microbienne tant en termes d’abondance et de richesse spécifique, qu’en termes de fonctions et de processus impliqués dans les flux de matière et d’énergie. Ce réservoir assure et supporte de nombreux services écosystémiques à la base de la durabilité des systèmes de production exploités par l’Homme. Cette grande biodiversité lui confère des capacités d’adaptation (résistance, résilience, redondance fonctionnelle,…) face aux activités anthropiques et aux changements globaux, et constitue ainsi une véritable assurance écologique pour l’Homme et ses moyens de production. Néanmoins, de nombreuses connaissances restent encore à acquéri…