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…

Impact of the use of wastewater for irrigation of cultivated plots on the soil microbiological quality in semi-arid zone (Tunisia): approaches at the plot and catchment area scales

Affiche, résumé. Session AS: Agricultural Soils: Biodiversity and Functioning; International audience

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…

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…

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…

Copper Dynamics and Impact on Microbial Communities in Soils of Variable Organic Status

International audience; The effect of soil organic status on copper impact was investigated by means of a microcosm study carried out on a vineyard soil that had been amended with varying types of organic matter during a previous long-term field experiment. Soil microcosms were contaminated at 250 mg Cu kg−1 and incubated for 35 days. Copper distribution and dynamics were assessed in the solid matrix by a sequential extraction procedure and in the soil solution by measuring total and free exchangeable copper concentrations. Copper bioavailability was also measured with a whole-cell biosensor. Modifications of microbial communities were assessed by means of biomass-C measurements and charact…

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 …

Optimisation de la procédure d'extraction d'ADN des sols pour caractériser la diversité microbienne tellurique par le pyroséquençage des gènes ribosomiques

Depuis plusieurs années, les communautés microbiennes du sol (bactériennes et fongiques) sont étudiées au travers de leur ADN. Le mode d’extraction de l’ADN du sol revêt donc une importance capitale pour décrire la biodiversité microbienne. A ce jour, de nombreuses procédures d’extraction d’ADN (commerciales ou non) des sols sont disponibles et utilisées. Il est cependant difficile de comparer les résultats d’études ayant utilisés différents protocoles d’extraction. L’emploi d’une méthode d’extraction standardisée est donc devenu indispensable pour comparer les résultats de différents laboratoires, comme la norme “ISO-11063: Soil quality – Method to directly extract DNA from soil” développé…

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…

Optimisation du pyroséquençage haut-débit pour caractériser la diversité taxonomique des communautés bactériennes des sols

Affiche, résumé; International audience; La diversité microbienne d’un sol (que l’on estime entre 100 000 et 1 000 000 d’espèces différentes par gramme de sol) est difficile à caractériser. Toutefois, d’importantes avancées en biologie moléculaire, comme le développement du pyroséquençage, ont permis d'obtenir plusieurs centaines de milliers de séquences à partir d’un ADN méta-génomique. Ces nouveaux développements permettent maintenant de caractériser la diversité des communautés microbiennes du sol en se basant sur un marqueur phylogénétique comme l'ADNr 16S, aussi appelée MetaTaxogénomique (Maron et coll., 2011). Toutefois, dans un contexte ou l’écologie microbienne du sol commence à s’a…

Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in two different soils

The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modi…

Atelier d'observation 3D des micro-organismes du sol, des champignons, des bactéries...

Effet du statut organique des sols pollués sur la dynamique et l'impact du cuivre sur les communautés microbiennes

National audience; L’effet du statut organique des sols (SOS) sur l’impact du cuivre a été évalué par une approche en microcosmes et lysimètres d’un sol de vigne amendé en diverses matières organiques lors d’une expérience de terrain de long terme. Des microcosmes et des lysimètres du sol de vigne ont été contaminés à 240 mg Cu kg-1 et incubés à 23°C pendant 12 mois. La distribution et la dynamique du cuivre ont été caractérisées par fractionnement granulométrique et spéciation solide en extraction séquentielles et par spéciation liquide par mesure de concentration de cuivre échangeable total (ICP-AES), libre (électrode sélective) et biodisponible (biosensor). L’impact du cuivre sur les com…

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…

Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques.

International audience; This work is the first report on the use of DNA-, RNA-SIP approaches to elucidate the dynamics and the diversity of bacterial populations actively assimilating C derived from plant residues labelled at more than 90% (13)C. Wheat-residues, were incorporated and incubated into soil microcosms for 28 days. At the end of the incubation time, no more than 55% of the total CO(2) released was (13)C-labelled, suggesting the occurrence of an important priming effect process. After 7 days, more than 30% of the whole DNA extracted were labelled, allowing an efficient separation of labelled from unlabelled DNA using density gradient centrifugation. The genetic structure of bacte…

The dynamics of soil bacterial community structure in response to yearly repeated agricultural copper treatments

International audience; The annual dynamics of soil bacterial community structure, including early, dose-dependent and transient modifications, was observed consecutively at different levels of copper contamination (high: 48 kg Cu ha−1, low: 16 kg Cu ha−1) repeated yearly over a three-year field experiment. Repeated low-level Cu contamination led to an increase in community stability to metal stress without a long-term shift in the population structure, whereas repeated high-level Cu contamination induced a novel and stable bacterial community structure. Furthermore, field experimentation highlighted that episodic climatic stress can modulate copper impact by enhancing community stability.

Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

National audience

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…

Valorisation des effluents dans les élevages mixtes bovins-porcins du Massif Central

National audience

Les communautés microbiennes présentes dans différents types de sols ont une réponse variable à l’apport de produits résiduaires organiques

National 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…

Soil Bacterial and Fungal Communities of Urban Areas in France

International audience

N2O Gaz hilarant, pas toujours drôle ! Atelier grand public

Le protoxyde d’azote (N2O) appelé aussi gaz hilarant fait partie des gaz à effet de serre. S’il est utilisé dans les siphons pour crème chantilly, il sert aussi en médecine comme anesthésiant.Nous vous proposons dans cet atelier de découvrir quels sont ses liens avec l’agriculture.Quels sont les leviers pour diminuer les émissions de ce gaz par l’agriculture ?Itinéraires techniques de l’agriculture, choix alimentaires des consommateurs : en quoi la recherche aide à faire baisser la teneur de ce gaz dans l’atmosphère ?

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

Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil

International audience; Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic compos…

Spatial patterns of microbial communities at a soil micro-scale

International audience

Optimisation du pyroséquençage haut-débit pour caractériser la diversité taxonomique des communautés bactériennes des sols

La diversité microbienne d’un sol (que l’on estime à 100000 à 1000000 d’espè ces différentes par gramme de sol) est difficile à caractériser. Toutefois, d’importantes avancé es en biologie moléculaire (comme le développement du pyrosé quençage), ont permis d'obtenir plusieurs centaines de milliers de sé quences à partir d’un ADN métagénomique, permettant une meilleure caracté risation de la diversité des communautés microbiennes du sol. Toutefois, dans un contexte ou l’écologie microbienne du sol commence à s’accaparer les é chantillonnages de grande envergure (spatial et temporelle) afin de mieux hié rarchiser les processus et paramètres impliqués dans la diversification de ces communauté …

Quel est l’impact des pratiques d’épandage des effluents d’élevages mixtes « Porcin-Bovin » en zone herbagère du Massif Central sur la microbiologie des sols ?

National audience; L’élevage porcin du Massif Central concerne 1 000 éleveurs répartis sur le territoire. Le maintien ou le renouvellement des ateliersest de moins en moins assuré pour des raisons sociales, économique et, environnementales. Dans le Massif Central, l’élevage porcinest souvent associé à l’élevage bovin. Les effluents porcins issus de ces systèmes mixtes peuvent être un réel atout pour la fertilisationorganique des prairies, étant elles-mêmes en retour une ressource alimentaire essentielle pour l’élevage bovin. Cependant, l’impactdu retour au sol des effluents d’élevage issus de ces systèmes mixtes sur la qualité biologique des sols est actuellement peu ou pasétudié. La présen…

Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination

A molecular fingerprinting assay was developed to assess the diversity of copA genes, one of the genetic determinants involved in bacterial resistance to copper. Consensus primers of the copA genes were deduced from an alignment of sequences from proteobacterial strains. A PCR detection procedure was optimized for bacterial strains and allowed the description of a novel copA genetic determinant in Pseudomonas fluorescens. The copA DNA fingerprinting procedure was optimized for DNA directly extracted from soils differing in their physico-chemical characteristics and in their organic status (SOS). Particular copA genetic structures were obtained for each studied soil and a coinertia analysis …

Utilization of microbial abundance and diversity as indicators of the origin of soil aggregates produced by earthworms

This study aimed at testing the capability of microbial community structure and abundance to be used as bioindicators of the origin of earthworm cast aggregates. Compact surface casts produced by Amynthas khami and surrounding aggregates lacking visible signs of biological activity (control) were left to disaggregate by natural rainfall and separated into four size classes (5-2, 2-0.5, 0.5-0.25 and <0.25 mm). The genetic structure and the abundance of the bacterial and fungal communities were characterized using B- and F-ARISA fingerprinting approach and quantitative PCR directly from DNA extracted from soil. Bacteria and to a lesser extent fungi were more abundant in casts than in control …

Contamination of soil by copper affects the dynamics, diversity, and activity of soil bacterial communities involved in wheat decomposition and carbon storage.

ABSTRACT A soil microcosm experiment was conducted to evaluate the influence of copper contamination on the dynamics and diversity of bacterial communities actively involved in wheat residue decomposition. In the presence of copper, a higher level of CO 2 release was observed, which did not arise from greater wheat decomposition but from a higher level of stimulation of soil organic matter mineralization (known as the priming effect). Such functional modifications may be related to significant modifications in the diversity of active bacterial populations characterized using the DNA stable-isotope probing approach.

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…

Lasting effect of solid waste composts on soil microbial communities

EABIOME; Lasting effect of solid waste composts on soil microbial communities. 16. International Symposium on Microbial Ecology - ISME16

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

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…

Jack et les légumineuses magiques face au réchauffement climatique. Atelier grand public

Avec le réchauffement climatique, les plantes sont soumises à différents stress, dont le stress hydrique et les fortes températures. Ces stress ont des conséquences négatives importantes sur les cultures et sur les éléments indispensables à la croissance et au développement des plantes, notamment l’azote et le fer.Dans cet atelier, nous allons vous montrer les pistes sur lesquelles les chercheurs se penchent pour comprendre comment les plantes peuvent résister à ces changements.

Protein and DNA fingerprinting of a soil bacterial community inoculated into three different sterile soils

The functional and genetic structures of a soil bacterial community were characterized after inoculation into three different sterile soils using a protein and DNA fingerprinting method, respectively. Principal component analysis (PCA) of profiles revealed that, depending on soil characteristics, bacterial communities with similar genetic structures harbored different functional structures and thus could potentially be of differing ecological significance for soil functioning. Co-inertia analysis between protein fingerprinting data and the corresponding sets of soil physicochemical characteristics demonstrated the correlation between the functional structure of the bacterial community and s…