Résumé
Grapevine downy mildew, caused by the oomycete Plasmopara viticola, is one of the most devastating diseases of grapevine worldwide. While primary inoculum plays a decisive role in disease epidemics, we still know very little about the abundance and the distribution of oospores, which are the overwintering forms of the pathogen resulting from sexual reproduction. In this study, we used ddPCR to describe the spatial distribution of P. viticola inoculum in a vineyard soil at the onset of the growing season. We found P. viticola oospores in all soil samples except one. The distribution of primary inoculum at the field scale was not random but characterized by 25 m-diameter patches of concentrically increasing oospore concentration. There was a positive coregionalization between soil inoculum and soil moisture spatial distributions, possibly mediated by disease incidence. The results indicated that oospores accumulated 5 times more in the ridge of soil below the vine stocks than in the inter-row. We conducted a leaf disc bioassay to assess soil infectious potential on a subset of samples collected in the field. Soil infectious potential estimated through infected leaf-disc area was positively correlated with our DNA-based quantification of oospores. Overall, the quantitative and spatially explicit survey of primary inoculum reservoir gained from these molecular and biological methods will contribute to the design of management strategies aimed at preventing primary inoculum accumulation in the vineyard from one season to the next.
Auteurs, date et publication :
Auteurs Charlotte Poeydebat , Eva Courchinoux , Isabelle Demeaux , Marie Rodriguez , Alexandre Chataigner , Mélanie Lelièvre , Jean-Pascal Goutouly , Jean-Pierre Rossi , Marc Raynal , Laurent Delière , François Delmotte
Date : 2024
Catégorie(s)
#Genosol #INRAEAuteurs, date et publication :
Auteurs Damien Costa , Anne Mercier , Kevin Gravouil , Jérôme Lesobre , Vincent Delafont , Anne Bousseau , Julien Verdon , Christine Imbert
Publication : Water Research
Date : 2025
Volume : 81
Pages : 223-231
Catégorie(s)
#Genosol #INRAERésumé
It is widely assumed that agricultural practices have a major impact on soil living organisms. However, the impact of agricultural practices on soil microbes is poorly known, notably for species richness, evenness, and taxonomic composition. The taxonomic diversity and composition of soil indigenous microbial community can be assessed now using pyrosequencing, a high throughput sequencing technology applied directly to soil DNA. Here, we studied the effect of agriculture management on soil bacterial and fungal diversity in a tropical grassland ecosystem of northeastern Laos using 454 pyrosequencing of 16S and 18S rRNA genes. We studied soil microbial diversity of agricultural soils 3 years after conversion from native grasslands. We compared five systems: one tillage, two no-tillage rotational, one no-tillage improved pasture, and one natural grassland. Our results show first that compared to the natural grassland, tillage decreases fungal richness and diversity by −40 % and −19 %, respectively and increases bacterial richness and diversity by +46 % and +13 %, respectively. This finding evidences an early impact of agricultural management on soil microbial diversity. Such an impact fits with the ecological concept of "intermediate perturbation"—the hump-backed model—leading to classify agricultural practices according to the level of environmental stress they generate. We found also that land use modified soil microbial taxonomic composition. Compared to the natural pasture, tillage decreased notably the relative abundance of Actinobacteria (by −6 %), Acidobacteria (by −3 %) and Delta-proteobacteria (by −4 %) phyla, and by contrast increased the relative abundance of Firmicutes (by +6 %), Gamma-proteobacteria (by +11 %), and Chytridiomycota (+2 %) phyla. We conclude that soil microbial diversity can be modified and improved by selecting suitable agricultural practices. Moreover no-till systems represented intermediate situations between tillage and the natural pasture and appear therefore as a fair trade-off between the need for agriculture intensification and soil ecological integrity preservation.
Auteurs, date et publication :
Auteurs Pascal Lienhard , Sébastien Terrat , Nicolas Chemidlin Prévost-Bouré , Virginie Nowak , Tiffanie Régnier , Sengphanh Sayphoummie , Khamkéo Panyasiri , Florent Tivet , Olivier Mathieu , Jean Levêque , Pierre-Alain Maron , Lionel Ranjard
Publication : Agronomy for Sustainable Development
Date : 2014
Volume : 34
Issue : 2
Pages : 525-533
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs Walid Horrigue , Samuel Dequiedt , Nicolas Chemidlin Prévost-Bouré , Claudy Jolivet , Nicolas P.A. Saby , Dominique Arrouays , Antonio Bispo , Pierre-Alain Maron , Lionel Ranjard
Publication : Ecological Indicators
Date : 2025
Volume : 64
Pages : 203-211
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
In France, about 90,000 ha per year of arable land become unsuitable for food production due to erosion, acidification, sealing and pollution by metallic and organic compounds. Bioenergy crops such as Miscanthus x giganteus are used to rehabilitate polluted soils for crop production. Although the economic potential of this crop is known, the crop abilities to regenerate the soil biological properties enabling sustainable crop production still remain unclear. Here, we evaluated the effects of the Miscanthus crop on the abundance and diversity of soil bacterial and fungal communities in a wastewater-contaminated soil, using synchronic and diachronic evaluation strategies. A 3-year field experiment, near Paris, was set up on an agricultural field irrigated with raw wastewater for more than 100 years, thus inducing a strong metal and organic contamination of the soil. We characterized the abundance and diversity of soil microbial communities using metagenomic techniques. Our results show that the Miscanthus crop had an early effect on microbial communities by stimulating bacterial diversity, by about 20 %, and fungal diversity, by about 10 %. This positive effect could be explained by the release of fresh organic matter from litter decomposition and root exudation, and by the absence of tillage and pesticide spraying, which are known to degrade soil microflora. On the other hand, no significant effect on microbial biomass has been recorded. Overall our findings show that Miscanthus cropping is a promising practice to enhance the regeneration of soil microbiological diversity and to reclame polluted soils.
Auteurs, date et publication :
Auteurs Emilie Bourgeois , Samuel Dequiedt , Mélanie Lelièvre , Folkert van Oort , Isabelle Lamy , Pierre-Alain Maron , Lionel Ranjard
Publication : Environmental Chemistry Letters
Date : 2015
Volume : 13
Issue : 4
Pages : 495-501
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Green infrastructures play a key role in the functionality and resilience of urban ecosystems. The physical, including thickness, chemical and biological properties of the Technosols of green infrastructures on rooftops are highly variable, leading to more or less favourable conditions for soil biodiversity. The aim of this study was to investigate the abundance and diversity of bacteria, fungi, nematodes, collembola and plants communities in relation with abiotic parameters of Technosols on 12 productive and extensive green roofs of the Paris region (France). Results showed that green roofs harboured a high level of abundance and diversity from microorganisms to micro and mesofauna. Microbial biomass ranged between 16.3 and 419.8 μg DNA g−1, with a predominance of bacteria, nematodes represented 820–60,700 individuals per kg of soil and between 1000 and 60,700 collembolan were present per m2 of soil. A total of 13,986 bacterial OTU (Operational Taxonomic Unit), 33,559 fungal OTU, 47 Collembola species, 28 nematodes families, 16 cultivated plant species and 48 spontaneous plant species was identified on all the green roofs studied. Microbial, animals and plants communities were significantly different between the two types of green roofs. Productive and extensive rooftops represent contrasted habitats, which can strongly influence the soil biota. Any voluntary action to enhance soil biodiversity in cities would need to take-into-account both soil properties and the landscape around.
Auteurs, date et publication :
Auteurs Sophie Joimel , Baptiste Grard , Claire Chenu , Pénélope Cheval , Samuel Mondy , Mélanie Lelièvre , Apolline Auclerc , Laure Vieublé Gonod
Publication : Ecological Engineering
Date : 2025
Volume : 175
Pages : 106475
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs Damien Costa , Anne Mercier , Kevin Gravouil , Jérôme Lesobre , Julien Verdon , Christine Imbert , Ake Forsberg
Publication : Pathogens and Disease
Date : 2025
Volume : 74
Issue : 7
Pages : ftw094
Catégorie(s)
#Genosol #INRAERésumé
CTX-M (extended spectrum beta-lactamase- ESBL) 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 blaCTX-M genes was determined directly from soil DNA extracts obtained from 120 sites in Burgundy (France) using real time PCR. blaCTX-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 presence of bla genes. Of the 13 strains, five and eight strains carried blaTEM-71 genes and blaCTX-M-1 genes respectively. Ten strains of CTX-M-1 producing E. coli were isolated from cultivated and pasture soils as well as from composted manure within 2 of these farms. The genotypic analysis revealed that environmental and animal strains were clonally related. Our study confirms the occurrence of CTX-M producing E. coli in cattle and reports for the first time the occurrence of such strains in cultivated soils. The environmental competence of such strains has to be determined and might explain their long term survival since CTX-M isolates were recovered from a soil that was last amended with manure one year before sampling.
Auteurs, date et publication :
Auteurs Alain Hartmann , Lucie Amoureux , Aude Locatelli , Geraldine Depret , Claudy Jolivet , Eric Gueneau , Catherine Neuwirth
Publication : Frontiers in Microbiology
Date : 2025
Volume : 3
Catégorie(s)
#Genosol #INRAERésumé
Agricultural practices affect the physical and chemical characteristics of the soil, which in turn may influence soil microorganisms with consequences on soil biological functioning. However, there is little knowledge on the interactions between agricultural management, soil physicochemical properties, and soil microbial communities, notably in tropical ecosystems with few studies conducted in strongly weathered and acid soils. Here, we investigated the early effect of tillage and crop residues management on top soil physical, chemical, and microbial properties in an acid savannah grassland of northeastern Laos. We initiated a 3-year rotation of rice/corn/soybean under three no-till systems (NTs) distinguished by the cover crops associated prior to and with the main crops, and one conventional tillage-based system (CT). The effect of agricultural management was evaluated 2 years after land reclamation in reference to the surrounding natural pasture (PAS). Our results demonstrate that NTs improve soil physicochemical characteristics (aggregate stability, organic carbon, and cation exchange capacity) as well as microbial abundance (total biomass, bacterial and fungal densities). A significant discrimination of the genetic structure of soil bacterial community was also observed between NTs, CT, and PAS. Interestingly, bacterial abundance and diversity were differently influenced by soil environment changes: microbial density was affected by the quantity and diversity of crop residues, soil organic carbon, and exchangeable base contents, whereas soil bacterial genetic structure was mainly determined by exchangeable aluminum content, pH, cation exchange capacity, and C/N ratio. Altogether, our study represents one of the most complete environmental evaluations of agricultural practices in tropical agrosystems and leads to recommend no-till systems with high residue restitutions to improve the physical, chemical, and microbial properties of tropical acid soils and thus contribute to the sustainability of agriculture in these ecosystems.
Auteurs, date et publication :
Auteurs Pascal Lienhard , Florent Tivet , André Chabanne , Samuel Dequiedt , Mélanie Lelièvre , Sengphanh Sayphoummie , Bounma Leudphanane , Nicolas Chemidlin Prévost-Bouré , Lucien Séguy , Pierre-Alain Maron , Lionel Ranjard
Publication : Agronomy for Sustainable Development
Date : 2013
Volume : 33
Issue : 2
Pages : 375-384
Catégorie(s)
#Genosol #INRAERésumé
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 1315 soil DNAs, prs was not detected. This suggested that the level of L. monocytogenes in French soils is generally less than 104L. monocytogenes per gram of dry soil. In order to confirm this hypothesis, we investigated the occurrence of L. monocytogenes in samples collected in the Burgundy region by culture-based and molecular detection methods on the same samples. By using cultivation-based detection, 17% of samples were positive for the presence of L. monocytogenes while only 2% were found positive by the molecular detection method. L. monocytogenes was repeatedly isolated from cow pasture soils but not from cultivated soils, meadows or forest soils. Isolates were grouped in the serovar 1/2a or 3a and 4b or 4d or 4e. Taken as a whole, molecular detection results globally demonstrate that the level of L. monocytogenes in French soils does not exceed 104CFU per gram of dry soil. However, in comparison with culture-based method, PCR-based detection underestimates the occurrence of L. monocytogenes in soils. Soil sampling procedure also appears critical and may also lead to the underestimation of the incidence of L. monocytogenes.
Auteurs, date et publication :
Auteurs Aude Locatelli , Géraldine Depret , Claudy Jolivet , Sonia Henry , Samuel Dequiedt , Pascal Piveteau , Alain Hartmann
Publication : Journal of Microbiological Methods
Date : 2013
Volume : 93
Issue : 3
Pages : 242-250