Résumé
Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km x 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making.
Auteurs, date et publication :
Auteurs Christophe Djemiel , Samuel Dequiedt , Arthur Bailly , Julie Tripied , Melanie Lelievre , Walid Horrigue , Claudy Jolivet , Antonio Bispo , Nicolas Saby , Matthieu Vale , Pierre-Alain Maron , Lionel Ranjard , Sebastien Terrat
Publication : MSPHERE
Date : 2023
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Anaerobic digestion of organic waste is a key process to produce renewable energy and meet the growing demand for sustainable energy. The residues of anaerobic digestion – called digestates – can be used as soil amendments to improve crop yields. However, the effect of digestates on the soil biota, especially on microorganisms, needs to be better documented before a large scale use of digestates in agriculture. In addition, how the quality and composition of the digestate may affect soil microbial communities has not been properly addressed yet. We designed a microcosm experiment under controlled experimental conditions to compare effects (42 days) of four digestates produced from varying intakes (cattle manure and/or energy crop and/or food residues and/or slurry) on soil microbial communities; a control microcosm made of undigested cattle manure was also used. Each digestate was applied on three contrasting soils representing contrasted pedo-climatic conditions (especially soil type and climate). These three soils presented different prokaryotic and fungal communities structures. The effect of digestate inputs on the soil microbial biomass and diversity was assessed using molecular DNA-based tools (quantification of extracted soil DNA and high-throughput sequencing, respectively) in comparison to the untreated cattle manure control condition. Our results show that 42 days after digestate application, significant differences of soil microbial communities were observed according to the digestate characteristics; these differences were soil-dependent. Thus, in the silty clay loam soil, no effect of digestates was observed on soil microbial biomass or diversity (P > 0.05), as compared to the undigested cattle manure. In the two other soil types (loam and sandy loam), soil microbial biomass decreased (around −40 %, P 0.05). Digestate application resulted in higher fungal diversity (around +35 %; P < 0.001) in soils with low C/N ratio (9.14 in average). The microbial community structure of coarse-textured soil appeared more impacted by organic inputs than fine-textured soils. To conclude, our results show that different soil types, harboring distinct microbial community structures, responded differently to different digestates application. This response was also digestate-dependent.
Auteurs, date et publication :
Auteurs F. Vautrin , P. Piveteau , M. Cannavacciuolo , P. Barré , C. Chauvin , C. Villenave , D. Cluzeau , K. Hoeffner , P. Mulliez , V. Jean-Baptiste , G. Vrignaud , J. Tripied , S. Dequiedt , P. A. Maron , L. Ranjard , S. Sadet-Bourgeteau
Publication : Applied Soil Ecology
Date : 2024
Volume : 193
Pages : 105105
Catégorie(s)
#Genosol #INRAE #PRO #PRO QualiAgroRésumé
The fungal kingdom is among the most diversified kingdoms on Earth, with estimations of up to 12 million species. However, it remains poorly understood, with only 150 000 fungal species currently described. Given the major ecological role of fungi in ecosystem functioning, these numbers stress the importance of investigating fungal diversity description across different ecosystem types. Here, we explored the spatial distribution of the soil fungal diversity on a broad geographical scale, using the French Soil Quality Monitoring Network that covers the whole French territory (2171 soils sampled along a systematic grid). Fungal alpha diversity was assessed directly from soil DNA using a meta-barcoding approach by targeting the 18S rDNA gene. The total accumulated fungal diversity across France included 136 219 operational taxonomic units (OTUs), i.e., about 1 % of worldwide soil fungal diversity (based on a maximum diversity estimate of 12 million) for a territory representing only 0.3 % of the terrestrial surface on Earth. Based on this dataset, the first extensive map of fungal alpha diversity was drawn and showed a heterogeneous and spatially structured distribution in large biogeographical patterns of 231 km radius for richness (Hill diversity of order 0) and smaller patterns of 36 km radius for dominant fungi (Hill diversity of order 2). As related to other environmental parameters, the spatial distribution of fungal diversity (Hill numbers based on different orders of diversity) was mainly influenced by local filters such as soil characteristics and land management and also by global filters such as climate conditions with various relative influences. Interestingly, cropped soils exhibited the highest pool of fungal diversity relative to forest and vineyard soils. To complement this, soil fungal OTU network interactions were calculated for the different land uses across France. They varied hugely and showed a loss of 75 % of the complexity in crop systems and grasslands compared to forests and up to 83 % in vineyard systems. Overall, our study revealed that a nationwide survey with a high spatial-resolution approach is relevant for deeply investigating the spatial distribution and determinism of soil fungal diversity. Our findings provide novel insights for a better understanding of soil fungal ecology across the 18S rDNA gene and upgrade biodiversity conservation policies by supplying representative repositories dedicated to soil fungi.
Auteurs, date et publication :
Auteurs Christophe Djemiel , Samuel Dequiedt , Walid Horrigue , Arthur Bailly , Mélanie Lelièvre , Julie Tripied , Charles Guilland , Solène Perrin , Gwendoline Comment , Nicolas P. A. Saby , Claudy Jolivet , Antonio Bispo , Line Boulonne , Antoine Pierart , Patrick Wincker , Corinne Cruaud , Pierre-Alain Maron , Sébastien Terrat , Lionel Ranjard
Publication : SOIL
Date : 2024
Volume : 10
Issue : 1
Pages : 251-273
Catégorie(s)
#Genosol #INRAERésumé
Microorganisms in soil are known to be a source and a sink of volatile organic compounds (VOCs). The role of the microbial VOCs on soil ecosystem regulation has been increasingly demonstrated in the recent years. Nevertheless, little is known about the influence of the microbial soil community structure and diversity on VOC emissions. This novel study analyzed the effect of reduced microbial diversity in soil on VOC emissions. We found that reduced levels of microbial diversity in soil increased VOC emissions from soils, while the number of different VOCs emitted decreased. Furthermore, we found that Proteobacteria, Bacteroidetes and fungi phyla were positively correlated to VOC emissions, and other prokaryotic phyla were either negatively correlated or very slightly positively correlated to VOCs emissions. Our interpretation is that Proteobacteria, Bacteroidetes and fungi were VOC producers while the other prokaryotic phyla were consumers. Finally, we discussed the possible role of VOCs as mediators of microbial interactions in soil.
Auteurs, date et publication :
Auteurs Letizia Abis , Benjamin Loubet , Raluca Ciuraru , Florence Lafouge , Sabine Houot , Virginie Nowak , Julie Tripied , Samuel Dequiedt , Pierre Alain Maron , Sophie Sadet-Bourgeteau
Publication : Scientific Reports
Date : 2020
Volume : 10
Issue : 1
Pages : 6104
Catégorie(s)
#ANR-Citation #Genosol #INRAE #PRORésumé
Abstract 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 post-clustering tool called ReClustOR aimed at improving the stability and reliability of OTUs whatever the initial clustering method. We compared several clustering methods: a homemade de novo method, VSEARCH, Swarm and ReClustOR associated with these three clustering methods, and the ESV definition, using two datasets (a simulated one and an environmental one). All methods were analysed for their ability to efficiently describe microbial diversity in terms of alpha-diversity, beta-diversity and phylogeny. Dataset analysis showed that post-clustering with ReClustOR improved OTU detection not only in terms of diversity, but also in terms of reliability and stability as compared to the initial clustering methods. More precisely, the post-clustering step improved the congruence of the results (alpha-diversity, beta-diversity, composition) whatever the initial clustering method. Moreover, ReClustOR, by defining a database of centroids, precludes the need to re-cluster all the reads each time when new reads are generated. ReClustOR is a new post-clustering method that overcomes problems (OTU stability and reliability) associated with classical clustering methods and thereby increases the quality and the congruence of the reconstructed OTUs. Moreover, the OTU database defined with ReClustOR can be used as a reference gradually enriched by merging new studies and samples. In this way, huge datasets (e.g. the Earth Microbiome Project or the Tara Oceans project) can be used as references for other projects within their range of application, and increase the quality of comparisons among studies and datasets.
Auteurs, date et publication :
Auteurs Sébastien Terrat , Christophe Djemiel , Corentin Journay , Battle Karimi , Samuel Dequiedt , Walid Horrigue , Pierre-Alain Maron , Nicolas Chemidlin Prévost-Bouré , Lionel Ranjard
Publication : Methods in Ecology and Evolution
Date : 2020
Volume : 11
Issue : 1
Pages : 168-180
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
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