Résumé
Theory surrounding landscape ecology has been built on the species distribution of birds and plants, but increasing evidence now exists for below-ground organisms, whose dispersal may also be affected by above-ground landscape structures. Uncertainties remain for how communities of microorganisms respond to landscape structure over time, and whether some groups of microorganisms react more than others. Here, we investigated if fungal or bacterial diversity is driven by the amount of forest cover in the current or the past landscape. We tested the habitat amount hypothesis (HAH) on ancient forests of the Cevennes national park, that experienced increased fragmentation 150 years ago, and are today surrounded by recent forests. As ancient forests are often more diverse in plant species, we hypothesized that the higher quantity of ancient forests in the landscape, the richer local fungal and bacterial communities would be. More precisely, we expected that ectomycorrhizal fungi, and pathotrophic fungi, often indicators of mature forests, would be also more sensitive to forest history and therefore to the quantity of ancient forests than bacteria and saprotrophic fungi. We sampled 40 soil cores per 0.5 ha, pooled in 8 composite samples per plot in 27 landscapes and sequenced ITS1 and 16S markers by Illumina-Mi seq. To identify functional groups of fungi, we relied on their taxonomy and the use of public databases. Our results partly follow the HAH, as fungal richness was positively related with the quantity of ancient forests in the landscape and not by the focal patch size. Ectomycorrhizal and pathotrophic fungi were positively affected by the ancient forest cover, and so were saprotrophic ones, but not bacteria. Local factors also shaped the communities such as soil composition and elevation, confirming classical patterns in soil microbial ecology. Interestingly, past landscape structure was better at explaining fungal community richness than contemporary landscape, suggesting a time lag in the response of communities to landscape modification and a potential extinction debt. Our results reveal the importance of below-ground communities in studies of landscape and historical ecology, with their structure and functions likely to be intimately linked with soil and landscape history.
Auteurs, date et publication :
Auteurs Sophie Mennicken , Floriane Kondratow , Florian Buralli , Sophie Manzi , Emilie Andrieu , Melanie Roy , Antoine Brin
Publication : FRONTIERS IN ECOLOGY AND EVOLUTION
Date : 2020
Volume : 8
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
BACKGROUND: The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.
RESULTS: BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.
CONCLUSIONS: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.
Auteurs, date et publication :
Auteurs Christophe Djemiel , Samuel Dequiedt , Battle Karimi , Aurélien Cottin , Thibault Girier , Yassin El Djoudi , Patrick Wincker , Mélanie Lelièvre , Samuel Mondy , Nicolas Chemidlin Prévost-Bouré , Pierre-Alain Maron , Lionel Ranjard , Sébastien Terrat
Publication : BMC bioinformatics
Date : 2020
Volume : 21
Issue : 1
Pages : 492
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.
Auteurs, date et publication :
Auteurs Laurie Dunn , Christophe Lang , Nicolas Marilleau , Sébastien Terrat , Luc Biju-Duval , Mélanie Lelièvre , Solène Perrin , Nicolas Chemidlin Prévost-Bouré
Publication : PLOS ONE
Date : 2025
Volume : 16
Issue : 6
Pages : e0252216
Catégorie(s)
#Genosol #INRAERésumé
Aphanomyces euteiches Drechs is a pathogenic soil-borne oomycete that causes root rot of legumes, one of the most serious diseases affecting legume production worldwide. There is currently no registered pesticide and no available resistant pea cultivar. Avoidance of infested fields based on disease risk assessment prior to pea sowing remains the main method available to manage the disease, but time-consuming bioassays are required to assess disease severity on susceptible plants grown in field soil samples. Direct quantification of A. euteiches inoculum in the soil by targeting multicopy genomic sequences of the internal transcribed spacer 1 with a qPCR-based method has been proposed as a rapid alternative for disease prediction. However, the method lacks sensitivity to accurately quantify low inoculum levels from naturally infested fields. We developed a suitable methodology based on droplet digital PCR (ddPCR) to quantify low A. euteiches inoculum levels in naturally infested soils. The methodology was validated on 200 soil samples taken from four naturally infested fields in the main pea cropping area in the north of France. The comparative analysis of inoculum density and disease severity of the 50 samples within each of the four fields revealed a non-homogeneous distribution of the A. euteiches population; this explains why the disease is visible in the form of foci. A significant relationship between pea root rot disease severity determined by bioassays and A. euteiches inoculum density was highlighted, and a linear mixed model is proposed to predict disease severity from inoculum density.
Auteurs, date et publication :
Auteurs Simon Gibert , Véronique Edel-Hermann , Rayanti Moussa Mcolo , Elodie Gautheron , Joël Michel , Eric Bernaud , Nadine Gautheron , Jean-Marie Sol , Gery Capelle , Rachel Galland , Arnaud Bardon-Debats , Claudine Lambert , Christian Steinberg
Publication : European Journal of Plant Pathology
Date : 2021
Volume : 161
Issue : 3
Pages : 503-528
Catégorie(s)
#Genosol #INRAERésumé
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered – public leisure, traffic, and urban agriculture – sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
Auteurs, date et publication :
Auteurs Amélie Christel , Samuel Dequiedt , Nicolas Chemidlin-Prevost-Bouré , Florian Mercier , Julie Tripied , Gwendoline Comment , Christophe Djemiel , Lionel Bargeot , Eric Matagne , Agnès Fougeron , Jean-Bertrand Mina Passi , Lionel Ranjard , Pierre-Alain Maron
Publication : Science of The Total Environment
Date : 2023
Pages : 163455
Catégorie(s)
#Genosol #INRAERésumé
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