Résumé

Using organic waste products (OWP) in agriculture makes it possible to increase productivity with less use of mineral fertilizers. However, the lasting effect on soil microbial communities of an OWP application repeated over several years needs further investigation. In the present study, soils were sampled from two long-term field experiments: QualiAgro and Colmar (France), where different types of OWP characterized by more or less stable organic matter had been applied for more than 10 years, and were compared to a control treatment. At QualiAgro, the carbon inputs due to OWP application were greater (∼4 t C ha−1 every two years) than at Colmar (∼1.7 t C ha−1 every two years). On both sites, soil samples were taken more than six months after the last OWP input. At QualiAgro, soil organic carbon, N and P2O5 concentrations, pH, and CEC were increased by repeated OWP inputs, as compared to the control. Soil microbial community parameters were also lastingly affected by OWP application. A 50% increase in microbial biomass was observed with OWP with the most stable organic matter contents. The prokaryotic community structure was influenced: directly by the OWP applied, and indirectly by soil properties changes. Soil pH appeared as a major driver for structure of the soil prokaryotic community. Fungal community structure was only directly influenced by the OWP applied. Contrastingly, at Colmar, OWP application had no impact on soil chemical characteristics or microbial communities’ parameters. This was probably due to the smaller amount of OWP applied than at QualiAgro, and/or a longer delay between the OWP application and soil sampling. Altogether, our results show that, depending on its type, the applied OWP could produce a lasting increase in soil microbial biomass and shape microbial community structure.

Auteurs, date et publication :

Auteurs S. Sadet-Bourgeteau , S. Houot , S. Dequiedt , V. Nowak , V. Tardy , S. Terrat , D. Montenach , V. Mercier , B. Karimi , N. Chemidlin Prévost-Bouré , P. A. Maron

Publication : Applied Soil Ecology

Date : 2018

Volume : 125

Pages : 278-287

Catégorie(s)

#ANR-Citation #Genosol #INRAE #PRO

Résumé

Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.

Auteurs, date et publication :

Auteurs Vincent Tardy , Abad Chabbi , Xavier Charrier , Christophe de Berranger , Tiffanie Reignier , Samuel Dequiedt , Celine Faivre-Primot , Sebastien Terrat , Lionel Ranjard , Pierre-Alain Maron

Publication : Plos One

Date : 2015

Volume : 10

Issue : 6

Catégorie(s)

#ACBB #ACBB Lusignan #ANR-Citation #Genosol

Résumé

Finding more sustainable ways to produce food is a major challenge for humanity in the face of biodiversity extinction and climate change. Consequently, research on the ability of agroecosystems to provide multiple functions is growing. In this regard, the relative importance of organic farming and landscape-scale measures for improving multifunctionality has recently been debated. We investigated the effects of farming system (conventional vs. organic) at field scale, total length of hedgerows in the landscape and their interaction on the multifunctionality of 40 winter cereal fields in Brittany (France). Our multifunctionality assessment integrated 21 indicators of five agroecosystem goods: biodiversity conservation, nutrient cycling and soil structure, pest and disease regulation, food production and socio-economic performance. Many indicators of biodiversity conservation, pest and disease regulation, and socio-economic performance were higher in organic than in conventional systems. However, indicators of nutrient cycling and soil structure did not improve and food production was much lower in organic systems. Total hedgerow length in the landscape had less influence than organic farming on indicators, although we observed positive interactions. Granivorous carabid abundance and semi-net margin were highest in organic fields located in well-preserved hedgerow landscapes. Synthesis and applications. Our study suggests that field-scale organic farming is necessary to promote biodiversity conservation and associated ecological functioning in crop fields, whereas landscape-scale preservation of semi-natural habitats alone is likely insufficient. Preservation of hedgerows in the landscape brings additional ecological and socio-economic benefits for organic systems without compromising agricultural production. More broadly, our results call for more ambitious research into the myriad possible combinations of farming practices and agri-environmental measures at both field and landscape scales, to improve both below-ground and above-ground functioning.

Auteurs, date et publication :

Auteurs Sébastien Boinot , Audrey Alignier , Stéphanie Aviron , Colette Bertrand , Nathalie Cheviron , Gwendoline Comment , Emma Jeavons , Cécile Le Lann , Samuel Mondy , Christian Mougin , Pierre-Antoine Précigout , Claire Ricono , Corinne Robert , Grégoire Saias , Philippe Vandenkoornhuyse , Cendrine Mony

Publication : Journal of Applied Ecology

Date : 2026

Volume : 62

Issue : 1

Pages : 53-63

Catégorie(s)

#BiochemEnv #CNRS #EcoGenO #Genosol

Résumé

A better understanding of the links between dissolved organic matter and biogeochemical processes in soil could help in evaluating global soil dynamics. To assess the effects of land cover and parental material on soil biogeochemistry, we studied 120 soil samples collected from various ecosystems in Burgundy, France. The potential solubility and aromaticity of dissolved organic matter was characterised by pressurised hot-water extraction of organic carbon (PH-WEOC). Soil physico-chemical characteristics (pH, texture, soil carbon and nitrogen) were measured, as was the δ13C signature both in soils and in PH-WEOC. We also determined bacterial and fungal abundance and the genetic structure of bacterial communities. Our results show that the potential solubility of soil organic carbon is correlated to carbon and clay content in the soil. The aromaticity of PH-WEOC and its δ13C signature reflect differences in the decomposition pathways of soil organic matter and in the production of water-extractable organic compounds, in relation to land cover. The genetic structure of bacterial communities is related to soil texture and pH, and to PH-WEOC, revealing that water-extractable organic matter is closely related to the dynamics of bacterial communities. This comprehensive study, at the regional scale, thus provides better definition of the relationships between water-extractable organic matter and soil biogeochemical properties.

Auteurs, date et publication :

Auteurs J. Guigue , J. Lévêque , O. Mathieu , P. Schmitt-Kopplin , M. Lucio , D. Arrouays , C. Jolivet , S. Dequiedt , N. Chemidlin Prévost-Bouré , L. Ranjard

Publication : Soil Biology and Biochemistry

Date : 2025

Volume : 84

Pages : 158-167

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

The use of herbicides for weed control is very common, but some of them represent a threat to human health, are environmentally detrimental and stimulate herbicide resistance. Therefore, using microorganisms as natural herbicides appears as a promising alternative. The mycoflorae colonizing different species of symptomatic and asymptomatic weeds were compared to characterize the possible mycoherbicidal candidates associated with symptomatic weeds. A collection of 475 symptomatic and asymptomatic plants belonging to 23 weed species was established. A metabarcoding approach based on amplification of the internal transcribed spacer (ITS) region combined with high-throughput amplicon sequencing revealed the diversity of fungal communities hosted by these weeds: 542 fungal genera were identified. The variability of the composition of fungal communities revealed a dispersed distribution of taxa governed neither by geographical location nor by the botanical species, suggesting a common core displaying non-specific interactions with host plants. Beyond this core, specific taxa were more particularly associated with symptomatic plants. Some of these, such as Alternaria, Blumeria, Cercospora, Puccinia, are known pathogens, while others such as Sphaerellopsis, Vishniacozyma and Filobasidium are not, at least on crops, and constitute new tracks to be followed in the search for mycoherbicidal candidates. IMPORTANCE: This approach is original because the diversity of weed-colonizing fungi has rarely been studied before. Furthermore, targeting both the ITS1 and ITS2 regions to characterize the fungal communities i) highlighted the complementarity of these two regions, ii) revealed a great diversity of weed-colonizing fungi, and iii) allowed for the identification of potential mycoherbicides, among which unexpected genera.

Auteurs, date et publication :

Auteurs Marion Triolet , Véronique Edel-Hermann , Nadine Gautheron , Samuel Mondy , Carole Reibel , Olivier André , Jean-Philippe Guillemin , Christian Steinberg

Publication : Applied and Environmental Microbiology

Date : 2022

Pages : aem0217721

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

The effects of different anthropic activities (vineyard: phytosanitary protection; winery: pressing and sulfiting) on the fungal populations of grape berries were studied. The global diversity of fungal populations (moulds and yeasts) was performed by pyrosequencing. The anthropic activities studied modified fungal diversity. Thus, a decrease in biodiversity was measured for three successive vintages for the grapes of the plot cultivated with Organic protection compared to plots treated with Conventional and Ecophyto protections. The fungal populations were then considerably modified by the pressing-clarification step. The addition of sulfur dioxide also modified population dynamics and favoured the domination of the species Saccharomyces cerevisiae during fermentation. The non-targeted chemical analysis of musts and wines by FT-ICR-MS showed that the wines could be discriminated at the end of alcoholic fermentation as a function of adding SO2 or not, but also and above all as a function of phytosanitary protection, regardless of whether these fermentations took place in the presence of SO2 or not. Thus, the existence of signatures in wines of chemical diversity and microbiology linked to vineyard protection has been highlighted.

Auteurs, date et publication :

Auteurs Cédric Grangeteau , Chloé Roullier-Gall , Sandrine Rousseaux , Régis D. Gougeon , Philippe Schmitt-Kopplin , Hervé Alexandre , Michèle Guilloux-Benatier

Publication : Microbial Biotechnology

Date : 2016

Pages : n/a-n/a

Catégorie(s)

#Genosol #INRAE

Résumé

Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR2/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.

Auteurs, date et publication :

Auteurs Christophe Djemiel , Damien Plassard , Sébastien Terrat , Olivier Crouzet , Joana Sauze , Samuel Mondy , Virginie Nowak , Lisa Wingate , Jérôme Ogée , Pierre-Alain Maron

Publication : Scientific Reports

Date : 2020

Volume : 10

Issue : 1

Pages : 5915

Catégorie(s)

#Genosol #INRAE

Résumé

The evaluation of the taxa–area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources.

Auteurs, date et publication :

Auteurs S. Terrat , S. Dequiedt , W. Horrigue , M. Lelievre , C. Cruaud , N. P. A. Saby , C. Jolivet , D. Arrouays , P.-A. Maron , L. Ranjard , N. Chemidlin Prévost-Bouré

Publication : Heredity

Date : 2025

Volume : 114

Issue : 5

Pages : 468-475

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

During the last 10 years, several attempts to map soil attributes at the scale of mainland France have been realised. We exemplify them by seven major outputs: maps of organic C stocks, trace elements (TE), microbial density and diversity, soil thickness, available water capacity (AWC), extractable P, and changes in soil pH. We first briefly describe the data and the methods used to produce these maps and summarise their main results. We then focus on their impacts on various categories of the public, i.e. the general public and citizens; farmers; private companies; non-governmental organisations; agricultural development organisations, stakeholders, and national agencies; French governmental bodies; and international organisations. We also analyse the demands that came to the French National Soil Information Centre from 2008 to 2018 and the impact that our activities had in various media. Soil organic C had the largest impact in nearly all categories of end-users, which may be linked to the recent `4 per 1000' initiative launched by the French governmentduring the COP21 and to the fact that farmers are interested in increasing the organic matter content of their soil for increasing the fertility. TE obtained high scores, which may be related to citizens' care about health and to the fact that governmental bodies and national agencies have a major interest in site contamination assessments. The soil P content, pH, and AWC exhibited major impacts on the agricultural sector. Maps of the soil P content and pH were used as geomarketing tools by private companies selling fertilisers and soil amendments, whereas the AWC was already incorporated into decision-making aid tools for irrigation management developed by development organisations for farmers. Microbial diversity generated collaborations with a large network of farmers and had a large media impact. Nevertheless, the visibility of soil information to the general public should be increased. This can be done by using new multimedia and interactive tools. Overall, these selected examples of digital soil mapping of soil attributes at the national scale in France clearly indicate that the soil attributes have substantial impact on various categories of end-users, such as farmers, professional organisations, stakeholders, and policymakers at different levels of decision-making, among others. However, the impacts on the general public and citizens are more difficult to quantify, and increasing the soil awareness of the general public should be of high priority. (C) 2020 Elsevier B.V. All rights reserved.

Auteurs, date et publication :

Auteurs Dominique Arrouays , Anne C. Richer-de-Forges , Florence Helies , Vera Leatitia Mulder , Nicolas P. A. Saby , Songchao Chen , Manuel P. Martin , Mercedes Roman Dobarco , Stephane Follain , Claudy Jolivet , Bertrand Laroche , Thomas Loiseau , Isabelle Cousin , Marine Lacoste , Lionel Ranjard , Benoit Toutain , Christine Le Bas , Thomas Eglin , Marion Bardy , Veronique Antoni

Publication : GEODERMA REGIONAL

Date : 2020

Volume : 23

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

The pea root rot complex is a major concern for green pea production worldwide. This study aimed at characterizing its composition and dynamics throughout a cropping season in northern France. To this end, fungi and oomycetes were isolated from green pea plant roots with symptoms sampled at the flowering stage in 22 fields in 2017, and at the pea emergence, elongation and flowering stages in two fields in 2018. Out of 646 isolates collected, 317 were identified using molecular markers. Fusarium oxysporum, F. solani and F. redolens were highly predominant. Pathogenicity tests separated the isolates into four aggressiveness groups. F. solani isolates were the most aggressive. Phylogenetic analysis of their TEF1 sequences showed that they mainly belonged to the F. pisi lineage, and that F. oxysporum isolates were genetically close to isolates from the UK that did not belong to the forma specialis pisi. In addition, several Clonostachys rhizophaga isolates are reported for the first time to cause pea root rot. The oomycetes were rarely found and were represented by a few Pythium spp. isolates. Lastly, this study shows that the fungal and oomycete communities associated with pea root rot change during the cropping season. The level of dissimilarity of the root-rot-associated communities decreased throughout the cropping season towards a more similar composition at the flowering stage, dominated by F. solani, F. oxysporum and F. redolens. The proportion of nonpathogenic to weakly pathogenic isolates decreased progressively during the growing season in favour of moderately to highly pathogenic isolates.

Auteurs, date et publication :

Auteurs Simon Gibert , Veronique Edel-Hermann , Elodie Gautheron , Nadine Gautheron , Eric Bernaud , Jean-Marie Sol , Gery Capelle , Rachel Galland , Arnaud Bardon-Debats , Claudine Lambert , Christian Steinberg

Publication : PLANT PATHOLOGY

Date : 2022

Volume : 71

Issue : 7

Pages : 1550-1569

Catégorie(s)

#ANR-Citation #Genosol #INRAE