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 #INRAERésumé
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 #INRAERésumé
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 #INRAERésumé
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 #INRAERésumé
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 #INRAERésumé
We compared pyrosequencing technology with the PCR-ITS-RFLP analysis of yeast isolates and denaturing gradient gel electrophoresis (DGGE). These methods gave divergent findings for the yeast population. DGGE was unsuitable for the quantification of biodiversity and its use for species detection was limited by the initial abundance of each species. The isolates identified by PCR-ITS-RFLP were not fully representative of the true population. For population dynamics, high-throughput sequencing technology yielded results differing in some respects from those obtained with other approaches. This study demonstrates that 454 pyrosequencing of amplicons is more relevant than other methods for studying the yeast community on grapes and during alcoholic fermentation. Indeed, this high-throughput sequencing method detected larger numbers of species on grapes and identified species present during alcoholic fermentation that were undetectable with the other techniques.
Auteurs, date et publication :
Auteurs Vanessa David , Sebastien Terrat , Khaled Herzine , Olivier Claisse , Sandrine Rousseaux , Raphaelle Tourdot-Marechal , Isabelle Masneuf-Pomarede , Lionel Ranjard , Herve Alexandre
Publication : JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
Date : 2014
Volume : 41
Issue : 5
Pages : 811-821
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Microbiological datasets and associated environmental parameters from the French soil quality monitoring network (RMQS) offer an opportunity for long-term and large-scale soil quality monitoring. Soils supply important ecosystem services e.g. carbon dynamics/storage or mineral element recycling, supported by the soil microbial diversity (bacteria, archaea and fungi). Based on the 2,240 sites of the 2000–2015 RMQS, molecular tools were applied to characterize soil microbiota. Soil DNA analysis yielded molecular microbial biomass for 2,168 sites, bacterial and fungal qPCR for 2,073 sites, and high-throughput amplicon sequencing of targeted 16S rDNA bacterial and archaeal genes for 1,842 sites. All these datasets were partially or completely unavailable, so raw results files from RMQS microbiological studies were harmonized and published in a Dataverse repository to facilitate their reusability. Altogether, these datasets allow for in-depth studies of soil microbial ecology and biogeography, and will be updated with fungal datasets and the second currently ongoing monitoring campaign (2016–2027).
Auteurs, date et publication :
Auteurs Aurélien Cottin , Samuel Dequiedt , Christophe Djemiel , Nicolas Chemidlin Prévost-Bouré , Julie Tripied , Mélanie Lelièvre , Lucie Terreau , Tiffanie Régnier , Battle Karimi , Claudy Jolivet , Antonio Bispo , Nicolas Saby , Pierre-Alain Maron , Lionel Ranjard , Sébastien Terrat
Publication : Scientific Data
Date : 2025
Volume : 12
Issue : 1
Pages : 34
Catégorie(s)
#Genosol #INRAERésumé
In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO2 emission by up to 40%, and (ii) shaped the source of CO2 emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil.
IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil.
Auteurs, date et publication :
Auteurs Pierre-Alain Maron , Amadou Sarr , Aurore Kaisermann , Jean Lévêque , Olivier Mathieu , Julien Guigue , Battle Karimi , Laetitia Bernard , Samuel Dequiedt , Sébastien Terrat , Abad Chabbi , Lionel Ranjard
Publication : Appl. Environ. Microbiol.
Date : 2018
Volume : 84
Issue : 9
Pages : e02738-17
Catégorie(s)
#ACBB #ACBB Lusignan #Genosol #INRAEAuteurs, date et publication :
Auteurs Francis Martin , Stephane Uroz , Samuel Dequiedt , Pierre-Alain Maron , Lionel Ranjard
Date : 2025
Volume : 1399
Pages : 55-60
Catégorie(s)
#Genosol #INRAERésumé
Many studies have focused on the impact of intense drought and rain events on soil functioning and diversity, but little attention has been paid to the response of microbial communities to non-extreme soil moisture variations. However, small fluctuations of soil water content represent a common situation that ought to be examined before understanding and deciphering the impact of extreme events. Here, we tested the impact of a decrease in average soil water content and small water content fluctuations in non-extreme conditions on microbial community composition and C mineralisation rate of a temperate meadow soil. Two soil microcosm sets were incubated at high and low constant moisture and a third set was subjected to 4 short dry–wet cycles between these two soil moistures. No robust change in bacterial community composition, molecular microbial biomass, and fungal:bacterial ratio were associated with soil water content change. On the contrary, the fungal community composition rapidly alternated between states corresponding to the high and low levels of soil moisture content. In addition, gross C mineralisation was correlated with soil moisture, with a noteworthy absence of a Birch effect (C over-mineralisation) during the wetting. This study suggests that some fungal populations could coexist by occupying different moisture niches, and high fungal community plasticity would classify them as more sensitive indicators of soil moisture than bacteria. Moreover, under non-stressed conditions, the community composition did not affect metabolic performance so a future decrease in average soil moisture content should not result in a supplemental loss in soil carbon stocks by a Birch effect.
Auteurs, date et publication :
Auteurs A. Kaisermann , P. A. Maron , L. Beaumelle , J. C. Lata
Publication : Applied Soil Ecology
Date : 2025
Volume : 86
Pages : 158-164