Résumé
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
Catégorie(s)
#Genosol #INRAEAuteurs, date et publication :
Auteurs Cédric Grangeteau , Daniel Gerhards , Sebastien Terrat , Samuel Dequiedt , Hervé Alexandre , Michèle Guilloux-Benatier , Christian von Wallbrunn , Sandrine Rousseaux
Publication : Journal of Microbiological Methods
Date : 2025
Volume : 121
Pages : 50-58
Catégorie(s)
#Genosol #INRAERésumé
Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.
Auteurs, date et publication :
Auteurs Pierre Plassart , Sébastien Terrat , Bruce Thomson , Robert Griffiths , Samuel Dequiedt , Mélanie Lelievre , Tiffanie Regnier , Virginie Nowak , Mark Bailey , Philippe Lemanceau , Antonio Bispo , Abad Chabbi , Pierre-Alain Maron , Christophe Mougel , Lionel Ranjard
Publication : Plos One
Date : 2012
Volume : 7
Issue : 9
Pages : e44279
Catégorie(s)
#ACBB #ACBB Lusignan #Genosol #INRAEAuteurs, date et publication :
Auteurs Naoise Nunan , Julie Leloup , Léo S. Ruamps , Valérie Pouteau , Claire Chenu
Publication : Scientific Reports
Date : 2025
Volume : 7
Issue : 1
Catégorie(s)
#Genosol #INRAERésumé
The soil microbial community plays important roles in nutrient cycling, plant pathogen suppression, decomposition of residues and degradation of pollutants; as such, it is often regarded as a good indicator of soil quality. Repeated applications of mixed organic and inorganic materials in agriculture improve the soil microbial quality and in turn crop productivity. The soil microbial quality following several years of repeated fertilizer inputs has received considerable attention, but the dynamic of this community over time has never been assessed. We used high-throughput sequencing targeting 16S ribosomal RNA genes to investigate the evolution of the bacterial and archaeal community throughout 6 years of repeated organic and inorganic fertilizer applications. Soils were sampled from a field experiment in La Mare (Reunion Island, France), where different mixed organic-inorganic fertilizer inputs characterized by more or less stable organic matter were applied regularly for 6 years. Soil samples were taken each year, more than 6 months after the latest fertilizer application. The soil molecular biomass significantly increased in some organically fertilized plots (by 35–45% on average), 3–5 years after the first fertilizers application. The significant variations in soil molecular microbial biomass were explained by the fertilization practices (cumulated organic carbon inputs) and sometimes by the soil parameters (sand and soil carbon contents). The structure of the bacterial and archaeal community was more influenced by time than by the fertilization type. However, repeated fertilizer applications over time tended to modify the abundance of the bacterial phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. To conclude, the present study highlights that the soil bacterial and archaeal community is lastingly modified after 6 years of repeated fertilizer inputs. These changes depend on the nature of the organic input and on the fertilization practice (frequency and applied quantity).
Auteurs, date et publication :
Auteurs Sophie Sadet-Bourgeteau , Christophe Djemiel , Nicolas Chemidlin Prévost-Bouré , Frederic Feder
Publication : Frontiers in Microbiology
Date : 2025
Volume : 13
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
In the French West Indies (FWI), the soil, andosols, ferralsols and nitisols, is highly polluted by chlordecone, although this organochlorine insecticide extensively applied to banana crops has been banned for 20years. This contamination has led to a major human health concern inducing the need for remediation of the contaminated soils. Work was conducted to help to evaluate the impact of remediation processes on the microbial communities from these soils. Microbial biomass was estimated after direct DNA extraction from three chlordecone-contaminated soils (an andosol, a ferralsol and a nitisol) and the bacterial community analyzed using t-RFLP. The FWI volcanic andosol was particularly recalcitrant to usual direct DNA extraction protocols hampering analysis of soil microbial communities until now, in contrast with the 2 other soils. For the first time, DNA was directly extracted from a FWI andosol based on yeast RNA addition at the lysis step. Differences in microbial biomass were thus observed between the 3 FWI soils. Moreover, the bacterial community structure was significantly distinct from each other’s and related to soil physico-chemical characteristics. Interestingly, differences in bacterial diversity could not be exclusively attributed to the level of chlordecone contamination.
Auteurs, date et publication :
Auteurs Anne Mercier , Marie-Christine Dictor , Jennifer Harris-Hellal , Dominique Breeze , Christophe Mouvet
Publication : Chemosphere
Date : 2013
Volume : 92
Issue : 7
Pages : 787-794