Auteurs, 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 #INRAE

Résumé

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 #INRAE

Auteurs, 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 #INRAE

Résumé

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 #INRAE

Résumé

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

Catégorie(s)

#Genosol #INRAE

Auteurs, date et publication :

Auteurs D Bru , A Ramette , N P A Saby , S Dequiedt , L Ranjard , C Jolivet , D Arrouays , L Philippot

Publication : The ISME Journal

Date : 2025

Volume : 5

Issue : 3

Pages : 532-542

Catégorie(s)

#Genosol #INRAE

Résumé

Aims To develop a qPCR approach for the detection of Pseudomonas aeruginosa in soil and manure and explore its efficacy and limitations compared with that of a classical culture-dependent approach. Methods and Results A Ps. aeruginosa ecfX qPCR assay was developed. This assay was optimized for soils of contrasting physico-chemical properties and evidenced a three-log dynamic range of detection [5 × 104 – 5 × 106 cells (g drywt soil)−1] in inoculated microcosms. Sensitivity was determined to be around 5 × 104 cells (g drywt soil)−1. In parallel, the minimum detection limit was estimated in the range of 10–100 CFU (g drywt soil)−1 using a culture-dependent approach based on the use of a selective medium (cetrimide agar base medium supplemented with nalidixic acid), coupled to ecfX gene amplification to confirm isolate identity. These soil samples led to the growth of abundant non-Ps. aeruginosa colonies mainly belonging to other Pseudomonas species but also some beta-Proteobacteria. These bacteria strongly impacted the detection threshold of this approach. Efficacy of these approaches was compared for Ps. aeruginosa enumeration among manure and agricultural soil samples from various sites in France, Tunisia and Burkina Faso. Conclusions The developed qPCR assay enabled a specific detection of Ps. aeruginosa in soil and manure samples. The culture-based approach was usually found more sensitive than the qPCR assay. However, abundance of non-Ps. aeruginosa species among the indigenous communities able to grow on the selective medium affected the sensitivity of this latter approach. Significance and Impact of the Study This study describes the first specific and sensitive qPCR assay for the detection and enumeration of Ps. aeruginosa in soil and manure and shows its complementarity with a culture-based approach.

Auteurs, date et publication :

Auteurs C. Colinon , A. Deredjian , E. Hien , E. Brothier , L. Bouziri , B. Cournoyer , A. Hartman , S. Henry , C. Jolivet , L. Ranjard , S. Nazaret

Publication : Journal of Applied Microbiology

Date : 2025

Volume : 114

Issue : 6

Pages : 1734-1749

Catégorie(s)

#Genosol #INRAE

Résumé

Candida albicans is the most common human fungal pathogen. This yeast is described as a commensal of human and animal mucosa, and very few studies have focused on its isolation in natural environments. We investigated the presence of C. albicans in a large panel of French soils. Because a culture-based method didn't allow isolation of the yeast in a panel of 70 soils, we adapted a nested-PCR for detecting C. albicans DNA in a panel of 460 soils. Only 7 of the 460 soil samples (1.5%) were PCR-positive for Candida albicans. To understand which parameters influence the survival of the yeast, we studied the decline of a population of C. albicans over a period of one month in a collection of 20 soils collected throughout France. C. albicans was able to survive up to 30 days in 80% of the soils tested. Using a Spearman correlation test, we showed that the short-term survival of C. albicans in soils was correlated with some soils chemical factors such as pH and presence of some minerals (Al, Mn, and Na). Concerning survival after 30 days, Cation Exchange Capacity (CEC) and clay content were identified as beneficial determinants of the long-term survival of C. albicans in soils.

Auteurs, date et publication :

Auteurs Marc Sautour , Jean-Paul Lemaître , Lionel Ranjard , Caroline Truntzer , Louise Basmaciyan , Géraldine Depret , Alain Hartmann , Frédéric Dalle

Publication : Environmental DNA

Date : 2025

Volume : n/a

Issue : n/a

Catégorie(s)

#Genosol #INRAE

Résumé

Two bacterial consortia prepared from a polychlorinated biphenyl (PCB)-contaminated soil enrichment were used as inocula, for aerobic PCB-degradation experiments in soil microcosms. The consortia were prepared either as a planktonic culture, or as a biofilm attached to granular activated carbon (GAC). Both consortia were mainly composed of members of the α-, β- and γ-subclasses of the phylum Proteobacteria. The most abundant bacteria, belonged to the genera Pseudomonas, Achromobacter, Ochrobactrum and Halomonas which are commonly associated with soil contaminated with biphenyl or PCBs. The decrease of the level of extractable PCB congeners was assessed in microcosms containing the same PCB-polluted soil from which the consortia were prepared and it was spiked or not with Aroclor 1242. When Aroclor 1242 was added to soil, mainly low-chlorinated congeners were removed, whereas in non-spiked soil, decreases of extractable PCBs levels were observed for a broader range of congeners. The biofilm-coated GAC was less efficient than the planktonic cells to decrease the total amount of extractable PCBs. This limitation was possibly due to the differences in the bacterial composition of the two inocula and to the reduced bioavailability the GAC-adsorbed PCBs. Nevertheless, the biofilm-coated GAC accelerated the aerobic removal of the extractable PCBs during the first three months of incubation, albeit limited in terms of total PCB-removal.

Auteurs, date et publication :

Auteurs A. Mercier , C. Michel , C. Joulian , S. Touzé , L. Amalric , P. Bataillard , C. Morlay , F. Battaglia-Brunet

Publication : International Biodeterioration & Biodegradation

Date : 2015

Volume : 105

Pages : 127-136

Catégorie(s)

#Genosol #INRAE

Auteurs, date et publication :

Auteurs Florentin Constancias , Nicolas P. A. Saby , Sébastien Terrat , Samuel Dequiedt , Wallid Horrigue , Virginie Nowak , Jean-Philippe Guillemin , Luc Biju-Duval , Nicolas Chemidlin Prévost-Bouré , Lionel Ranjard

Publication : MicrobiologyOpen

Date : 2025

Volume : 4

Issue : 3

Pages : 518-531

Catégorie(s)

#ANR-Citation #Genosol #INRAE