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

Résumé

The horse’s hindgut bacterial ecosystem has often been studied using faecal samples. However few studies compared both bacterial ecosystems and the validity of using faecal samples may be questionable. Hence, the present study aimed to compare the structure of the equine bacterial community in the hindgut (caecum, right ventral colon) and faeces using a fingerprint technique known as Automated Ribosomal Intergenic Spacer Analysis (ARISA). Two DNA extraction methods were also assessed. Intestinal contents and faeces were sampled 3 h after the morning meal on four adult fistulated horses fed meadow hay and pelleted concentrate. Irrespective of the intestinal segment, Principal Component Analysis of ARISA profiles showed a strong individual effect (P<0.0001). However, across the study, faecal bacterial community structure significantly (P<0.001) differed from those of the caecum and colon, while there was no difference between the two hindgut communities. The use of a QIAamp® DNA Stool Mini kit increased the quality of DNA extracted irrespective of sample type. The differences observed between faecal and hindgut bacterial communities challenge the use of faeces as a representative for hindgut activity. Further investigations are necessary to compare bacterial activity between the hindgut and faeces in order to understand the validity of using faecal samples.

Auteurs, date et publication :

Auteurs S. Sadet-Bourgeteau , C. Philippeau , S. Dequiedt , V. Julliand

Publication : animal

Date : 2014

Volume : 8

Issue : 12

Pages : 1928-1934

Catégorie(s)

#Genosol #INRAE

Résumé

Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive or non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, seventeen OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.

Auteurs, date et publication :

Auteurs Katarzyna Siegel-Hertz , Véronique Edel-Hermann , Emilie Chapelle , Sébastien Terrat , Jos M. Raaijmakers , Christian Steinberg

Publication : Frontiers in Microbiology

Date : 2025

Volume : 9

Catégorie(s)

#Genosol #INRAE

Auteurs, date et publication :

Auteurs Anne Mercier , Joanne Bertaux , Jérôme Lesobre , Kevin Gravouil , Julien Verdon , Christine Imbert , Eric Valette , Yann Héchard

Publication : Biofouling

Date : 2016

Volume : 32

Issue : 3

Pages : 287-299

Catégorie(s)

#Genosol #INRAE

Résumé

The Biological Resource Centre for the Environment BRC4Env is a network of Biological Resource Centres (BRCs) and collections whose leading objectives are to improve the visibility of genetic and biological resources maintained by its BRCs and collections and to facilitate their use by a large research community, from agriculture research to life sciences and environmental sciences. Its added value relies on sharing skills, harmonizing practices, triggering projects in comparative biology, and ultimately proposing a single-entry portal to facilitate access to documented samples, taking into account the partnership policies of research institutions as well as the legal frame which varies with the biological nature of resources. BRC4Env currently includes three BRCs: the Centre for Soil Genetic Resources of the platform GenoSol, in partnership with the European Conservatory of Soil Samples; the Egg Parasitoids Collection (EP-Coll); and the collection of ichthyological samples, Colisa. BRC4Env is also associated to several biological collections: microbial consortia (entomopathogenic bacteria, freshwater microalgae…), terrestrial arthropods, nematodes (plant parasitic, entomopathogenic, animal parasitic...), and small mammals. The BRCs and collections of BRC4Env are involved in partnership with academic scientists, as well as private companies, in the fields of medicinal mining, biocontrol, sustainable agriculture, and additional sectors. Moreover, the staff of the BRCs is involved in many training courses for students from French licence degree to Ph.D, engineers, as well as ongoing training.

Auteurs, date et publication :

Auteurs Christian Mougin , Emmanuelle Artige , Frédéric Marchand , Samuel Mondy , Céline Ratié , Nadine Sellier , Philippe Castagnone-Sereno , Armelle Cœur D’Acier , Daniel Esmenjaud , Céline Faivre-Primot , Laurent Granjon , Valérie Hamelet , Frederic Lange , Sylvie Pagès , Frédéric Rimet , Nicolas Ris , Guillaume Sallé

Publication : Environmental Science and Pollution Research

Date : 2018

Volume : 25

Issue : 34

Pages : 33849-33857

Catégorie(s)

#BiochemEnv #Genosol #INRAE

Résumé

Arbuscular mycorrhizal fungal (AMF) communities have been demonstrated to respond to a variety of biotic and abiotic factors, including various aspects of land management. Numerous studies have specifically addressed the impact of land use on AMF communities, but usually have been confined to one or a few sites. In this study, soil AMF assemblages were described in four different long-term observatories (LTOs) across Europe, each of which included a site-specific high-intensity and a low-intensity land use. AMF communities were characterized on the basis of 454 sequencing of the internal transcribed spacer 2 (ITS2) rDNA region. The primary goals of this study were (i) to determine the main factors that shape AMF communities in differentially managed sites in Europe and (ii) to identify individual AMF taxa or combinations of taxa suitable for use as biomarkers of land use intensification. AMF communities were distinct among LTOs, and we detected significant effects of management type and soil properties within the sites, but not across all sites. Similarly, indicator species were identified for specific LTOs and land use types but not universally for high- or low-intensity land uses. Different subsets of soil properties, including several chemical and physical variables, were found to be able to explain an important fraction of AMF community variation alone or together with other examined factors in most sites. The important factors were different from those for other microorganisms studied in the same sites, highlighting particularities of AMF biology.

Auteurs, date et publication :

Auteurs M.-L. Bouffaud , C. Bragalini , A. Berruti , M. Peyret-Guzzon , S. Voyron , H. Stockinger , D. van Tuinen , E. Lumini , D. Wipf , P. Plassart , P. Lemanceau , V. Bianciotto , D. Redecker , M. Girlanda

Publication : Mycorrhiza

Date : 2017

Volume : 27

Issue : 4

Pages : 331-343

Catégorie(s)

#Genosol #INRAE