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 #INRAERésumé
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 #INRAERésumé
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 #INRAEAuteurs, date et publication :
Auteurs Victor Frossard , Laurent Millet , Valérie Verneaux , Jean-Philippe Jenny , Fabien Arnaud , Michel Magny , Marie-Elodie Perga
Publication : Freshwater Biology
Date : 2025
Volume : 59
Issue : 1
Pages : 26-40
Catégorie(s)
#INRAE #OLARésumé
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 #INRAEAuteurs, date et publication :
Auteurs Elisa Adriano , Jean-Paul Laclau , João Domingos Rodrigues
Publication : Trees
Date : 2025
Volume : 31
Issue : 1
Pages : 285-297
Catégorie(s)
#CIRAD #FORET Itatinga #INRAERésumé
Abstract
Globally, lake surface water temperatures have warmed rapidly relative to air temperatures, but changes in deepwater temperatures and vertical thermal structure are still largely unknown. We have compiled the most comprehensive data set to date of long-term (1970–2009) summertime vertical temperature profiles in lakes across the world to examine trends and drivers of whole-lake vertical thermal structure. We found significant increases in surface water temperatures across lakes at an average rate of + 0.37 °C decade
−1
, comparable to changes reported previously for other lakes, and similarly consistent trends of increasing water column stability (+ 0.08 kg m
−3
decade
−1
). In contrast, however, deepwater temperature trends showed little change on average (+ 0.06 °C decade
−1
), but had high variability across lakes, with trends in individual lakes ranging from − 0.68 °C decade
−1
to + 0.65 °C decade
−1
. The variability in deepwater temperature trends was not explained by trends in either surface water temperatures or thermal stability within lakes, and only 8.4% was explained by lake thermal region or local lake characteristics in a random forest analysis. These findings suggest that external drivers beyond our tested lake characteristics are important in explaining long-term trends in thermal structure, such as local to regional climate patterns or additional external anthropogenic influences.
Auteurs, date et publication :
Auteurs Rachel M. Pilla , Craig E. Williamson , Boris V. Adamovich , Rita Adrian , Orlane Anneville , Sudeep Chandra , William Colom-Montero , Shawn P. Devlin , Margaret A. Dix , Martin T. Dokulil , Evelyn E. Gaiser , Scott F. Girdner , K. David Hambright , David P. Hamilton , Karl Havens , Dag O. Hessen , Scott N. Higgins , Timo H. Huttula , Hannu Huuskonen , Peter D. F. Isles
Publication : Scientific Reports
Date : 2025
Volume : 10
Issue : 1
Pages : 20514
Catégorie(s)
#INRAE #OLARésumé
Agricultural lands are subject to changes in use for a variety of environmental and economic reasons. Among these changes, shifts between crops and grasslands are particularly common. Understanding the effects of these changes on soil functioning is crucial to anticipating crop productivity and environmental impacts and yet has rarely been studied. The purpose of this study was to investigate the in situ temporal dynamics of soil N cycling and C pools after grassland/cropland conversions and risks of N losses from such systems. The experiment was conducted in western France at a long-term experimental site with a temperate oceanic climate. We followed soil N cycling and C pools for four experimental treatments over 36 months: (i) continuous grassland, (ii) continuous rotation of annual crops, (iii) conversion from grassland to a rotation of annual crops, and (iv) conversion from a rotation of annual crops to grassland. Gross N mineralization, potential N immobilization and potential nitrification were estimated using the 15N dilution/enrichment technique and FLUAZ model, based on samples from the 0e10 cm soil layer (0, 0.75, 3, 12, 24 and 36 months after change in land use) and 10e30 cm soil layer (after 24 and 36 months) in all 4 treatments. Nitrogen pools (NH4þ, NO3À, and organic N), total carbon (C), dissolved organic C, microbial biomass C, and C mineralization were also determined on all soil samples.
Auteurs, date et publication :
Auteurs E. Attard , X. Le Roux , X. Charrier , O. Delfosse , N. Guillaumaud , G. Lemaire , S. Recous
Publication : Soil Biology and Biochemistry
Date : 2025
Volume : 97
Pages : 31-39
Catégorie(s)
#ACBB #ACBB Lusignan #INRAEAuteurs, date et publication :
Auteurs Salima Taibi-Hassani , Jeanne-Chantal Thoisy , Patrice Lepelletier , Jeanne Bodin , Nadia Bennegadi-Laurent , Jean-Jacques Bessoule , Antonio Bispo , Josselin Bodilis , Rémi Chaussod , Nathalie Cheviron , Jérôme Cortet , Stephan Criquet , Jérôme Dantan , Samuel Dequiedt , Olivier Faure , Christophe Gangneux , Jennifer Harris-Hellal , Mickaël Hedde , Adnane Hitmi , Marina Le Guédard
Publication : Etude et Gestion des Sols
Date : 2025
Volume : 20
Issue : 2
Pages : 127-136
Catégorie(s)
#INRAE #PROAuteurs, date et publication :
Auteurs Muhammad Sanaullah , Abad Chabbi , Jens Leifeld , Gerard Bardoux , Daniel Billou , Cornelia Rumpel
Publication : Plant and Soil
Date : 2025
Volume : 338
Issue : 1-2
Pages : 127–141