Résumé

Green infrastructures play a key role in the functionality and resilience of urban ecosystems. The physical, including thickness, chemical and biological properties of the Technosols of green infrastructures on rooftops are highly variable, leading to more or less favourable conditions for soil biodiversity. The aim of this study was to investigate the abundance and diversity of bacteria, fungi, nematodes, collembola and plants communities in relation with abiotic parameters of Technosols on 12 productive and extensive green roofs of the Paris region (France). Results showed that green roofs harboured a high level of abundance and diversity from microorganisms to micro and mesofauna. Microbial biomass ranged between 16.3 and 419.8 μg DNA g−1, with a predominance of bacteria, nematodes represented 820–60,700 individuals per kg of soil and between 1000 and 60,700 collembolan were present per m2 of soil. A total of 13,986 bacterial OTU (Operational Taxonomic Unit), 33,559 fungal OTU, 47 Collembola species, 28 nematodes families, 16 cultivated plant species and 48 spontaneous plant species was identified on all the green roofs studied. Microbial, animals and plants communities were significantly different between the two types of green roofs. Productive and extensive rooftops represent contrasted habitats, which can strongly influence the soil biota. Any voluntary action to enhance soil biodiversity in cities would need to take-into-account both soil properties and the landscape around.

Auteurs, date et publication :

Auteurs Sophie Joimel , Baptiste Grard , Claire Chenu , Pénélope Cheval , Samuel Mondy , Mélanie Lelièvre , Apolline Auclerc , Laure Vieublé Gonod

Publication : Ecological Engineering

Date : 2025

Volume : 175

Pages : 106475

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Auteurs, date et publication :

Auteurs Damien Costa , Anne Mercier , Kevin Gravouil , Jérôme Lesobre , Julien Verdon , Christine Imbert , Ake Forsberg

Publication : Pathogens and Disease

Date : 2025

Volume : 74

Issue : 7

Pages : ftw094

Catégorie(s)

#Genosol #INRAE

Résumé

CTX-M (extended spectrum beta-lactamase- ESBL) producing Escherichia coli are increasingly involved in human infections worldwide. The aim of this study was to investigate potential reservoirs for such strains: soils, cattle and farm environment. The prevalence of blaCTX-M genes was determined directly from soil DNA extracts obtained from 120 sites in Burgundy (France) using real time PCR. blaCTX-M targets were found in 20% of the DNA extracts tested. Samples of cattle feces (n=271) were collected from 182 farms in Burgundy. Thirteen ESBL-producing isolates were obtained from 12 farms and further characterized for the presence of bla genes. Of the 13 strains, five and eight strains carried blaTEM-71 genes and blaCTX-M-1 genes respectively. Ten strains of CTX-M-1 producing E. coli were isolated from cultivated and pasture soils as well as from composted manure within 2 of these farms. The genotypic analysis revealed that environmental and animal strains were clonally related. Our study confirms the occurrence of CTX-M producing E. coli in cattle and reports for the first time the occurrence of such strains in cultivated soils. The environmental competence of such strains has to be determined and might explain their long term survival since CTX-M isolates were recovered from a soil that was last amended with manure one year before sampling.

Auteurs, date et publication :

Auteurs Alain Hartmann , Lucie Amoureux , Aude Locatelli , Geraldine Depret , Claudy Jolivet , Eric Gueneau , Catherine Neuwirth

Publication : Frontiers in Microbiology

Date : 2025

Volume : 3

Catégorie(s)

#Genosol #INRAE

Résumé

Agricultural practices affect the physical and chemical characteristics of the soil, which in turn may influence soil microorganisms with consequences on soil biological functioning. However, there is little knowledge on the interactions between agricultural management, soil physicochemical properties, and soil microbial communities, notably in tropical ecosystems with few studies conducted in strongly weathered and acid soils. Here, we investigated the early effect of tillage and crop residues management on top soil physical, chemical, and microbial properties in an acid savannah grassland of northeastern Laos. We initiated a 3-year rotation of rice/corn/soybean under three no-till systems (NTs) distinguished by the cover crops associated prior to and with the main crops, and one conventional tillage-based system (CT). The effect of agricultural management was evaluated 2 years after land reclamation in reference to the surrounding natural pasture (PAS). Our results demonstrate that NTs improve soil physicochemical characteristics (aggregate stability, organic carbon, and cation exchange capacity) as well as microbial abundance (total biomass, bacterial and fungal densities). A significant discrimination of the genetic structure of soil bacterial community was also observed between NTs, CT, and PAS. Interestingly, bacterial abundance and diversity were differently influenced by soil environment changes: microbial density was affected by the quantity and diversity of crop residues, soil organic carbon, and exchangeable base contents, whereas soil bacterial genetic structure was mainly determined by exchangeable aluminum content, pH, cation exchange capacity, and C/N ratio. Altogether, our study represents one of the most complete environmental evaluations of agricultural practices in tropical agrosystems and leads to recommend no-till systems with high residue restitutions to improve the physical, chemical, and microbial properties of tropical acid soils and thus contribute to the sustainability of agriculture in these ecosystems.

Auteurs, date et publication :

Auteurs Pascal Lienhard , Florent Tivet , André Chabanne , Samuel Dequiedt , Mélanie Lelièvre , Sengphanh Sayphoummie , Bounma Leudphanane , Nicolas Chemidlin Prévost-Bouré , Lucien Séguy , Pierre-Alain Maron , Lionel Ranjard

Publication : Agronomy for Sustainable Development

Date : 2013

Volume : 33

Issue : 2

Pages : 375-384

Catégorie(s)

#Genosol #INRAE

Résumé

Soil is a potential reservoir of human pathogens and a possible source of contamination of animals, crops and water. In order to study the distribution of Listeria monocytogenes in French soils, a real-time PCR TaqMan assay targeting the phosphoribosylpyrophosphate synthetase (prs) gene of L. monocytogenes was developed for the specific detection and quantification of this bacterium within a collection of 1315 soil DNAs originated from the French Soil Quality Monitoring Network. The prs real-time PCR TaqMan assay was specific for L. monocytogenes and could quantify accurately down to 104L. monocytogenes per gram of dry soil. Among the 1315 soil DNAs, prs was not detected. This suggested that the level of L. monocytogenes in French soils is generally less than 104L. monocytogenes per gram of dry soil. In order to confirm this hypothesis, we investigated the occurrence of L. monocytogenes in samples collected in the Burgundy region by culture-based and molecular detection methods on the same samples. By using cultivation-based detection, 17% of samples were positive for the presence of L. monocytogenes while only 2% were found positive by the molecular detection method. L. monocytogenes was repeatedly isolated from cow pasture soils but not from cultivated soils, meadows or forest soils. Isolates were grouped in the serovar 1/2a or 3a and 4b or 4d or 4e. Taken as a whole, molecular detection results globally demonstrate that the level of L. monocytogenes in French soils does not exceed 104CFU per gram of dry soil. However, in comparison with culture-based method, PCR-based detection underestimates the occurrence of L. monocytogenes in soils. Soil sampling procedure also appears critical and may also lead to the underestimation of the incidence of L. monocytogenes.

Auteurs, date et publication :

Auteurs Aude Locatelli , Géraldine Depret , Claudy Jolivet , Sonia Henry , Samuel Dequiedt , Pascal Piveteau , Alain Hartmann

Publication : Journal of Microbiological Methods

Date : 2013

Volume : 93

Issue : 3

Pages : 242-250

Catégorie(s)

#Genosol #INRAE

Résumé

To reduce the environmental footprint of human activities, the quality of environmental media such as water, soil and the atmosphere should be first assessed. Microorganisms are well suited for a such assessment because they respond fast to environmental changes, they have a huge taxonomic and genetic diversity, and they are actively involved in biogeochemical cycles. Here, we review microbiological methods that provide sensitive and robust indicators for environmental diagnosis. Methods include genomics, transcriptomics, proteomics and metabolomics to study the abundance, diversity, activity and functional potentials of indigenous microbial communities in various environmental matrices such as water, soil, air and waste. We describe the advancement, technical limits and sensitivity of each method. Examples of method application to farming, industrial and urban impact are presented. We rank the most advanced indicators according to their level of operability in the different environmental matrices based on a technology readiness level scale.

Auteurs, date et publication :

Auteurs T. Bouchez , A. L. Blieux , S. Dequiedt , I. Domaizon , A. Dufresne , S. Ferreira , J. J. Godon , J. Hellal , C. Joulian , A. Quaiser , F. Martin-Laurent , A. Mauffret , J. M. Monier , P. Peyret , P. Schmitt-Koplin , O. Sibourg , E. D’oiron , A. Bispo , I. Deportes , C. Grand

Publication : Environmental Chemistry Letters

Date : 2016

Volume : 14

Issue : 4

Pages : 423-441

Catégorie(s)

#Genosol #INRAE

Auteurs, date et publication :

Auteurs Sébastien Terrat , Richard Christen , Samuel Dequiedt , Mélanie Lelièvre , Virginie Nowak , Tiffanie Regnier , Dipankar Bachar , Pierre Plassart , Patrick Wincker , Claudy Jolivet , Antonio Bispo , Philippe Lemanceau , Pierre-Alain Maron , Christophe Mougel , Lionel Ranjard

Publication : Microbial Biotechnology

Date : 2025

Volume : 5

Issue : 1

Pages : 135-141

Catégorie(s)

#Genosol #INRAE

Résumé

Wastewater can be recycled in agricultural soil as fertilizer to increase crop yields. However, adding wastewater induces sometimes ecotoxicological issues such as pollution by toxic compounds, which may lead to the loss of arable land. Bioenergy crops such as Miscanthus x giganteus have been tested to rehabilitate polluted soils, but the impact of Miscanthus on soil microbes is unknown. Here, we evaluated the effects of Miscanthus cropping on bacterial and fungal taxonomic composition in a wastewater-contaminated soil using synchronic and diachronic evaluation strategies. A 3-year field experiment close to Paris was set up on an agricultural site irrigated by raw wastewater for more than one century, thus resulting in strong metal and organic contamination. Soil microbial taxonomic composition was characterized by direct analysis of soil DNA using metagenomic tools such as 454 pyrosequencing of ribosomal genes. Our results demonstrate that Miscanthus cropping stimulates specific populations of bacteria such as Rhizobiales, increased by 1.4 in relative abundance, Nistrospira (x1.5), Azospira (x2), and Gemmatimonas (x2), and fungi: Glomeromycota (x3) and Mortierella (x1.5) for fungi. Noteworthy, these microbial genera are known to be strongly involved in plant symbiosis, organic matter mineralization, and nutrient cycling. Overall our findings show that Miscanthus cropping enhances regeneration of soil microbiological functions and services in polluted soil by stimulating populations beneficial for soil fertility and crop production.

Auteurs, date et publication :

Auteurs Emilie Bourgeois , Samuel Dequiedt , Melanie Lelievre , Folkert van Oort , Isabelle Lamy , Lionel Ranjard , Pierre Alain Maron

Publication : Environmental Chemistry Letters

Date : 2025

Volume : 13

Issue : 4

Pages : 503-511

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

Soil microbes play major agricultural functions such as the transformation of soil organic matter into plant fertilizers. The effects of agricultural practices on soil microbes at the scale of plots, from meters to hectare, are well documented. However, the impact at soil microscale, from micrometers to millimeters, is much less known. Therefore, we studied bacterial community density and diversity at microscale in crop soil under grassland, tillage, and no tillage. We fractionated macroaggregates, from 2,000 to 250 μm and from 250 to 63 μm; microaggregates, from 63–20 μm and 20–2 μm; and clay particles, lower than 2 μm. We measured the bacterial density and diversity by real-time PCR and 454-pyrosequencing of 16S rRNA genes of soil DNA, respectively. Results show that bacterial density and diversity were heterogeneous among size aggregates. Tillage decreased bacterial density from 22 to 74 %, and diversity from 4 to 11 %, and changed taxonomic groups in micro- and macroaggregates. This change led to the homogenization of bacterial communities and is explained by a higher protection of microaggregates. As a consequence, microaggregates contained similar bacterial communities whatever the land management is, whereas strong differences were observed between communities inhabiting macroaggregates. These findings demonstrate that bacterial diversity in microaggregates was mainly controlled by historical contingency, whereas bacterial communities in macroaggregates are shaped by contemporary perturbations. Our findings thus revealed unprecedented insights of the effect of agriculture on soil microbes. Potential applications include using crop management options that preserve macroaggregate structure to promote soil heterogeneity and therefore microbial diversity.

Auteurs, date et publication :

Auteurs Florentin Constancias , Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Simon Aussems , Virginie Nowak , Jean-Philippe Guillemin , Aline Bonnotte , Luc Biju-Duval , Aline Navel , Jean MF Martins , Pierre-Alain Maron , Lionel Ranjard

Publication : Agronomy for Sustainable Development

Date : 2014

Volume : 34

Issue : 4

Pages : 831-840

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.

Auteurs, date et publication :

Auteurs Anne-Laure Vivant , Dominique Garmyn , Pierre-Alain Maron , Virginie Nowak , Pascal Piveteau

Publication : Plos One

Date : 2013

Volume : 8

Issue : 10

Pages : e76991

Catégorie(s)

#ANR-Citation #Genosol #INRAE