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 #INRAEAuteurs, 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 #INRAERésumé
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 #INRAERésumé
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 #INRAERésumé
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 #INRAEAuteurs, date et publication :
Auteurs Sebastien Terrat , Pierre Plassart , Emilie Bourgeois , Stéphanie Ferreira , Samuel Dequiedt , Nathalie Adele-Dit-De-Renseville , Philippe Lemanceau , Antonio Bispo , Abad Chabbi , Pierre-Alain Maron , others
Publication : Microbial biotechnology
Date : 2025
Volume : 8
Issue : 1
Pages : 131–142
Catégorie(s)
#ACBB #ACBB Lusignan #Genosol #INRAERésumé
Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across France, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i. e. OTU number) was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance), the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively), and the land use (1.4%). Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R-adj(2) of 0.56) and provides a reference value for a given pedoclimatic condition.
Auteurs, date et publication :
Auteurs Sebastien Terrat , Walid Horrigue , Samuel Dequietd , Nicolas P. A. Saby , Melanie Lelievre , Virginie Nowak , Julie Tripied , Tiffanie Regnier , Claudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Battle Karimi , Antonio Bispo , Pierre Alain Maron , Nicolas Chemidlin Prevost-Boure , Lionel Ranjard
Publication : PloS One
Date : 2017
Volume : 12
Issue : 10
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs Robert I. Griffiths , Bruce C. Thomson , Pierre Plassart , Hyun S. Gweon , Dorothy Stone , Rachael E. Creamer , Philippe Lemanceau , Mark J. Bailey
Publication : Applied Soil Ecology
Date : 2025
Volume : 97
Pages : 61-68
Catégorie(s)
#Genosol #INRAERésumé
Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity.
Auteurs, date et publication :
Auteurs Florentin Constancias , Sébastien Terrat , Nicolas P. A. Saby , Walid Horrigue , Jean Villerd , Jean-Philippe Guillemin , Luc Biju-Duval , Virginie Nowak , Samuel Dequiedt , Lionel Ranjard , Nicolas Chemidlin Prévost-Bouré
Publication : MicrobiologyOpen
Date : 2025
Volume : 4
Issue : 3
Pages : 505-517
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
The occurrence of Pseudomonas aeruginosa was monitored at a broad spatial scale in French agricultural soils, from various soil types and under various land uses to evaluate the ability of soil to be a natural habitat for that species. To appreciate the impact of agricultural practices on the potential dispersion of P. aeruginosa, we further investigated the impact of organic amendment at experimental sites in France and Burkina Faso. A real-time quantitative PCR (qPCR) approach was used to analyze a set of 380 samples selected within the French RMQS (“Réseau de Mesures de la Qualité des Sols”) soil library. In parallel, a culture-dependent approach was tested on a subset of samples. The results showed that P. aeruginosa was very rarely detected suggesting a sporadic presence of this bacterium in soils from France and Burkina Faso, whatever the structural and physico-chemical characteristics or climate. When we analyzed the impact of organic amendment on the prevalence of P. aeruginosa, we found that even if it was detectable in various manures (at levels from 103 to 105 CFU or DNA targets (g drywt)−1 of sample), it was hardly ever detected in the corresponding soils, which raises questions about its survival. The only case reports were from a vineyard soil amended with a compost of mushroom manure in Burgundy, and a few samples from two fields amended with raw urban wastes in the sub-urban area of Ouagadougou, Burkina Faso. In these soils the levels of culturable cells were below 10 CFU (g drywt)−1.
Auteurs, date et publication :
Auteurs Amélie Deredjian , Céline Colinon , Edmond Hien , Elisabeth Brothier , Benjamin Youenou , Benoit Cournoyer , Samuel Dequiedt , Alain Hartmann , Claudy Jolivet , Sabine Houot , Lionel Ranjard , Nicolas P. A. Saby , Sylvie Nazaret
Publication : Frontiers in Cellular and Infection Microbiology
Date : 2014
Volume : 4