Publications by authors named "Claudy Jolivet"

19 Publications

  • Page 1 of 1

Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity.

Sci Rep 2019 03 7;9(1):3812. Epub 2019 Mar 7.

Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F- 21000, Dijon, France.

Although land use drives soil bacterial diversity and community structure, little information about the bacterial interaction networks is available. Here, we investigated bacterial co-occurrence networks in soils under different types of land use (forests, grasslands, crops and vineyards) by sampling 1798 sites in the French Soil Quality Monitoring Network covering all of France. An increase in bacterial richness was observed from forests to vineyards, whereas network complexity respectively decreased from 16,430 links to 2,046. However, the ratio of positive to negative links within the bacterial networks ranged from 2.9 in forests to 5.5 in vineyards. Networks structure was centered on the most connected genera (called hub), which belonged to Bacteroidetes in forest and grassland soils, but to Actinobacteria in vineyard soils. Overall, our study revealed that soil perturbation due to intensive cropping reduces strongly the complexity of bacterial network although the richness is increased. Moreover, the hub genera within the bacterial community shifted from copiotrophic taxa in forest soils to more oligotrophic taxa in agricultural soils.
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http://dx.doi.org/10.1038/s41598-019-40422-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405751PMC
March 2019

Biogeography of soil bacteria and archaea across France.

Sci Adv 2018 07 4;4(7):eaat1808. Epub 2018 Jul 4.

Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France.

Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 16 ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 16 rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism.
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http://dx.doi.org/10.1126/sciadv.aat1808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031370PMC
July 2018

Mapping and predictive variations of soil bacterial richness across France.

PLoS One 2017 23;12(10):e0186766. Epub 2017 Oct 23.

Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France.

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 (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0186766PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653302PMC
November 2017

Microbial Diversity Indexes Can Explain Soil Carbon Dynamics as a Function of Carbon Source.

PLoS One 2016 23;11(8):e0161251. Epub 2016 Aug 23.

UMR SAS 1069, INRA, Rennes, France.

Mathematical models do not explicitly represent the influence of soil microbial diversity on soil organic carbon (SOC) dynamics despite recent evidence of relationships between them. The objective of the present study was to statistically investigate relationships between bacterial and fungal diversity indexes (richness, evenness, Shannon index, inverse Simpson index) and decomposition of different pools of soil organic carbon by measuring dynamics of CO2 emissions under controlled conditions. To this end, 20 soils from two different land uses (cropland and grassland) were incubated with or without incorporation of 13C-labelled wheat-straw residue. 13C-labelling allowed us to study residue mineralisation, basal respiration and the priming effect independently. An innovative data-mining approach was applied, based on generalized additive models and a predictive criterion. Results showed that microbial diversity indexes can be good covariates to integrate in SOC dynamics models, depending on the C source and the processes considered (native soil organic carbon vs. fresh wheat residue). Specifically, microbial diversity indexes were good candidates to help explain mineralisation of native soil organic carbon, while priming effect processes seemed to be explained much more by microbial composition, and no microbial diversity indexes were found associated with residue mineralisation. Investigation of relationships between diversity and mineralisation showed that higher diversity, as measured by the microbial diversity indexes, seemed to be related to decreased CO2 emissions in the control soil. We suggest that this relationship can be explained by an increase in carbon yield assimilation as microbial diversity increases. Thus, the parameter for carbon yield assimilation in mathematical models could be calculated as a function of microbial diversity indexes. Nonetheless, given limitations of the methods used, these observations should be considered with caution and confirmed with more experimental studies. Overall, along with other studies on relationships between microbial community composition and SOM dynamics, this study suggests that overall measures of microbial diversity may constitute relevant ways to include microbial diversity in models of SOM dynamics.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161251PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995005PMC
July 2017

Occurrence of Stenotrophomonas maltophilia in agricultural soils and antibiotic resistance properties.

Res Microbiol 2016 May 14;167(4):313-324. Epub 2016 Jan 14.

Université de Lyon, Université Lyon 1, CNRS UMR 5557 Ecologie Microbienne, Villeurbanne cedex F-69622, France. Electronic address:

The occurrence of Stenotrophomonas maltophilia was monitored in organic amendments and agricultural soils from various sites in France and Tunisia. S. maltophilia was detected in horse and bovine manures, and its abundance ranged from 0.294 (±0.509) × 10(3) to 880 (±33.4) × 10(3) CFU (g drywt)(-1) of sample. S. maltophilia was recovered from most tested soil samples (104/124). Its abundance varied from 0.33 (±0.52) to 414 (±50) × 10(3) CFU (g drywt)(-1) of soil and was not related to soil characteristics. Antibiotic resistance properties of a set of environmental strains were compared to a clinical set, and revealed a high diversity of antibiotic resistance profiles, given both the numbers of resistance and the phenotypes. Manure strains showed resistance phenotypes, with most of the strains resisting between 7 and 9 antibiotics. While French soil strains were sensitive to most antibiotics tested, some Tunisian strains displayed resistance phenotypes close to those of clinical French strains. Screening for metal resistance among 66 soil strains showed a positive relationship between antibiotic and metal resistance. However, the prevalence of antibiotic resistance phenotypes in the studied sites was not related to the metal content in soil samples.
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http://dx.doi.org/10.1016/j.resmic.2016.01.001DOI Listing
May 2016

Vegetation ecology meets ecosystem science: Permanent grasslands as a functional biogeography case study.

Sci Total Environ 2015 Nov 20;534:43-51. Epub 2015 Apr 20.

Laboratoire des Sciences du climat et de l'Environnement (UMR 8212 CEA/CNRS/UVSQ), Orme des Merisiers, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.

The effect of biodiversity on ecosystem functioning has been widely acknowledged, and the importance of the functional roles of species, as well as their diversity, in the control of ecosystem processes has been emphasised recently. However, bridging biodiversity and ecosystem science to address issues at a biogeographic scale is still in its infancy. Bridging this gap is the primary goal of the emerging field of functional biogeography. While the rise of Big Data has catalysed functional biogeography studies in recent years, comprehensive evidence remains scarce. Here, we present the rationale and the first results of a country-wide initiative focused on the C3 permanent grasslands. We aimed to collate, integrate and process large databases of vegetation relevés, plant traits and environmental layers to provide a country-wide assessment of ecosystem properties and services which can be used to improve regional models of climate and land use changes. We outline the theoretical background, data availability, and ecoinformatics challenges associated with the approach and its feasibility. We provide a case study of upscaling of leaf dry matter content averaged at ecosystem level and country-wide predictions of forage digestibility. Our framework sets milestones for further hypothesis testing in functional biogeography and earth system modelling.
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http://dx.doi.org/10.1016/j.scitotenv.2015.03.141DOI Listing
November 2015

Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

PLoS One 2014 3;9(11):e111667. Epub 2014 Nov 3.

Unité Mixte de Recherche 1347 Agroécologie, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France; Unité Mixte de Recherche 1347 Agroécologie-Plateforme GenoSol, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France.

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111667PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4218796PMC
August 2015

Low occurrence of Pseudomonas aeruginosa in agricultural soils with and without organic amendment.

Front Cell Infect Microbiol 2014 29;4:53. Epub 2014 Apr 29.

CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Université de Lyon Villeurbanne, France.

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 10(3) to 10(5) 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).
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http://dx.doi.org/10.3389/fcimb.2014.00053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010769PMC
January 2015

Distribution and speciation of ambient selenium in contrasted soils, from mineral to organic rich.

Sci Total Environ 2014 May 15;479-480:93-101. Epub 2014 Feb 15.

Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), IPREM, Université de Pau et des Pays de l'Adour/CNRS UMR 5254, Hélioparc, 2 Avenue du Président Angot, 64053 Pau Cedex 9, France.

Selenium adsorption onto oxy-hydroxides mainly controls its mobility in volcanic soils, red earths and soils poor in organic matter (OM) while the influence of OM was emphasized in podzol and peat soils. This work aims at deciphering how those solid phases influence ambient Se mobility and speciation under less contrasted conditions in 26 soils spanning extensive ranges of OM (1-32%), Fe/Al oxy-hydroxides (0.3-6.1%) contents and pH (4.0-8.3). The soil collection included agriculture, meadow and forest soils to assess the influence of OM quality as well. Trace concentrations of six ambient Se species (Se(IV), Se(VI) and 4 organo-Se compounds) were analyzed by HPLC-ICP-MS in three extractants (ultrapure water, phosphate and sodium hydroxide) targeting Se associated to different soil phases. The Kd values determined from ultrapure water extraction were higher than those reported in commonly used short-term experiments after Se-spiking. Correlations of ambient Se content and distribution with soil parameters explained this difference by an involvement of slow processes in Se retention in soils. The 26 Kd values determined here for a wide variety of soils thus represent a relevant database for long-term prediction of Se mobility. For soils containing less than 20% OM, ambient Se solubility is primarily controlled by its adsorption onto crystalline oxy-hydroxides. However, OM plays an important role in Se mobility by forming organo-mineral associations that may protect adsorbed Se from leaching and/or create anoxic zones (aggregates) where Se is immobilized after its reduction. Although for the first time, inorganic Se(IV), Se(VI) and organo-Se compounds were simultaneously investigated in a large soil collection, high Se proportions remain unidentified in each soil extract, most probably due to Se incorporation and/or binding to colloidal-sized OM. Variations of environmental factors regulating the extent of OM-mineral associations/aggregation may thus lead to changes in Se mobility and bio-availability.
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http://dx.doi.org/10.1016/j.scitotenv.2014.01.079DOI Listing
May 2014

Biotic and abiotic soil properties influence survival of Listeria monocytogenes in soil.

PLoS One 2013 7;8(10):e75969. Epub 2013 Oct 7.

INRA, UMR1347 Agroécologie, Dijon, France.

Listeria monocytogenes is a food-borne pathogen responsible for the potentially fatal disease listeriosis and terrestrial ecosystems have been hypothesized to be its natural reservoir. Therefore, identifying the key edaphic factors that influence its survival in soil is critical. We measured the survival of L. monocytogenes in a set of 100 soil samples belonging to the French Soil Quality Monitoring Network. This soil collection is meant to be representative of the pedology and land use of the whole French territory. The population of L. monocytogenes in inoculated microcosms was enumerated by plate count after 7, 14 and 84 days of incubation. Analysis of survival profiles showed that L. monocytogenes was able to survive up to 84 days in 71% of the soils tested, in the other soils (29%) only a short-term survival (up to 7 to 14 days) was observed. Using variance partitioning techniques, we showed that about 65% of the short-term survival ratio of L. monocytogenes in soils was explained by the soil chemical properties, amongst which the basic cation saturation ratio seems to be the main driver. On the other hand, while explaining a lower amount of survival ratio variance (11%), soil texture and especially clay content was the main driver of long-term survival of L. monocytogenes in soils. In order to assess the effect of the endogenous soils microbiota on L. monocytogenes survival, sterilized versus non-sterilized soils microcosms were compared in a subset of 9 soils. We found that the endogenous soil microbiota could limit L. monocytogenes survival especially when soil pH was greater than 7, whereas in acidic soils, survival ratios in sterilized and unsterilized microcosms were not statistically different. These results point out the critical role played by both the endogenous microbiota and the soil physic-chemical properties in determining the survival of L. monocytogenes in soils.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075969PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792134PMC
June 2014

Nation-wide study of the occurrence of Listeria monocytogenes in French soils using culture-based and molecular detection methods.

J Microbiol Methods 2013 Jun 6;93(3):242-50. Epub 2013 Apr 6.

INRA, UMR1347 Agroécologie, Dijon, France.

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 10(4)L. 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 10(4)L. 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 10(4)CFU 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.
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http://dx.doi.org/10.1016/j.mimet.2013.03.017DOI Listing
June 2013

Analyzing the spatial distribution of PCB concentrations in soils using below-quantification limit data.

J Environ Qual 2012 Nov-Dec;41(6):1893-905

INRA, US 1106 InfoSol, Orleans, France.

Polychlorinated biphenyls (PCBs) are highly toxic environmental pollutants that can accumulate in soils. We consider the problem of explaining and mapping the spatial distribution of PCBs using a spatial data set of 105 PCB-187 measurements from a region in the north of France. A large proportion of our data (35%) fell below a quantification limit (QL), meaning that their concentrations could not be determined to a sufficient degree of precision. Where a measurement fell below this QL, the inequality information was all that we were presented with. In this work, we demonstrate a full geostatistical analysis-bringing together the various components, including model selection, cross-validation, and mapping-using censored data to represent the uncertainty that results from below-QL observations. We implement a Monte Carlo maximum likelihood approach to estimate the geostatistical model parameters. To select the best set of explanatory variables for explaining and mapping the spatial distribution of PCB-187 concentrations, we apply the Akaike Information Criterion (AIC). The AIC provides a trade-off between the goodness-of-fit of a model and its complexity (i.e., the number of covariates). We then use the best set of explanatory variables to help interpolate the measurements via a Bayesian approach, and produce maps of the predictions. We calculate predictions of the probability of exceeding a concentration threshold, above which the land could be considered as contaminated. The work demonstrates some differences between approaches based on censored data and on imputed data (in which the below-QL data are replaced by a value of half of the QL). Cross-validation results demonstrate better predictions based on the censored data approach, and we should therefore have confidence in the information provided by predictions from this method.
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http://dx.doi.org/10.2134/jeq2011.0478DOI Listing
May 2013

Occurrence of CTX-M Producing Escherichia coli in Soils, Cattle, and Farm Environment in France (Burgundy Region).

Front Microbiol 2012 9;3:83. Epub 2012 Mar 9.

INRA, UMR Microbiologie des Sols et de l'Environnement (MSE), The Institut National de la Recherche Agronomique Dijon, France.

CTX-M [a major type of 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 bla(CTX-M) genes was determined directly from soil DNA extracts obtained from 120 sites in Burgundy (France) using real-time PCR. bla(CTX-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 bla(TEM-71) genes and bla(CTX-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 two 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 1 year before sampling.
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http://dx.doi.org/10.3389/fmicb.2012.00083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297819PMC
October 2012

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure.

Microb Biotechnol 2012 Jan 12;5(1):135-41. Epub 2011 Oct 12.

INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France.

Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.
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http://dx.doi.org/10.1111/j.1751-7915.2011.00307.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815280PMC
January 2012

Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR.

PLoS One 2011 8;6(9):e24166. Epub 2011 Sep 8.

INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, Dijon, France.

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1/FF390. This in silico analysis of the specificity of FR1/FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1/FF390 for Fungi was validated in vitro by cloning--sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024166PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169588PMC
March 2012

Which persistent organic pollutants can we map in soil using a large spacing systematic soil monitoring design? A case study in Northern France.

Sci Total Environ 2011 Sep 3;409(19):3719-31. Epub 2011 Jul 3.

INRA, US1106 Unité Infosol, Centre de recherches d'Orléans, CS 40001, Ardon, 45075 Orléans Cedex 2, France.

Persistent organic pollutants (POPs) impact upon human and animal health and the wider environment. It is important to determine where POPs are found and the spatial pattern of POP variation. The concentrations of 90 molecules which are members of four families of POPs and two families of herbicides were measured within a region of Northern France as part of the French National Soil Monitoring Network (RMQS: Réseau de Mesures de la Qualité des Sols). We also gather information on five covariates (elevation, soil organic carbon content, road density, land cover and population density) which might influence POP concentrations. The study region contains 105 RMQS observation sites arranged on a regular square grid with spacing of 16 km. The observations include hot-spots at sites of POP application, smaller concentrations where POPs have been dispersed and observations less than the limit of quantification (LOQ) where the soil has not been impacted by POPs. Fifty nine of the molecules were detected at less than 50 sites and hence the data were unsuitable for spatial analyses. We represent the variation of the remaining 31 molecules by various linear mixed models which can include fixed effects (i.e. linear relationships between the molecule concentrations and covariates) and spatially correlated random effects. The best model for each molecule is selected by the Akaike Information Criterion. For nine of the molecules, spatial correlation is evident and hence they can potentially be mapped. For four of these molecules, the spatial correlation cannot be wholly explained by fixed effects. It appears that these molecules have been transported away from their application sites and are now dispersed across the study region with the largest concentrations found in a heavily populated depression. More complicated statistical models and sampling designs are required to explain the distribution of the less dispersed molecules.
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http://dx.doi.org/10.1016/j.scitotenv.2011.05.048DOI Listing
September 2011

Spatial distribution of lindane in top soil of Northern France.

Chemosphere 2009 Nov 30;77(9):1249-55. Epub 2009 Sep 30.

INRA, US 1106, InfoSol Unit, CS 40001 Ardon, F-45075 Orléans Cedex 2, France.

Lindane is a persistent organochlorine insecticide and the use of this insecticide in agriculture was banned in France in 1998. In this study we investigated the concentrations of lindane in top soil in Northern France and used robust geostatistics to map the geographical distribution of lindane. The study was based on a 16 km x 16 km grid covering an area of ca 25,000 km(2). Lindane was found in all soils, even those from non-agricultural-application areas. Very low ratios of alpha-/gamma-HCH and delta-/gamma-HCH suggested that a long time had passed since technical HCH was used in the studied area, or that emission sources of lindane were still present. A strong gradient in lindane concentration was observed, with the highest lindane concentrations in an area located in the northern region. Results suggested that some of the lindane observed in the high concentration area may have come from volatilization of old lindane applied to intensively cultivated areas, which was then transported by prevailing winds coming from the south-west and deposited in a densely inhabited depression.
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http://dx.doi.org/10.1016/j.chemosphere.2009.08.060DOI Listing
November 2009

Biogeographical patterns of soil bacterial communities.

Environ Microbiol Rep 2009 Aug 22;1(4):251-5. Epub 2009 Jun 22.

INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon, Cedex, France. Université de Bourgogne, UMR 1229, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon, Cedex, France. Platform GenoSol, INRA-Université de Bourgogne, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon, Cedex, France. Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne Cedex, France. INRA Orléans - US 1106, Unité INFOSOL, Avenue de la Pomme de Pin - BP 20619 Ardon 45166 Olivet, Cedex, France.

This study provides the first maps of variations in bacterial community structure on a broad scale based on genotyping of DNA extracts from 593 soils from four different regions of France (North, Brittany, South-East and Landes). Soils were obtained from the soil library of RMQS ('Réseau de Mesures de la Qualité des Sols' = French soil quality monitoring network). The relevance of a biogeographic approach for studying bacterial communities was demonstrated by the great variability in community structure and specific geographical patterns within and between the four regions. The data indicated that the distribution of bacterial community composition might be more related to local factors such as soil type and land cover than to more global factors such as climatic and geomorphologic characteristics. Furthermore, the regional pools of biodiversity could be ordered: South-East ≥ North > Brittany > Landes, according to the observed regional variability of the bacterial communities, which could be helpful for improving land use in accordance with soil biodiversity management.
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http://dx.doi.org/10.1111/j.1758-2229.2009.00040.xDOI Listing
August 2009
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