Pesticide Residues in French Soils: Occurrence, Risks, and Persistence.

Contamination of the environment by pesticide residues is a growing concern given their widespread presence in the environment and their effects on ecosystems. Only a few studies have addressed the occurrence of pesticides in soils, and their results highlighted the need for further research on the persistence and risks induced by those substances. We monitored 111 pesticide residues (48 fungicides, 36 herbicides, 25 insecticides and/or acaricides, and two safeners) in 47 soils sampled across France under various land uses (arable lands, vineyards, orchards, forests, grasslands, and brownfields). Pesticides were found in 98% of the sites (46 of the 47 sampled), including untreated areas such as organic fields, forests, grasslands, and brownfields, with up to 33 different substances detected in one sample, mostly fungicides and herbicides. The concentrations of herbicides were the highest in soils with glyphosate, and its transformation product, AMPA, contributed 70% of the cumulative herbicides. Risk assessment underlined a moderate to high risk for earthworms in arable soils mostly attributed to insecticides and/or acaricides. Finally, the comparison with pesticide application by farmers underlines the presence of some residues long after their supposed 90% degradation and at concentrations higher than predicted environmental concentrations, leading to questions their real persistence in soils.

First national reference of microplastic contamination of French soils.

The recent emergence of studies on plastic contamination of terrestrial environments has revealed the presence of microplastics (MP) in a variety of soil types, from the most densely populated areas to the most remote ones. However, the concentrations and chemical natures of MP in soils vary between studies, and only a few ones have focused on this issue in France. The MICROSOF project aimed to establish the first national references for French soil contamination by microplastics. 33 soil samples randomly chosen on the French soil quality-monitoring network were analyzed. The study collected data on the abundance of microplastics in the [315-5000] µm range, their chemical nature and size, as well as mass abundance estimates and other relevant information. Results demonstrated that 76 % of the soil samples contained microplastics, in concentrations ranging from <6.7 to 80 MP.kg-1 (dry soil). Most samples from croplands, grasslands and vineyards and orchards were contaminated, whereas only one sample from forest contained MP, suggesting an increased risk of microplastic contamination in soils exposed to agricultural practices. The MP abundances are not statistically different from similar studies, indicating an intermediate level of contamination in French soils. Despite intervention reports and surveys, the sources remain unclear at this stage. For the first time, an overview of the state of soil contamination in France, as well as the potential risks is provided.

Selection of soil health indicators for modelling soil functions to promote smart urban planning.

The contribution of soil health to global health receives a growing interest, especially in urban environment. Therefore, there is a true need to develop methods to evaluate ecological functions provided by urban soils in order to promote smart urban planning. This work aims first at identifying relevant soil indicators based either on in situ description, in situ measurement or lab analysis. Then, 9 soil functions and sub-functions were selected to meet the main expectations regarding soil health in urban contexts. A crucial step of the present research was then to select adequate indicators for each soil function and then to create adapted reference frameworks; they were in the form of 4 classes with scores ranging from 0 to 3. All the reference frameworks were developed to evaluate soil indicators in order to score soil functions, either by using existing scientific or technical standards or references or based on the expertise of the co-authors. Our model was later tested on an original database of 109 different urban soils located in 7 cities of Western Europe and under various land uses. The scores calculated for 8 soil functions of 109 soils followed a Gaussian distribution. The scoring successfully expressed the strong contrasts between the various soils; the lowest scores were calculated for sealed soils and soils located in urban brownfields, whereas the highest were found for soils located in city parks or urban agriculture. Despite requiring a soil expertise, the proposed approach is easy to implement and could help reveal the true potential of urban soils in order to promote smart urban planning and enhance their contribution to global health.

Biogeographical patterns of the soil fungal:bacterial ratio across France.

Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.

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

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.

Systems knowledge for sustainable soil and land management.

While soils and land are pivotal elements of many Sustainable Development Goals (SDGs) and societal challenges, they face degradation and reduction of related functions and services worldwide. Societal demands on soils and land are increasing, including contributions to climate change mitigation and adaptation, ecosystem services, biodiversity and biomass production for food, feed, fiber and energy. This adverse combination of reducing capacities and increasing demands requires rapid transition towards sustainable soil and land management that mitigates trade-offs and creates synergies. Likewise, a transformation of soil and land research is required to scientifically support the sustainable transformation. Based on a literature analysis combined with engagement of soil and land scientists, we developed a systemic research framework for sustainable soil and land management to support the implementation of the Horizon Europe Mission "A Soil Deal for Europe". The framework summarizes soil and land related topics into six societal challenges and associates them with eight knowledge types that outline integrated research for development and implementation of sustainable soil and land management. We propose that research should be aligned with living labs and lighthouses to leverage local solutions, innovation, training and education. We outline the role of experimentation, data analysis, assessment, modelling and the importance of research for institutions, governance and policy support. For encouraging a swift transition towards a systems approach for sustainable soil and land management, we concluded that among all knowledge types, those addressing socio-economic interrelations with soil health and related policies currently represent the biggest bottleneck.

Correction: Mapping and predictive variations of soil bacterial richness across France.

[This corrects the article DOI: 10.1371/journal.pone.0186766.].

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

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.

Biogeography of soil bacteria and archaea across 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 16S 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 16S 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.

Mapping and predictive variations of soil bacterial richness across 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.

Correction: Mapping and predictive variations of soil bacterial richness across France.

[This corrects the article DOI: 10.1371/journal.pone.0186766.].

Selecting a battery of bioassays for ecotoxicological characterization of wastes.

This study was conducted in France within the context of waste classification (Hazardous Waste Council Directive 91/689/EEC), and focused on "ecotoxic" property (H14). In 1998, an experimental test strategy was developed to assess ecotoxicological properties of wastes using a battery of six standardized bioassays. This combined direct and indirect approaches integrating two solid-phase tests: emergence and growth inhibition of Lactuca sativa (14 days), mortality of Eisenia fetida (14 days) and four standardized tests performed on water extracts from wastes: growth inhibition of Pseudokirchneriella subcapitata (3 days), inhibition of mobility of Daphnia magna (48 h), inhibition of reproduction of Ceriodaphnia dubia (7 days), inhibition of light emission of Vibrio fischeri (30 min). This study aimed to set up preliminary conclusions on relevancy of this experimental test strategy, based on data obtained since 1998. Results were analyzed from the combined use of Hierarchical Cluster Analysis, Principal Component Analysis and Nonlinear Mapping. These multivariate analyses clearly showed that it was possible to reduce this number of tests without changing the typology of the wastes. A battery of bioassays including one solid phase test and two tests performed on water extracts (L. sativa, V. fischeri and C. dubia) was found as an optimal solution for characterizing the toxicity of the studied wastes. This optimal battery represents a good basis for determining the H14 property.

DNA damage measured by the single-cell gel electrophoresis (Comet) assay in mammals fed with mussels contaminated by the 'Erika' oil-spill.

This research aimed to estimate potential genotoxicity for consumers resulting from the ingestion of seafood contaminated with polycyclic aromatic hydrocarbons (PAHs) released into the marine environment after the 'Erika' shipwreck along the coasts of south Brittany, in France. Mussels (Mytilus sp.) collected from sites on the Atlantic coast that were affected by the oil slick in various degrees, were used to feed rats daily for 2 and 4 weeks. DNA damage was measured by use of the Comet assay in the liver, bone marrow and blood of rats receiving food contaminated with 312 microg of 16PAHs/kg dry weight (d.w.) equivalent to 33.8 microg TEQs (toxic equivalent quantities to benzo(a)pyrene (BaP))/kg d.w. mussels, 569 microg/kg d.w. (83.6 microg TEQs/kg) and 870 microg/kg d.w. (180.7 microg TEQs/kg). A dose-effect-time relationship was observed between the amount of DNA damage in the liver and bone marrow of the rats and the PAH contamination level of the mussels. Genotoxicity increased during the period between 15 and 30 days in rats that received food at the highest two PAH levels. On the other hand, no significant change in liver and bone marrow of rats fed with mussels containing 33.8 microg TEQs/kg d.w. was recorded at 30 days compared with 15 days, indicating efficient DNA repair capacity at low levels of exposure. No signs of genotoxicity were found in peripheral blood. Globally, the observed effects were rather moderate. These results show that oil-contaminated food caused DNA damage in predators, and underline the bioavailability to consumers of pollutants in mussels contaminated with fuel oil. The usefulness of the Comet assay as a sensitive tool in biomonitoring studies analyzing responses of PAH transfer through food webs was also confirmed.

Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition.

This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard.

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

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.

Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure.

Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.

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

Spatial distribution of lindane in top soil of Northern 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.

Genotoxicity related to transfer of oil spill pollutants from mussels to mammals via food.

Heavy fuel oils containing high levels of polycyclic aromatic hydrocarbons (PAHs) were released into the marine environment after the Erika oil spill on the Atlantic coast. As highly condensed PAH pollutants can bioaccumulate in invertebrates, their transfer to vertebrates through the food chain was of concern. This study aimed to estimate potential genotoxic effects in rats fed for 2 or 4 weeks with the marine mussel Mytilus edulis contaminated by oil pollutants. Two levels of PAH contamination were studied, around 100 and 500 microg of total PAHs/kg dry weight (d.w.) in mussels. Genotoxic damage in rats was investigated by single-cell gel electrophoresis (Comet assay) and micronucleus assays in liver, bone marrow, and peripheral blood. DNA damage was observed in the liver of rats fed with the most contaminated mussels (500 microg PAHs/kg d.w.).DNA damage also was observed in the bone marrow but less than that in the liver. A small increase in micronuclei frequency was registered as well. This work underlines the bioavailability of pollutants in fuel-oil-contaminated mussels to consumers and the usefulness of the Comet assay as a sensitive tool in biomonitoring to analyze responses to PAH transfer in food. The occurrence of substituted PAHs and related compounds such as benzothiophenes in addition to nonsubstituted PAHs in fuel oils and mussels raised the question of whether they were implicated in the genotoxic effects registered in rats.