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Abstract: Considering the limited number of bioindicators available to assess soil quality, a national research programme was set up in France to develop such indicators (2006–2012), the “Bioindicator” programme. This programme tested 47 biological parameters (i.e. microorganisms, fauna, flora) including earthworms, in several sites differing in terms of land use, contamination type – PAHs or metals – and pollution levels. The present study proposes some study objectives for bioindicator approaches, based on the earthworm results from the programme. Therefore, different earthworm descriptors were tested at the community level (e.g. abundance, biomass, species and functional structures, and ecological traits) as well as the organism level (i.e. measuring the metallothionein coding gene expression level in earthworms). The present results, obtained from the programme''s spring 2009 sampling campaign, discriminated among the different descriptors and showed that earthworm and endogeic abundance as well as the individual weight of endogeics seem to be good indicators in non-contaminated (cultivated) sites, while the ecological structure, namely the proportion of anecic vs. endogeic species, and the proportion of non-vulnerable species should be used as indicators of contaminated soils. Furthermore, the first results obtained for Lumbricus terrestris and L. rubellus rubellus are encouraging as they show that metallothionein expression increases in metal-contaminated soils. The relevance of these descriptors, which have to be considered in study objectives, requires the analysis of 2010 results. [Copyright &y& Elsevier]

Soil health is a key concept in worldwide efforts to reverse soil degradation, but to be used as a tool to improve soils, it must be definable at a policy level and quantifiable in some way. Soil indicators can be used to define soil health and quantify the degree to which soils fulfil expected functions. Indicators are assessed using target and/or threshold values, which define achievable levels of the indicators or functions. However, defining robust targets and thresholds is not a trivial task, as they should account for soil, climate, land-use, management, and history, among others. This paper introduces and discusses (through theory and stakeholder feedback) four approaches to setting targets and thresholds: fixed, reference, distribution and relative change. Three approaches (not including relative change) are then illustrated using a case study, located in Denmark, Italy, and France, which highlights key strengths and weaknesses of each approach. Finally, a framework is presented that facilitates both choosing the most appropriate target/threshold method for a given context, and using targets/thresholds to trigger follow-up actions to promote soil health., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

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., Competing Interests: One of the co-authors is currently working for AUREA AgroSciences, a private agri-environmental testing and consultancy laboratory. Although this society coordinated the project Agro-Eco Sol in partnership with INRAE, the funders had no role in study design, data interpretation, or the decision to submit the work for publication.

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.

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., Competing Interests: Declaration of competing interest The authors declare no known conflicts of interests or personal relationships that could have influenced the content reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

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.

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 S 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 S 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.

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., (© 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)

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.