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Recycling organic waste products (OWPs) is known to influence soil physical, chemical, and biological properties, yet few studies have compared the long-term effects of different OWP type across multiple sites. This study examined the impacts of repeated OWP application on soil properties in two French long-term field experiments: QualiAgro and PROspective (20 and 18 years, respectively). The OWP included dehydrated urban sewage sludge (SLU), green waste and SLU compost, biowaste compost from source-separated municipal organic waste co-composted with green waste, municipal solid waste compost, farmyard manure from a dairy cow farm (FYM), and composted FYM from open-air composting on a concrete platform. The application of OWP led to increased soil nutrient levels and trace element availability, and stimulated microbial biomass and enzyme activities, while the response of nematode varied depending on site and OWP type. Biological properties were less affected than physico-chemical properties, though the OWP application enhanced soil microbial biomass and specific enzyme activities. The impact on soil nematode communities varied depending on OWP type and site. Strong correlations were observed among soil property changes, with exogenous carbon and nutrient inputs from OWP identified as key drivers. Larger changes were noted in QualiAgro, where OWP application rates were higher and initial soil quality lower. These findings highlight that OWP applications, depending on their type, rate, and initial soil conditions, can significantly alter soil properties.

The evaluation of soil quality requires the use of robust methods to assess biologically based indicators. Among them, enzyme activities are used for several decades, but there is a clear need to update their measurement methods for routine use, in combining feasibility, accuracy, and reliability. To this end, the platform Biochem-Env optimized a miniaturized method to measure enzyme activities in soils using colorimetric substrates in micro-well plates. The standardization of the method was carried out within the framework of ISO/TC 190/SC 4/WG 4 “Soil quality – Biological methods” workgroup, recommending an inter-laboratory evaluation for the publication of a full ISO standard. That evaluation, managed by the platform, was based on the measurement, in six soils of contrasted physicochemical properties, of the ten soil enzyme activities described in the standard. Eight laboratories were involved in the validation study. Only 2.7% of outliers were identified from the analyses of the whole dataset. The repeatability and reproducibility of the method were determined by computing, respectively, the intra-laboratory ( CV r ,) and inter-laboratory ( CV R ) coefficients of variation for each soil and enzyme. The mean CV r ranged from 4.5% (unbuffered phosphatase) to 9.9% (α-glucosidase), illustrating a reduced variability of enzyme activities within laboratories. The mean CV R ranged from 13.8% (alkaline phosphatase) to 30.9% (unbuffered phosphatase). Despite this large CV R noticed for unbuffered phosphatase, the method was repeatable, reproducible, and sensitive. It also proved to be applicable for measuring enzyme activities in different types of soils. These results have been found successful by ISO/TC 190/SC4 and resulted in the publication of ISO 20130:2018 standard.

Improvement of the catalytic properties of fungal laccases is a current challenge for the efficient bioremediation of natural media polluted by xenobiotics. We developed the heterologous expression of a laccase from the white-rot fungus Trametes versicolor in the yeast Yarrowia lipolytica as a first step for enzyme evolution. The full-length cDNA consisted of a 1,561-bp open reading frame encoding lacIIIb, a 499-amino-acid protein and a 21-amino-acid signal peptide. Native and yeast secretion signals were used to direct the secretion of the enzyme, with the native signal yielding higher enzyme activity in the culture medium. The level of laccase activity secreted by the transformed yeast was similar to that observed for the non-induced wild-type strain of T. versicolor. The identity of the recombinant enzyme was checked by Western blot and matrix-assisted laser desorption/ionization time-of-flight analysis. Electrophoresis separation in native conditions indicated a molecular mass of the recombinant protein slightly higher (5 kDa) than that of the mature T. versicolor laccase IIIb, suggesting a limited excess of glycosylation. The laccase production level reached 2.5 mg/l (0.23 units/ml), which is suitable for engineering purpose.

The aims of this study were to investigate (i) the influence of aging grassland in the recovery of soil state by the comparison of permanent grassland, two restored grasslands, two temporary grasslands, and a continuous crop in the same pedoclimatic conditions, (ii) the extent and the persistence of the potential changes following a grassland/or cropland phase. We hypothesized that the level of microbial communities and enzyme activities could achieve a profile close to that of permanent grassland after the introduction of grassland for a few years in crop rotations. Soil biophysicochemical properties were studied. Our results indicated that the abundance of microbial communities and enzyme activities were positively correlated to soil C and N contents and negatively correlated to soil pH. The changes in microbial abundance level were strongly linked to the changes in functional level when grasslands are introduced into crop rotations. We also showed that a continuous crop regime had a stronger legacy on the soil biota and functions. By contrast, the legacy of a grassland regime changed quickly when the grassland regime is interrupted by recent culture events. A grassland regime enabled the restoration of functions after more than five cumulative years in the grassland regime.

Neonicotinoids are the most widely used class of insecticides in the world but they have raised numerous concerns regarding their effects on biodiversity. Thus, the objective of this work was to do a critical review of the contamination of the environment (soil, water, air, biota) by neonicotinoids (acetamiprid, clothianidin, imidacloprid, thiacloprid, thiamethoxam) and of their impacts on terrestrial and aquatic biodiversity. Neonicotinoids are very frequently detected in soils and in freshwater, and they are also found in the air. They have only been recently monitored in coastal and marine environments, but some studies already reported the presence of imidacloprid and thiamethoxam in transitional or semi-enclosed ecosystems (lagoons, bays and estuaries). The contamination of the environment leads to the exposure and to the contamination of non-target organisms, and to negative effects on biodiversity. Direct impacts of neonicotinoids are mainly reported on terrestrial invertebrates (e.g., pollinators, natural enemies, earthworms) and vertebrates (e.g., birds), and on aquatic invertebrates (e.g., arthropods). Impacts on aquatic vertebrate populations and communities, as well as on microorganisms, are less documented. In addition to their toxicity to directly exposed organisms, neonicotinoid induce indirect effects via trophic cascades as demonstrated in several species (terrestrial and aquatic invertebrates). However, more data are needed to reach firmer conclusions and to get a clearer picture of such indirect effects. Finally, we identified specific knowledge gaps that need to be filled to better understand the effects of neonicotinoids on terrestrial, freshwater and marine organisms, as well as on ecosystem services associated with these biotas.

The use of pesticides in agriculture has highly increased during the last 40 years to increase crop yields. However, today most pesticides are polluting water, soil, atmosphere and food. Pesticides are also impact soil enzymes, which are essential catalysts ruling the quality of soil life. In particular, the activity of soil enzymes control nutrient cycles, and, in turn, fertilization. Here, we review the effects of pesticides on the activity of soil enzymes in terrestrial ecosystems. Enzymes include dehydrogenase, fluorescein diacetate hydrolase, acid phosphatase, alkaline phosphatase, phosphatase, beta-glucosidase, cellulase, urease and aryl-sulfatase. Those enzymes are involved in the cycles of carbon, nitrogen, sulfur and phosphorus. The main points of our analysis are (1) the common inhibition of dehydrogenase in 61 % of studies, stimulation of cellulase in 56 % of studies and no response of aryl-sulfatase in 67 % of studies. (2) Fungicides have mainly negative effects on enzymatic activities. (3) Insecticides can be classified into two groups, the first group represented by endosulfan having an overall positive impact while the second group having a negative effect. (4) Herbicides can be classified into two groups, one group with few positive effect and another group with negative effect.

Ecotoxicological tests with earthworms are widely used and are mandatory for the risk assessment of pesticides prior to registration and commercial use. The current model species for standardized tests is Eisenia fetida or Eisenia andrei. However, these species are absent from agricultural soils and often less sensitive to pesticides than other earthworm species found in mineral soils. To move towards a better assessment of pesticide effects on non-target organisms, there is a need to perform a posteriori tests using relevant species. The endogeic species Aporrectodea caliginosa (Savigny, 1826) is representative of cultivated fields in temperate regions and is suggested as a relevant model test species. After providing information on its taxonomy, biology, and ecology, we reviewed current knowledge concerning its sensitivity towards pesticides. Moreover, we highlighted research gaps and promising perspectives. Finally, advice and recommendations are given for the establishment of laboratory cultures and experiments using this soil-dwelling earthworm species.

The activity of microorganisms in soil is important for a robust functioning of soil and related ecosystem services. Hence, there is a necessity to identify the composition, diversity, and function of the soil microbiome in order to determine its natural properties, functioning, and operating range as well as to assess ecotoxicological effects due to anthropogenic activities. Numerous microbiological methods currently exist in the literature and new, more advanced methods continue to be developed; however, only a limited number of these methods are standardised. Consequently, there is a need to identify the most promising non-standardised methods for assessing soil quality and to transform them into standards. In agreement with the “Ecosystem Service Approach”, new methods should focus more on soil microbial functions, including nutrient cycling and greenhouse gas emission, pest control and plant growth promotion, carbon cycling and sequestration, as well as soil structure development and filter function. The few existing standardised methods available that focus on the function of the soil microbiome mostly include measurements, like basal respiration, enzyme activities, and biodegradation of organic matter, under well-defined conditions in the lab. This paper sets out to summarise and expand on recent discussions within the International Organization for Standardization (ISO), Soil Quality – Biological Characterization sub-committee (ISO TC 190/SC 4), where a need was identified to develop scientifically sound methods which would best fulfil the practical needs of future users for assessing soil quality, going beyond the existing test systems. Of particular note is the current evolution of molecular methods in microbial ecology that use quantitative real-time PCR (qPCR) to produce a large number of new functional endpoints which are more sensitive as compared to “classical” methods. Quantitative PCR assesses the abundance of microbes that catalyse major transformation steps in nitrogen and phosphorus cycling, greenhouse gas emissions, chemical transformations including pesticide degradation, and plant growth promotion pathways based on the assessment of marker gene sequences that drive the related processes. In the assessment of soil quality methods, it was found that most methods focus on bacteria and related endpoints. Techniques to describe fungal communities as well as their functional traits are far less represented. As such, techniques to analyse fungal enzyme activities are proposed. Additionally, methods for the determination of microbial growth rates and efficiencies, including the use of glomalin as a biochemical marker for soil aggregation, are discussed. Furthermore, field methods indicative of carbon turnover, including the litter bag test and a modification to the tea bag test, are presented. However, it is obvious that with increasing developments in high throughput sequencing technologies and big data analyses, including metagenomics analysis, it will be possible to implement these technologies into the standardisation process for assessing the functions of the soil microbiome. Overall, it is suggested that endpoints should represent a potential function of soil microorganisms rather than actual activity levels, as the latter can largely be dependent on short-term variable soil properties such as pedoclimatic conditions, nutrient availability, and anthropogenic soil cultivation activities.