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Soils host highly diverse organism communities organized in complex food webs that strongly contribute to biological soil functions. However, it is a problem to evaluate these contributions because there are only few methods available which directly address soil functioning and ecosystem services. In fact, there are just two functional methods, which are useful for assessing quantitavely the activity of soil organisms, especially invertebrates. Both are related to organic matter decomposition (and thus nutrient cycling): the litter-bag-test in which mass loss of organic material is measured, but takes a long time, and the bait-lamina test, which is used to measure soil invertebrates’ feeding activity and its vertical distribution in situ. Both methods are internationally standardized. Currently, the use of the bait-lamina test seems to increase, mainly because it has been recommended for regulatory applications. The experiences with the bait-lamina test as described in the literature including the paper of Musso et al. (2014) are a good basis for improvements to be recommended, such as performing a preliminary test for the identification of the most appropriate study duration, using a standard bait material (i.e. to facilitate the comparison of data sets from different studies), and optimizing the “classic” study design in order to increase the statistical power of the test.

BackgroundGlyphosate-based herbicides (GBHs) are among the most often used pesticides. The hundreds of GBHs used worldwide consist of the active ingredient (AI) glyphosate in form of different salts, possibly other AIs, and various mostly undisclosed co-formulants. Pesticide risk assessments are commonly performed using single AIs or GBHs at standard soil conditions without vegetation. In a greenhouse experiment, we established a weed population with common amaranth (Amaranthus retroflexus) to examine the effects of three GBHs (Roundup LB Plus, Roundup PowerFlex, Touchdown Quattro) and their corresponding AIs (salts of glyphosate isopropylammonium, potassium, diammonium) on the activity and physiological biomarkers (glutathione S-transferase, GST; acetylcholine esterase, AChE) of an ecologically relevant earthworm species (Lumbricus terrestris). GBHs and AIs were applied at recommended doses; hand weeding served as control. Experiments were established with two soil types differing in organic matter content (SOM; 3.0% vs. 4.1%) and other properties.ResultsEarthworm activity (casting and movement activity) decreased after application of glyphosate formulations or active ingredients compared to hand weeding. We found no consistent pattern that formulations had either higher or lower effects on earthworm activity than their active ingredients; rather, differences were substance-specific. Earthworm activity was little affected by soil organic matter levels. Biomarkers remained unaffected by weed control types; GST but not AChE was decreased under high SOM. Water infiltration after a simulated heavy rainfall was interactively affected by weed control types and SOM. Leachate amount was higher after application of formulations than active ingredients and was higher under low SOM. Glyphosate concentrations in soil and leachate were strongly affected by application of formulations or active ingredients and varied with SOM (significant weed control type x SOM interaction).ConclusionsWe found that both commercial formulations and pure active ingredients can influence earthworms with consequences on important soil functions. Glyphosate products showed increased, reduced or similar effects than pure glyphosate on particular soil functions; soil properties can substantially alter this. Especially at lower SOM, heavy rainfalls could lead to more glyphosate leaching into water bodies. A full disclosure of co-formulants would be necessary to further decipher their specific contributions to these inconsistent effects.

Metagenomics – shotgun sequencing of all DNA fragments from a community DNA extract – is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene‐based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies. We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes. We recovered over 95% of the species, and observed relatively high false‐positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon‐specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass–read relationships. Results were similar among different sequencing efforts. The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low‐ and high‐sequencing efforts yield similar results, suggesting high cost‐efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics‐based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality. Shotgun metagenomics is increasingly applicable to study eukaryotic community composition. Theoretically, metagenomics should inform about species’ biomass, since it omits a taxonomically biased PCR step. Here, we evaluate how well metagenomics records composition and biomass in mock communities, and how its performance is affected by reference genome properties.

In the present review, we compiled and evaluated the available information supporting the assessment of population and community recovery after pesticide application. This information is crucial for the environmental risk assessment of pesticides. We reviewed more than 3900 manuscripts on those organism groups relevant or likely to become relevant for the risk assessment procedures in Europe, that is, aquatic invertebrates, algae, aquatic plants, fish, aquatic microbes, amphibians, as well as birds and mammals, non-target terrestrial arthropods including honeybees, non-arthropod invertebrates, terrestrial microbes, non-target terrestrial plants, nematodes, and reptiles. Finally, 106 aquatic and 76 terrestrial studies met our selection criteria and were evaluated in detail. We extracted the following general conclusions. (i) Internal recovery depends strongly on reproduction capacity. For aquatic invertebrates, recovery was generally observed within a maximum of five generation times. (ii) In cases where recovery occurred within one generation, migration from uncontaminated areas was identified as the main pathway for aquatic and terrestrial invertebrates, in particular, for insect species with the ability for aerial recolonization. (iii) Community composition in general did not recover within the study duration in the majority of cases. (iv) The ecological context, including factors such as food resources, habitat quality, and recolonization potential, is a crucial factor for recovery from pesticide effects. (v) Indirect effects acting through food chain processes, including predation and competition, are highly relevant for increasing the magnitude of effect and for prolonging recovery time. Based on our findings, we recommend defining realistic scenarios for risk assessment regarding exposure, taxa considered, environmental conditions, and ecological context. In addition to experimental studies, field monitoring was shown to yield valuable information to identify relevant taxa, long-term effects, and the conditions for recovery, and should therefore be considered to validate approaches of risk assessment. Likewise, ecological modelling was found to be a valuable tool for assessing recovery. Finally, both study design and interpretation of results still often suffer from missing ecological information or from neglect of the available knowledge. Hence, a more rigorous utilization of existing knowledge (e.g., from general disturbance ecology) and the generation of systematic ecological knowledge on the various factors influencing recovery are needed.

Glyphosate-based herbicides (GBH) are currently the most widely used agrochemicals for weed control. Environmental risk assessments (ERA) on nontarget organisms mostly consider the active ingredients (AIs) of these herbicides, while much less is known on effects of commercial GBH formulations that are actually applied in the field. Moreover, it is largely unknown to what extent different soil characteristics alter potential side effects of herbicides. We conducted a greenhouse experiment growing a model weed population of Amaranthus retroflexus in arable field soil with either 3.0 or 4.1% soil organic matter (SOM) content and treated these weeds either with GBHs (Roundup LB Plus, Touchdown Quattro, Roundup PowerFlex) or their respective AIs (isopropylammonium, diammonium or potassium salts of glyphosate) at recommended dosages. Control pots were mechanically weeded. Nontarget effects were assessed on the surface activity of the springtail species Sminthurinus niger (pitfall trapping) and litter decomposition in the soil (teabag approach). Both GBHs and AIs increased the surface activity of springtails compared to control pots; springtail activity was higher under GBHs than under corresponding AIs. Stimulation of springtail activity was much higher in soil with higher SOM content than with low SOM content (significant treatment x SOM interaction). Litter decomposition was unaffected by GBHs, AIs or SOM levels. We suggest that ERAs for pesticides should be performed with actually applied herbicides rather than only on AIs and should also consider influences of different soil properties.

The most important reason for the lack of a German nationwide and standardised survey of soil organisms is probably the time‐consuming and expensive identification of soil invertebrates. The present contribution should contribute to solving this problem. Earthworms and soil were sampled at 25 sites, the animals were identified morphologically and by community DNA (comDNA) and environmental DNA (eDNA) metabarcoding. The comparison of results showed that comDNA detected more species (3.6 on average) than eDNA (3.0) and morphological identification (2.8). In contrast, eDNA, on average, detected a similar number of species as morphological identification. However, some species appear to have a different probability of being detected by eDNA than others, depending on their abundance, behaviour, biology or body size. All three identification methods can differentiate between sites with different species composition, and the degree of separation can vary depending on the identification method. The relative proportion of eDNA reads shows potential as a surrogate of relative abundance/biomass for endogeic but not for anecic species. The overall aim of the ‘MetaSOL’ project (which the present contribution originated from) was to develop recommendations for efficient and routinely implementable monitoring of soil fauna. The results showed that genetic identification methods are suitable for earthworms. Before genetic identification methods can be introduced into official practice, key preconditions such as comprehensive, well‐curated and quality‐controlled DNA reference databases and method standardisation must be addressed. Robust indices of soil health based on soil organism data need to be developed. The inclusion of further groups in addition to earthworms should be examined. The present contribution should contribute to solving the problem of the time‐consuming and expensive identification of soil invertebrates in the standardised survey of soil organisms. Earthworms and soil were sampled at 25 sites; the animals were identified morphologically and by community DNA (comDNA) and environmental DNA (eDNA) metabarcoding, and the results compared. The results showed that genetic identification methods for earthworms are generally suitable to be included in an efficient and routinely implementable monitoring of soil fauna, but that several preconditions must first be met.

According to the Millennium Ecosystem Assessment, common indicators are needed to monitor the loss of biodiversity and the implications for the sustainable provision of ecosystem services. However, a variety of indicators are already being used resulting in many, mostly incompatible, monitoring systems. In order to synthesise the different indicator approaches and to detect gaps in the development of common indicator systems, we examined 531 indicators that have been reported in 617 peer-reviewed journal articles between 1997 and 2007. Special emphasis was placed on comparing indicators of biodiversity and ecosystem services across ecosystems (forests, grass- and shrublands, wetlands, rivers, lakes, soils and agro-ecosystems) and spatial scales (from patch to global scale). The application of biological indicators was found most often focused on regional and finer spatial scales with few indicators applied across ecosystem types. Abiotic indicators, such as physico-chemical parameters and measures of area and fragmentation, are most frequently used at broader (regional to continental) scales. Despite its multiple dimensions, biodiversity is usually equated with species richness only. The functional, structural and genetic components of biodiversity are poorly addressed despite their potential value across habitats and scales. Ecosystem service indicators are mostly used to estimate regulating and supporting services but generally differ between ecosystem types as they reflect ecosystem-specific services. Despite great effort to develop indicator systems over the past decade, there is still a considerable gap in the widespread use of indicators for many of the multiple components of biodiversity and ecosystem services, and a need to develop common monitoring schemes within and across habitats. Filling these gaps is a prerequisite for linking biodiversity dynamics with ecosystem service delivery and to achieving the goals of global and sub-global initiatives to halt the loss of biodiversity.

BackgroundA field study lasting one year was performed to study the effects of a calcium cyanamide fertiliser (trade name: Perlka®) on Collembola in order to support the terrestrial risk assessment under the REACH (Registration, Evaluation, Authorisation and Restriction of Chemicals) regulation. Due to the lack of an appropriate guidance document, the design of the study was based on the ISO Guideline 11268–3, originally developed for earthworm field studies. However, the sampling procedure was adapted accordingly by applying ISO Guideline 23611–2, i.e. taking soil core and pitfall trap samples. Two groups of four plots each were treated with 200 kg/ha and 400 kg/ha Perlka®, respectively. A third group served as a fertiliser control, i.e. it was treated with a standard urea fertiliser (172.9 kg Piagran®/ha) at the same total nitrogen rate (79.5 kg/ha) as provided by the high Perlka® application rate. The fourth group served as negative control without any fertiliser treatment and the fifth group was treated with the reference item Agriclor® (480 g a.i./L chlorpyrifos), known to be toxic to springtails.ResultsIn total 16 different Collembola species were determined. For seven species, covering all life form types, a reliable statistical evaluation was possible, which was reflected in correspondingly low MDD values in the study. A statistically significant decrease of the abundance (at least 50%) on the reference item plots compared to the untreated control was observed for six species, thus demonstrating the sensitivity of the Collembola community.ConclusionNo long-lasting effects of the Perlka® application rates could be observed for any of the Collembola species. In order to support risk assessors in both industry and authorities in the interpretation of large and complex data sets typical for field studies with chemicals, further guidance on implementation and data interpretation is urgently needed.

The contamination left by abandoned mines demands sustainable mitigation measures. Hence, the aim of this study was to examine the phytoremediator ability of Eucalyptus globulus Labill. to be used for cleaning up metal-contaminated soils from an African abandoned iron (Fe) mine (Ait Ammar, Oued Zem, Morocco). Plantlets of this species were exposed to a control (CTL), a reference (REF), and a mine-contaminated soil (CS). Morphological (growth, leaf area) and physiological stress biomarkers (photosynthetic efficiency, pigments content, leaf relative water, and malondialdehyde (MDA) levels) and metal bioaccumulation were assessed. The growth and leaf area of E. globulus increased overtime in all soils, although at a lower rate in the CS. Its photosynthetic efficiency was not markedly impaired, as well as MDA levels decreased throughout the experiment in CS. In this soil, higher metal contents were detected in E. globulus roots than in leaves, especially Fe (roots: 15.98–213.99 μg g −1 ; leaves: 5.97–15.98 μg g −1 ) and Zn (roots: 1.64–1.99 μg g −1 ; leaves: 0.67–1.19 μg g −1 ), indicating their reduced translocation. Additionally, though at low extent, the plants bioaccumulated some metals (Pb > Zn > Cu) from CS. Overall, E. globulus may be potentially used for the phytoremediation of metals in metal-contaminated soils.

The ability of organisms to avoid contaminated soils can act as an indicator of toxic potential in a particular soil. Based on the escape response of earthworms and Collembola, avoidance tests with these soil organisms have great potential as early screening tools in site-specific assessment. These tests are becoming more common in soil ecotoxicology, because they are ecologically relevant and have a shorter duration time compared with standardized soil toxicity tests. The avoidance response of soil invertebrates, however, can be influenced by the soil properties (e.g., organic matter content and texture) that affect behavior of the test species in the exposure matrix. Such an influence could mask a possible effect of the contaminant. Therefore, the effects of soil properties on performance of test species in the exposure media should be considered during risk assessment of contaminated soils. Avoidance tests with earthworms (Eisenia andrei) and springtails (Folsomia candida) were performed to identify the influence of both organic matter content and texture on the avoidance response of representative soil organisms. Distinct artificial soils were prepared by modifying quantities of the standard artificial soil components described by the Organization for Economic Co-operation and Development to achieve different organic matter and texture classes. Several combinations of each factor were tested. Results showed that both properties influenced the avoidance response of organisms, which avoided soils with low organic matter content and fine texture. Springtails were less sensitive to changes in these soil constituents compared with earthworms, indicating springtails can be used for site-specific assessments of contaminated soils with a wider range of respective soil properties.