Soil Biodiversity: State-of-the-Art and Possible Implementation in Chemical Risk Assessment.

Protecting the structure and functioning of soil ecosystems is one of the central aims of current regulations of chemicals. This is, for instance, shown by the emphasis on the protection of key drivers and ecosystem services as proposed in the protection goal options for soil organisms by the European Food Safety Authority (EFSA). Such targets require insight into soil biodiversity, its role in the functioning of ecosystems, and the way it responds to stress. Also required are tools and methodologies for properly assessing biodiversity. To address these issues, the Society of Environmental Toxicology and Chemistry (SETAC) Europe 14th Special Science Symposium (SESSS14) was held 19 to 20 November 2019 in Brussels, Belgium. The central aim of the SESSS14 was to provide information on how to include soil biodiversity and soil functions as protection goal options in the risk assessment and quantification of the effects of chemicals and other stressors (including their respective regulations). This paper is based on the presentations and discussions at the SESSS14 and will give a brief update on the scientific state-of-the art on soil biodiversity, novel scientific developments, experimental and modeling approaches, as well as case studies. It will also discuss how these approaches could inform future risk assessment of chemicals and other stressors in the regulatory context of protecting soil ecosystems. Integr Environ Assess Manag 2021;17:541-551. © 2020 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Effects of Dutch livestock production on human health and the environment.

Observed multiple adverse effects of livestock production have led to increasing calls for more sustainable livestock production. Quantitative analysis of adverse effects, which can guide public debate and policy development in this area, is limited and generally scattered across environmental, human health, and other science domains. The aim of this study was to bring together and, where possible, quantify and aggregate the effects of national-scale livestock production on 17 impact categories, ranging from impacts of particulate matter, emerging infectious diseases and odor annoyance to airborne nitrogen deposition on terrestrial nature areas and greenhouse gas emissions. Effects were estimated and scaled to total Dutch livestock production, with system boundaries including feed production, manure management and transport, but excluding slaughtering, retail and consumption. Effects were expressed using eight indicators that directly express Impact in the sense of the Drivers-Pressures-State-Impact-Response framework, while the remaining 14 express Pressures or States. Results show that livestock production may contribute both positively and negatively to human health with a human disease burden (expressed in disability-adjusted life years) of up to 4% for three different health effects: those related to particulate matter, zoonoses, and occupational accidents. The contribution to environmental impact ranges from 2% for consumptive water use in the Netherlands to 95% for phosphorus transfer to soils, and extends beyond Dutch borders. While some aggregation across impact categories was possible, notably for burden of disease estimates, further aggregation of disparate indicators would require normative value judgement. Despite difficulty of aggregation, the assessment shows that impacts receive a different contribution of different animal sectors. While some of our results are country-specific, the overall approach is generic and can be adapted and tuned according to specific contexts and information needs in other regions, to allow informed decision making across a broad range of impact categories.

Towards an integrative understanding of soil biodiversity.

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

Global distribution of earthworm diversity.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

Ecological Risk Assessment of a Metal-Contaminated Area in the Tropics. Tier II: Detailed Assessment.

This study presents data on the detailed evaluation (tier 2) of a site-specific ecological risk assessment (ssERA) in a former smelter area contaminated with metals (Santo Amaro, Bahia, Brazil). Combining information from three lines of evidence (LoE), chemical (ChemLoE), ecotoxicological (EcotoxLoE) and ecological (EcoLoE), in the Triad approach, integrated risk values were calculated to rank sites and confirm the potential risk disclosed with tier 1. Risk values were calculated for the habitat and for the retention functions in each sampling point. Habitat function included the ChemLoE calculated from total metal concentrations. The EcotoxLoE was based on reproduction tests with terrestrial invertebrates (Folsomia candida, Enchytraeus crypticus, Eisenia andrei), shoot length and plant biomass (Avena sativa, Brassica rapa). For the EcoLoE, ecological parameters (microbial parameters, soil invertebrate community, litter breakdown) were used to derive risk values. Retention function included the ChemLoE, calculated from extractable metal concentrations, and the EcotoxLoE based on eluate tests with aquatic organisms (Daphnia magna reproduction and Pseudokirchneriella subcapitata growth). Results related to the habitat function indicated that the metal residues are sufficient to cause risk to biota, while the low metal levels in extracts and the general lack of toxicity in aquatic tests indicated a high soil retention capacity in most sampling points. Integrated risk of tier 2 showed the same trend of tier 1, suggesting the need to proceed with remediation actions. The high risk levels were related to direct toxicity to organisms and indirect effects, such as failure in the establishment of vegetation and the consequent loss of habitat quality for microorganisms and soil fauna. This study shed some light on the selection of tools for the tier 2 of an ssERA in tropical metal-contaminated sites, focusing on ecological receptors at risk and using available chemical methods, ecological surveys and ecotoxicity tests.

Choice of resolution by functional trait or taxonomy affects allometric scaling in soil food webs.

Belowground organisms often display a shift in their mass-abundance scaling relationships due to environmental factors such as soil chemistry and atmospheric deposition. Here we present new empirical data that show strong differences in allometric scaling according to whether the resolution at the local scale is based on a taxonomic or a functional classification, while only slight differences arise according to soil environmental conditions. For the first time, isometry (an inverse 1:1 proportion) is recognized in mass-abundance relationships, providing a functional signal for constant biomass distribution in soil biota regardless of discrete trophic levels. Our findings are in contrast to those from aquatic ecosystems, in that higher trophic levels in soil biota are not a direct function of increasing body mass.

The practicalities and pitfalls of establishing a policy-relevant and cost-effective soil biological monitoring scheme.

A large number of biological indicators have been proposed over the years for assessing soil quality. Although many of those have been applied in monitoring schemes across Europe, no consensus exists on the extent to which these indicators might perform best and how monitoring schemes can be further optimized in terms of scientific and policy relevance. Over the past decade, developments in environmental monitoring and risk assessment converged toward the use of indicators and endpoints that are related to soil functioning and ecosystem services. In view of the proposed European Union (EU) Soil Framework Directive, there is an urgent need to identify and evaluate indicators for soil biodiversity and ecosystem services. The recently started integrated project, Ecological Function and Biodiversity Indicators in European Soils (EcoFINDERS), aims to address this specific issue within the EU Framework Program FP7. Here, we 1) discuss how to use the concept of ecosystem services in soil monitoring, 2) review former and ongoing monitoring schemes, and 3) present an analysis of metadata on biological indicators in some EU member states. Finally, we discuss our experiences in establishing a logical sieve approach to devise a monitoring scheme for a standardized and harmonized application at European scale.

Field effects of pollutants at the community level--experimental challenges and significance of community shifts for ecosystem functioning.

In the Stimulation Program System-oriented Ecotoxicological Research (SSEO) three sites in The Netherlands were investigated for field effects of the grey veil of pollutants. At each site several studies were performed in order to arrive at an adequate weight of evidence and to improve causal inference of pollutant effects. This paper contains a synthesis of results of the studies, performed at one of the sites, the Demmerikse polder. This site is characterized by an anthropogenic layer of soil (in old Dutch: 'toemaakdek') on top of the natural peat. Lead, copper and zinc concentrations were elevated, with lead concentrations above a Netherlands environmental quality criterion (Intervention Value) in 66% of the samples. Issues discussed in the paper are: the sampling strategy, selection of maximum gradient and suitable community end-points, both in space and in time. Specific emphasis was given to causal inference of ecological effects of pollutants, related to direct versus indirect effects, functioning of ecosystems, normal operation range and risk assessment. The plausibility of metal effects could be demonstrated on a number of occasions. In the Demmerikse polder changes in the bacterial and nematode communities could be related significantly to metal concentrations and separated from other environmental variables, such as organic matter content and pH.

Integration of bioavailability, ecology and ecotoxicology by three lines of evidence into ecological risk indexes for contaminated soil assessment.

A Weight of Evidence approach was applied to define three integrated effect indexes estimating the impairment on terrestrial ecosystems caused by the stressor(s) of concern. According to a Triad approach, the integrated effect indexes combined the information provided by the measurement endpoints of each line of evidence (chemistry/bioavailability, ecology and ecotoxicology) and allowed to analyse the impairment degree highlighted by each measurement endpoint as difference from the reference condition. Multi-Criteria Decision Analysis (MCDA) was used for the aggregation of the complementary Triad information, including expert judgement and a weighted procedure based on the endpoint sensitivity and the sensitivity of the test for ecosystem effects. The developed methodology was implemented in the DSS-ERAMANIA, Module 2, and is presented in this paper as "Integrated Effect Indexes" (IEI) sub-module. The latter has been preliminary applied to the Acna di Cengio (Italy) contaminated site; the results of this application are presented and discussed.

Development of a site-specific Ecological Risk Assessment for contaminated sites: part II. A multi-criteria based system for the selection of bioavailability assessment tools.

A comparison procedure based on Multi-Criteria Decision Analysis (MCDA) and expert judgment was developed in order to allow the comparison of bioavailability tests to implement the chemical Line of Evidence (LoE) within a TRIAD based site-specific Ecological Risk Assessment framework including three tires of investigation. The proposed methodology was included in the Module 1 of the Decision Support System DSS-ERAMANIA and the obtained rank supported the selection of a suitable set of available tests to be applied to the case study. A simplified application of the proposed procedure is described and results obtained by the system software are discussed.

Can transgenic maize affect soil microbial communities?

The aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the microbial community (ability to metabolize sources belonging to different chemical guilds) and/or a change in numerical abundance of their cells. Litter placement is known for its strong influence on the soil decomposer communities. The effects of the addition of crop residues on respiration and catabolic activities of the bacterial community were examined in microcosm experiments. Four cultivars of Zea mays L. of two different isolines (each one including the conventional crop and its Bacillus thuringiensis cultivar) and one control of bulk soil were included in the experimental design. The growth models suggest a dichotomy between soils amended with either conventional or transgenic maize residues. The Cry1Ab protein appeared to influence the composition of the microbial community. The highly enhanced soil respiration observed during the first 72 h after the addition of Bt-maize residues can be interpreted as being related to the presence of the transgenic crop residues. This result was confirmed by agar plate counting, as the averages of the colony-forming units of soils in conventional treatments were about one-third of those treated with transgenic straw. Furthermore, the addition of Bt-maize appeared to induce increased microbial consumption of carbohydrates in BIOLOG EcoPlates. Three weeks after the addition of maize residues to the soils, no differences between the consumption rate of specific chemical guilds by bacteria in soils amended with transgenic maize and bacteria in soils amended with conventional maize were detectable. Reaped crop residues, comparable to post-harvest maize straw (a common practice in current agriculture), rapidly influence the soil bacterial cells at a functional level. Overall, these data support the existence of short Bt-induced ecological shifts in the microbial communities of croplands' soils.

Functional recovery of biofilm bacterial communities after copper exposure.

Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 micromol/l copper amended surface water and a reference and subsequently to un-amended surface water. Transitions of bacterial communities were characterised with denaturing gradient gel electrophoresis (DGGE) and community-level physiological profiles (CLPP). Exposure to 6.8 micromol/l copper provoked distinct changes in DGGE profiles of bacterial consortia, which did not reverse upon copper depuration. Exposure to 2.1 and 6.8 micromol/l copper was found to induce marked changes in CLPP of bacterial communities that proved to be reversible during copper depuration. Furthermore, copper exposure induced the development of copper-tolerance, which was partially lost during depuration. It is concluded that bacterial communities exposed to copper contaminated water for a period of 26 days are capable to restore their metabolic attributes after introduction of unpolluted water in aquaria for 28 days.

Legislation and ecological quality assessment of soil: implementation of ecological indication systems in Europe.

Nationally and internationally there are an increasing number of legal initiatives to protect the ecological processes in soil. This article describes the legal situation concerning the protection of natural functions of soil in Europe (mainly The Netherlands (since 1987) and Germany (since 1998)). Examples of processes to be protected comprise the element cycles, the degradation of pollutants, and the conversion of organic matter. These processes are performed by organisms, and therefore, there is a growing consensus that protection of soil biodiversity is necessary for the survival of humans and the above-ground ecosystems. It is discussed that protection of soil ecosystems needs requires definitions and aims for the ecological quality of soil (as already provided for aquatic ecosystems). Taking into account that most soils are privately owned, legal initiatives are necessary to clarify responsibilities and to direct research toward the implementation of reproducible and standardized methods to determine the ecological quality of soil.

The use of microorganisms in ecological soil classification and assessment concepts.

Microbial communities are integral parts of soil and their activity is very important to the functioning of soil. Therefore, microorganisms should be included in soil quality classification and assessment concepts. The challenges of using microbial indicators are to identify the best choice among the many techniques available to assess soil quality and to convert the information obtained from the microbial indicator into a form relevant for policy makers. In this article, we present a wide range of possible microbial indicators, some of them standardized; each provides slightly different information on soil quality. Experience with the use of indicators for assessment of microbial communities and soil quality is discussed. At present, as many microbial indicators as possible should be included to gain experience. At a minimum, measures of microbial biomass, respiration, and N mineralization and a community profiling method (e.g., DGGE, PLFA, or CLPP) should be included.

Effects of copper and temperature on aquatic bacterial communities.

The present study aimed to characterise effects of copper and temperature on bacterial communities in photosynthetic biofilms using a suit of supplementary methods: pollution-induced community tolerance (PICT), DNA profiles with denaturing gradient gel electrophoresis (DGGE) and physiological profiles with community-level physiological profiling (CLPP). Biofilms of algae and bacteria were grown in a ditch of a Dutch polder and exposed in the laboratory to copper (3 microM and a reference) at three different temperatures (10, 14 and 20 degrees C). Bacterial communities sampled from the field showed heterogeneity in their physiological profiles, however the heterogeneity decreased during laboratory incubation. After 3 days laboratory incubation, the copper treated biofilms were different from the reference biofilms, as revealed by DGGE and CLPP analyses. Effects of temperature were not observed in the CLPPs, or in the DGGE profiles. PICT was observed for the bacterial communities at all temperatures. The copper-tolerance at 10 and 14 degrees C increased about 3 times, whereas copper-tolerance at 20 degrees C increased about 6 times. Temperature had an effect on the community tolerance, but not on the structure or on the physiological profile, suggesting that temperature was not a major factor causing successional changes under these laboratory conditions. In contrast, temperature had an effect on tolerance development indicating that the exposure to copper was enhanced at higher temperature.

Location-specific ecotoxicological risk assessment of metal-polluted soils.

When chemical analysis indicates metal pollution, a second-tier method is needed to evaluate whether toxic effects occur at the polluted sites. A method based on pollution-induced community tolerance (PICT) was developed using samples taken from locations polluted with sewage more than 20 years ago. Microorganisms extracted from soil samples were exposed to a concentration range of zinc, nickel, copper, chromium (III), or chromium (VI) salts in a buffer suspension. The remaining activity of the intoxicated microorganisms was determined by color formation with 31 different organic substrates in microtiter plates. Microorganisms from moderately Zn-polluted sites (>45 mg/kg) showed an increased tolerance for zinc. Nickel tolerance was observed at 51 mg Ni/kg soil, chromium (VI) tolerance at 923 mg Cr/kg. In most cases, tolerance also was observed at higher concentrations. High concentrations of 1,494 mg Cu/kg or 3,935 mg Cr/kg did not show PICT, indicating a limited bioavailability of Cu and Cr at these sites. The benefits of our method are its greater sensitivity compared to other tests used at these sites, and its specificity for those metals that exceed allowable levels.

Copper-induced modifications of the trophic relations in riverine algal-bacterial biofilms.

The effects of copper (Cu) on photosynthetic riverine biofilms were studied in artificial stream channels. Direct effects on the composition and functioning of the biofilms were investigated using plant pigments, community-level physiological profiles (CLPP), and pulse-amplitude-modulated (PAM) fluorescence. Copper caused a significant reduction of microalgal biomass and induced a shift in the population from diatoms to cyanobacteria. However, a decrease in biomass indicated that the replacement of species was not totally effective to counteract the toxic effects of Cu. A direct effect of Cu could also be shown in the bacterial community, and, furthermore, changes in the CLPP could be related to the Cu treatment. Copper-exposed biofilms lost the capacity to use between 11 and 15% of the substrates, but many of the remaining capacities became more robust, indicating an increased Cu tolerance due to the exposure. The change in the biofilm microbial composition points to the indirect effects of Cu on biofilms due to the close interdependence between biofilm autotrophic and heterotrophic compartments. Grazing by snails, which appeared to be an important factor structuring biofilms without any Cu addition, had a very minor effect on Cu-exposed biofilms. Although grazing changed the bacterial composition, its effects were not detected either on the algal community or on the biofilm community tolerance to Cu.

Biodegradation kinetics of toluene, m-xylene, p-xylene and their intermediates through the upper TOL pathway in Pseudomonas putida (pWWO).

Pseudomonas putida mt-2, harbouring TOL plasmid pWWO, is capable of degrading toluene and a range of di- and tri-alkylbenzenes. In this study, chemostat-grown cells (D = 0.05 h-1, toluene or m-xylene limitation) of this strain were used to assess the kinetics of the degradation of toluene, m-xylene, p-xylene, and a number of their pathway intermediates. The conversion kinetics for the three hydrocarbons showed significant differences: the maximal conversion rates were rather similar [11-14 mmol h-1 (g dry wt)-1] but the specific affinity (the slope of the v vs s curve near the origin) of the cells for toluene [1300 I (g dry wt)-1 h-1] was only 5% and 14% of those found for m-xylene and p-xylene, respectively. Consumption kinetics of mixtures of the hydrocarbons confirmed that xylenes are strongly preferred over toluene at low substrate concentrations. The maximum flux rates of pathway intermediates through the various steps of the TOL pathway as far as ring cleavage were also determined. Supply of 0-5 mM 3-methylbenzyl alcohol or 3-methylbenzaidehyde to fully induced cells led to the transient accumulation of 3-methylbenzoate. Accumulation of the corresponding carboxylic acid (benzoate) was also observed after pulses of benzyl alcohol and benzaldehyde, which are intermediates in toluene catabolism. Analysis of consumption and accumulation rates for the various intermediates showed that the maximal rates at which the initial monooxygenation step and the conversion of the carboxylic acids by toluate 1,2-dioxygenase may occur are two- to threefold lower than those measured for the two intermediate dehydrogenation steps.