Standard methods for the assessment of structural and functional diversity of soil organisms: A review

Additional organic and bacterium fertilizer input regulated soybean root architecture and dry matter distribution for a sustainable yield in the semi-arid Region of China

In the dryland area of the Loess Plateau in northwest China, long-term excessive fertilization has led to soil compaction and nutrient loss, which in turn limits crop yield and soil productivity. To address this issue, we conducted experiments using environmentally friendly organic fertilizer and bacterium fertilizer. Our goal was to investigate the effects of additional organic and bacterium fertilizer inputs on soil water migration, crop root architecture, and yield formation. We implemented six different fertilizer strategies, namely: Nm (mulching, N 30 kg/ha), NPK1m (mulching, N 60 kg/ha; P 30 kg/ha; K 30 kg/ha), NPK2m (mulching, N 90 kg/ha; P 45 kg/ha; K 30 kg/ha), NPKOm (mulching, N 90 kg/ha; P 45 kg/ha; K 30 kg/ha; organic fertilizer 2 t/ha), NPKBm (mulching, N 60 kg/ha; P 30 kg/ha; K 30 kg/ha; bacterium fertilizer 10 kg/ha), and N (N 30 kg/ha; no mulching). The results revealed that the addition of bacterium fertilizer (NPKBm) had a positive impact on soybean root system development. Compared with the other treatments, it significantly increased the total root length, total root surface area, and total root length density by 25.96% ~ 94.89%, -19.63% ~ 36.28%, and 9.36% ~ 28.84%, respectively. Furthermore, NPKBm enhanced soil water consumption. In 2018, water storage during the flowering and podding periods decreased by 12.63% and 19.65%, respectively, while water consumption increased by 0.97% compared to Nm. In 2019, the flowering and harvest periods decreased by 23.49% and 11.51%, respectively, while water consumption increased by 0.65%. Ultimately, NPKBm achieved high grain yield and significantly increased water use efficiency (WUE), surpassing other treatments by 76.79% ~ 78.97% and 71.22% ~ 73.76%, respectively. Subsequently, NPK1m also exhibited significant increases in yield and WUE, with improvements of 35.58% ~ 39.27% and 35.26% ~ 38.16%, respectively. The use of bacterium fertilizer has a profound impact on soybean root architecture, leading to stable and sustainable grain yield production.

Spent coffee grounds as a suitable alternative to standard soil in ecotoxicological tests

Eisenia andrei is considered in OECD and ISO guidelines to be a suitable replacement for Eisenia fetida in ecotoxicological assays. This suggests that other alternative materials and methods could also be used in standard procedures for toxicity testing. The guidelines also favor using less time-consuming procedures and reducing costs and other limitations to ecotoxicological assessments. In recent years, spent coffee grounds (SCG) have been used to produce vermicompost and biochar and as an additive to organic fertilizers. In addition, the physicochemical characteristics of SCG indicate that the material is a suitable substrate for earthworms, with the organisms performing as well as in natural soil. In the present study, a battery of ecotoxicological tests was established with unwashed and washed SCG and a natural reference soil (LUFA 2.2). The test substrates were spiked with different concentrations of silver nitrate. Survival and reproduction of the earthworm E. andrei were assessed under different conditions, along with substrate basal respiration (SBR) as a proxy for microbial activity. Seedling emergence and the germination index of Lepidium sativum were also determined, following standard guidelines. Exposure to silver nitrate had similar effects on earthworm survival and reproduction, as the estimated effective concentrations (EC10 and EC50) in unwashed SCG and LUFA 2.2 overlapped. A hormetic effect was observed for SBR in LUFA 2.2 spiked with 12.8 mg/kg but not in unwashed SCG. Both SBR and root development were inhibited by similar concentrations of silver nitrate in washed SCG. The findings indicate that unwashed SCG could potentially be used as a substrate in E. andrei toxicity tests and support the eventual inclusion of this material in the standard guidelines.

Continued Organic Fertigation after Basal Manure Application Does Not Impact Soil Fungal Communities, Tomato Yield or Soil Fertility

There is currently a limited understanding of the complex response of fungal microbiota diversity to organic fertigation. In this work, a 2-year field trial with organic tomato crops in a soil previously amended with fresh sheep manure was conducted. Two hypotheses were compared: (i) fertigation with organic liquid fertilizers versus (ii) irrigation with water. At the end of both years, soils were analyzed for physical-chemical parameters and mycobiome variables. Plate culture and DNA metabarcoding methods were performed in order to obtain a detailed understanding of soil fungal communities. Fertigation did not increase any of the physical-chemical parameters. Concerning soil fungal communities, differences were only found regarding the identification of biomarkers. The class Leotiomycetes and the family Myxotrichaceae were identified as biomarkers in the soil fungal community analyzed by means of DNA metabarcoding of the "fertigation" treatment at the end of Year 1. The Mortierella genus was detected as a biomarker in the "water" treatment, and Mucor was identified in the "fertigation" treatment in the cultivable soil fungi at the end of Year 2. In both years, tomato yield and fruit quality did not consistently differ between treatments, despite the high cost of the fertilizers added through fertigation.

The Smart Soil Organism Detector: An instrument and machine learning pipeline for soil species identification

Understanding the diversity of soil organisms is complicated by both scale and substrate. Every footprint we leave in the soil covers hundreds to millions of organisms yet we cannot see them without extremely laborious extraction and microsopy endeavors. Studying them is also challenging. Keeping them alive so that we can understand their lifecycles and ecological roles ranges from difficult to impossible. Functional and taxonomic identification of soil organisms, while possible, is also challenging. Here we present the Smart Soil Organism Detector, an instrument and machine learning pipeline that combines high-resolution imaging, multi-spectral sensing, large-bore flow cytometry, and machine learning to extract, isolate, count, identify, and separate soil organisms in a high-throughput, high-resolution, non-destructive, and reproducible manner. This system is not only capable of separating alive nematodes, dead nematodes, and nematode cuticles from soil with 100% out-of-sample accuracy, but also capable of identifying nematode strains (sub-species) with 95.5% out-of-sample accuracy and 99.4% specificity. Soil micro-arthropods were identified to class with 96.1% out-of-sample accuracy. Broadly applicable across soil taxa, the Smart SOD system is a tool for understanding global soil biodiversity.

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).

Oppia nitens C.L. Koch, 1836 (Acari: Oribatida): Current Status of Its Bionomics and Relevance as a Model Invertebrate in Soil Ecotoxicology

The oribatid soil mite Oppia nitens C.L. Koch, 1836, is a model microarthropod in soil ecotoxicity testing. This species has a significant role in supporting soil functions and as a suitable indicator of soil contamination. Despite its significance to the environment and to ecotoxicology, however, very little is known of its biology, ecology, and suborganismal responses to contaminants in the soil. In the present review, we present detailed and critical insights into the biology and ecology of O. nitens in relation to traits that are crucial to its adaptive responses to contaminants in soil. We used a species sensitivity distribution model to rank the species sensitivity to heavy metals (cadmium and zinc) and neonicotinoids (imidacloprid and thiacloprid) compared with other standardized soil invertebrates. Although the International Organization for Standardization and Environment and Climate Change Canada are currently standardizing a protocol for the use of O. nitens in soil toxicity testing, we believe that O. nitens is limited as a model soil invertebrate until the molecular pathways associated with its response to contaminants are better understood. These pathways can only be elucidated with information from the mites' genome or transcriptome, which is currently lacking. Despite this limitation, we propose a possible molecular pathway to metal tolerance and a putative adverse outcome pathway to heavy metal toxicity in O. nitens. Environ Toxicol Chem 2019;38:2593-2613. © 2019 SETAC.

Effects of herbicide on non-target microorganisms: Towards a new class of biomarkers?

Conventional agriculture still relies on the general use of agrochemicals (herbicides, fungicides and insecticides) to control various pests (weeds, fungal pathogens and insects), to ensure the yield of crop and to feed a constantly growing population. The generalized use of pesticides in agriculture leads to the contamination of soil and other connected environmental resources. The persistence of pesticide residues in soil is identified as a major threat for in-soil living organisms that are supporting an important number of ecosystem services. Although authorities released pesticides on the market only after their careful and thorough evaluation, the risk assessment for in-soil living organisms is unsatisfactory, particularly for microorganisms for which pesticide toxicity is solely considered by one global test measuring N mineralization. Recently, European Food Safety Authority (EFSA) underlined the lack of standardized methods to assess pesticide ecotoxicological effects on soil microorganisms. Within this context, there is an obvious need to develop innovative microbial markers sensitive to pesticide exposure. Biomarkers that reveal direct effects of pesticides on microorganisms are often viewed as the panacea. Such biomarkers can only be developed for pesticides having a mode of action inhibiting a specific enzyme not only found in the targeted organisms but also in microorganisms which are considered as "non-target organisms" by current regulations. This review explores possible ways of innovation to develop such biomarkers for herbicides. We scanned the herbicide classification by considering the mode of action, the targeted enzyme and the ecotoxicological effects of each class of active substance in order to identify those that can be tracked using sensitive microbial markers.