Terrestrial ecologists and soil modelers have traditionally portrayed the inhabitants of soil as a black box labeled as "soil fauna" or "decomposers or detritivores” assuming that they just merely recycle the deposited dead plant material. Soil is one of the most diverse habitats on Earth and contains one of the most diverse assemblages of living organisms; however, the opacity of this world has severely limited our understanding of their functional contributions to soil processes and to ecosystem resilience. Traditional taxonomy, based on morphological and anatomical aspects, is becoming replaced by rapid processing molecular techniques (e.g. with marker gene-based approaches). However, this may be impracticable in many ecological studies and consequently, the majority of the current knowledge, still contributes little to our understanding of their role in ecosystem functioning. Over the years, different workers have produced several ‘functional classifications’ based on the body width, feeding regime, certain behavioral and reproductive aspects and ecological niches of soil organisms. Unfortunately, the information available is severely restricted to ‘major’ groups. A better physiological and metabolic understanding of when and how a complex community of soil organisms access nutrients, alter their environment and in turn, affect soil processes, will allow a more realistic quantitative evaluation of their ecological roles in the biogeochemical cycles. Here, I review the applicability of the available approaches, highlight future research challenges and propose a dynamic conceptual framework that could improve our ability to solve this functional puzzle.

Soil fauna is crucial to soil formation, litter decomposition, nutrient cycling, biotic regulation, and for promoting plant growth. Yet soil organisms remain underrepresented in soil processes and in existing modeling exercises. This is a consequence of assuming that much of the below-ground diversity is just ecologically “redundant” and that soil food webs exhibit a higher degree of omnivory. However, evidence is accumulating on the strong influence of abiotic filters (temperature, moisture, soil pH) and soil habitat characteristics in controlling their spatial and temporal patterns. From this, new emerging concepts such as “hot moments,” “biological accessibility,” and “trophic cascades” have been coined to enable plausible explanations of the observed faunal responses to environmental changes. Here, I argue that many of these findings are indeed “happy accidents” (i.e., “eureka discoveries”) that remain disjointed between disciplines, impeding us from making significant breakthroughs. Therefore, here I provide some new perspectives on soil fauna research and highlight some experimental approaches to better explore the great variety of organisms living in soils and their complex interactions. A more comprehensive and dynamic holistic approach is needed to couple soil pedological and biological processes and to combine current experimental and theoretical knowledge if we aim to improve our predictive capacities in determining the persistence of soil organic matter and soil ecosystem functioning.

Pesticides are widely distributed in soils ^1–3 , yet their effects on soil biodiversity remain poorly understood ^4–7 . Here we examined the effects of 63 pesticides on soil archaea, bacteria, fungi, protists, nematodes, arthropods and key functional gene groups across 373 sites spanning woodlands, grasslands and croplands in 26 European countries. Pesticide residues were detected in 70% of sites and emerged as the second strongest driver of soil biodiversity patterns after soil properties. Our analysis further revealed organism- and function-specific patterns, emphasizing complex and widespread non-target effects on soil biodiversity. Pesticides altered microbial functions, including phosphorus and nitrogen cycling, and suppressed beneficial taxa, including arbuscular mycorrhizal fungi and bacterivore nematodes. Our findings highlight the need to integrate functional and taxonomic characteristics into future risk assessment methodology to safeguard soil biodiversity, a cornerstone of ecosystem functioning.