Soil ecotoxicology: state of the art and future directions

Developments in soil ecotoxicology started with observations on pesticide effects on soil invertebrates in the 1960s. To support the risk assessment of chemicals, in the 1980s and 1990s development of toxicity tests was the main issue, including single species tests and also more realistic test systems like model ecosystems and field tests focusing on structural and functional endpoints. In the mean time, awareness grew about issues like bioavailability and routes of exposure, while biochemical endpoints (biomarkers) were proposed as sensitive and potential early-warning tools. In recent years, interactions between different chemicals (mixture toxicity) and between chemical and other stressors attracted scientific interest. With the development of molecular biology, omics tools are gaining increasing interest, while the ecological relevance of exposure and effects is translating into concepts like (chemical) stress ecology, ecological vulnerability and trait-based approaches. This contribution addresses historical developments and focuses on current issues in soil ecotoxicology. It is concluded that soil ecotoxicological risk assessment would benefit from extending the available battery of toxicity tests by including e.g. isopods, by paying more attention to exposure, bioavailability and toxicokinetics, and by developing more insight into the ecology of soil organisms to support better understanding of exposure and long-term consequences of chemical exposure at the individual, population and community level. Ecotoxicogenomics tools may also be helpful in this, but will require considerable further research before they can be applied in the practice of soil ecotoxicological risk assessment.     

Bridging the gap between micro - and macro-scale perspectives on the role of microbial communities in global change ecology

In order to understand the role microbial communities play in mediating ecosystem response to disturbances it is essential to address the methodological and conceptual gap that exists between micro- and macro-scale perspectives in ecology. While there is little doubt microorganisms play a central role in ecosystem functioning and therefore in ecosystem response to global change-induced disturbance, our ability to investigate the exact nature of that role is limited by disciplinary and methodological differences among microbial and ecosystem ecologists. In this paper we present results from an interdisciplinary graduate-level seminar class focused on this topic. Through the medium of case studies in global change ecology (soil respiration, nitrogen cycling, plant species invasion and land use/cover change) we highlight differences in our respective approach to ecology and give examples where disciplinary perspective influences our interpretation of the system under study. Finally, we suggest a model for integrating perspectives that may lead to greater interdisciplinary collaboration and enhanced conceptual and mechanistic modeling of ecosystem response to disturbance.     

Interactive effects of global change drivers as determinants of the link between soil biodiversity and ecosystem functioning

Biodiversity, both aboveground and belowground, is negatively affected by global changes such as drought or warming. This loss of biodiversity impacts Earth's ecosystems, as there is a positive relationship between biodiversity and ecosystem functioning (BEF). Even though soils host a large fraction of biodiversity that underlies major ecosystem functions, studies exploring the relationship between soil biodiversity and ecosystem functioning (sBEF) as influenced by global change drivers (GCDs) remain scarce. Here we highlight the need to decipher sBEF relationships under the effect of interactive GCDs that are intimately connected in a changing world. We first state that sBEF relationships depend on the type of function (e.g., C cycling or decomposition) and biodiversity facet (e.g., abundance, species richness, or biomass) considered. Then, we shed light on the impact of single and interactive GCDs on soil biodiversity and sBEF and show that results from scarce studies studying interactive effects range from antagonistic to additive to synergistic when two individual GCDs cooccur. This indicates the need for studies quantitatively accounting for the impacts of interactive GCDs on sBEF relationships. Finally, we provide guidelines for optimized methodological and experimental approaches to study sBEF in a changing world that will provide more valuable information on the real impact of (interactive) GCDs on sBEF. Together, we highlight the need to decipher the sBEF relationship in soils to better understand soil functioning under ongoing global changes, as changes in sBEF are of immediate importance for ecosystem functioning.     

A Striking Profile: Soil Ecological Knowledge in Restoration Management and Science

Available evidence suggests that research in terrestrial restoration ecology has been dominated by the engineering and botanical sciences. Because restoration science is a relatively young discipline in ecology, the theoretical framework for this discipline is under development and new theoretical offerings appear regularly in the literature. In reviewing this literature, we observed an absence of in‐depth discussion of how soils, and in particular the ecology of soils, can be integrated into the developing theory of restoration science. These observations prompted us to assess the current role of soil ecological knowledge in restoration research and restoration practice. Although soils are universally regarded as critical to restoration success, and much research has included manipulations of soil variables, we found that better integration of soil ecological principles could still contribute much to the practice of ecosystem restoration. Here we offer four potential points of departure for increased dialog between restoration ecologists and soil ecologists. We hope to encourage the view that soil is a complex, heterogeneous, and vital entity and that adoption of this point of view can positively affect restoration efforts worldwide.     

生物多样性与生态系统功能:进展与争论

生物多样性与生态系统功能的关系已成为当前人类社会面临的一个重大科学问题,生物多样性的空前丧失,促使人们开展了大量研究工作来描述物种多样性-生态系统功能关系,并试图揭示多样性与系统功能关系的内在机制,本文将多样性对生态系统功能作用机制的有关假说分为统计学与生物学两大类：前者是从统计学角度来解释观察到的多样性-系统功能模式,包括抽样效应,统计均衡效应等;而后者是基于多样性的生物学效应给出的,包括生态位互补,种间正相互作用,保险效应等,本文较为详细地介绍了该领域内有代表性的实验工作,包括“生态箱”实验,Cedar Creek草地多样性实验,微宇宙实验,欧洲草地实验,以及在这些实验结果解释上的激烈争论。     

青藏高原高寒草地生物多样性与生态系统功能的关系

生物多样性和生态系统功能(BEF)之间的关系是目前陆地生态系统生态学研究的热点, 对于生态系统的高效利用与管理意义重大, 而且对于退化生态系统功能的恢复及生物多样性的保护有重要的指导作用。高寒草地是青藏高原生态系统的主体, 近年来, 在气候变化与人为干扰等因素的驱动下, 高寒草地生态系统功能严重衰退。为此, 本文在综述物种多样性和生态系统功能及其相互关系研究进展的基础上, 首先从地下生态学过程研究、全球变化对生态系统多功能性的影响等方面解析了目前关于草地生物多样性和生态系统功能研究中存在的问题。继而, 从不同草地类型、草地退化程度、放牧、模拟气候变化、刈割、施肥、封育和补播等干扰利用方式对高寒草地物种多样性与生态系统功能的影响进行了全面的评述。并指出了高寒草地BEF研究中存在的不足, 今后应基于物种功能多样性开展高寒草地BEF研究, 全面且综合地考虑非生物因子(养分资源、外界干扰、环境波动等)对生物多样性与生态系统功能之间关系的影响, 关注尺度效应和要素耦合在全球气候变化对高寒草地BEF研究中的作用。最后, 以高寒草地BEF研究进展和结论为支撑依据, 综合提出了高寒草地资源利用和生物多样性保护的措施与建议: 加强放牧管理, 保护生物多样性; 治理退化草地, 维持生物多样性功能; 加强创新保护理念, 增强生态系统功能。     

Addressing chemical pollution in biodiversity research

Climate change, biodiversity loss, and chemical pollution are planetary-scale emergencies requiring urgent mitigation actions. As these “triple crises” are deeply interlinked, they need to be tackled in an integrative manner. However, while climate change and biodiversity are often studied together, chemical pollution as a global change factor contributing to worldwide biodiversity loss has received much less attention in biodiversity research so far. Here, we review evidence showing that the multifaceted effects of anthropogenic chemicals in the environment are posing a growing threat to biodiversity and ecosystems. Therefore, failure to account for pollution effects may significantly undermine the success of biodiversity protection efforts. We argue that progress in understanding and counteracting the negative impact of chemical pollution on biodiversity requires collective efforts of scientists from different disciplines, including but not limited to ecology, ecotoxicology, and environmental chemistry. Importantly, recent developments in these fields have now enabled comprehensive studies that could efficiently address the manifold interactions between chemicals and ecosystems. Based on their experience with intricate studies of biodiversity, ecologists are well equipped to embrace the additional challenge of chemical complexity through interdisciplinary collaborations. This offers a unique opportunity to jointly advance a seminal frontier in pollution ecology and facilitate the development of innovative solutions for environmental protection.     

Soil microbial diversity: Methodological strategy, spatial overview and functional interest

Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have resulted in modifications of the taxonomic diversity and functioning of the indigenous microbial communities. As a consequence, the functional significance of these losses/modifications of biodiversity, in terms of the capacity of ecosystems to maintain the functions and services on which humanity depends, is now of pivotal importance. In this context, one of the main challenges in soil microbial ecology is to better understand and predict the processes that drive soil microbial diversity and the link between diversity and ecosystem process. This review describes past, present and ongoing conceptual and methodological strategies employed to better assess and understand the distribution and evolution of soil microbial diversity with the aim of increasing our capacity to translate such diversity into soil biological functioning and, more widely, into ecosystem services.     

Some aspects of forest soil and litter ecology in the Dawyck Cryptogamic Sanctuary with a particular reference to fungi

Here we report on ecology and biodiversity of fungi in a unique mycological sanctuary in Britain, where data on species composition have been collected since 1994. To complement the biodiversity data by the information on the fungal ecological interactions and their role in the overall ecosystem functioning, soil properties and the composition of forest litter and field layer, bacterial population numbers and fungal biomass (in terms of ergosterol) were measured in 8 plots covered with different vegetations (beech, birch, birch-oak-beech, grass) over a May–Aug. period, and the results were analysed by correlation analysis and stepwise regression modelling together with data on protozoa and nematodes available from parallel research. The results highlighted the complexity of factors influencing temporal dynamics and spatial variability of fungal biomass in soil and forest litter. Most of the registered interactions appeared to be transient, and this should be taken into account while interpreting environmental observations. Interpretation of the specific relationships is given and implications for further research and overall ecosystem functioning are discussed.     

英国多克隐花植物保护区森林土壤和凋落叶特性及其与真菌的关系

报道了英国独特的真菌保护区里真菌的生态学和生物多样性,而该保护区内有关物种构成的数据自1994年就开始进行收集了。关于真菌的生态学相互关系以及它们在总的生态系统功能中的作用可以作为生物多样性数据的补充。5~8月期间,在8块覆盖着不同植被（山毛榉,桦树,桦栎山毛榉,禾本科植物）实验区里,研究了森林凋落叶和叶本层土壤的特性和构成,测量了细菌种群数量和真菌的生物量（针对麦角固醇而言）。用相关分析和分段回归建模方法,结合可通过并行研究采集到的原生动物和线虫数据,得到了一系列结果。这些结果强调了某些因素的复杂性,这些因素影响着森林土壤和森林凋落叶中真菌生物量空间可变性的时间动态。大多数的相互作用看起来是瞬时的,在解释环境观测记录时应该对这一点给予充分考虑。最后,解释了若干具体关系,给出了进一步研究的方向,讨论了对整个生态系统功能研究的必要性。     

Patterns in Species Persistence and Biomass Production in Soil Microcosms Recovering from a Disturbance Reject a Neutral Hypothesis for Bacterial Community Assembly

The neutral theory of biodiversity has emerged as a major null hypothesis in community ecology. The neutral theory may sufficiently well explain the structuring of microbial communities as the extremely high microbial diversity has led to an expectation of high ecological equivalence among species. To address this possibility, we worked with microcosms of two soils; the microcosms were either exposed, or not, to a dilution disturbance which reduces community sizes and removes some very rare species. After incubation for recovery, changes in bacterial species composition in microcosms compared with the source soils were assessed by pyrosequencing of bacterial 16S rRNA genes. Our assays could detect species with a proportional abundance ≥ 0.0001 in each community, and changes in the abundances of these species should have occurred during the recovery growth, but not be caused by the disturbance per se. The undisturbed microcosms showed slight changes in bacterial species diversity and composition, with a small number of initially low-abundance species going extinct. In microcosms recovering from the disturbance, however, species diversity decreased dramatically (by > 50%); and in most cases there was not a positive relationship between species initial abundance and their chance of persistence. Furthermore, a positive relationship between species richness and community biomass was observed in microcosms of one soil, but not in those of the other soil. The results are not consistent with a neutral hypothesis that predicts a positive abundance-persistence relationship and a null effect of diversity on ecosystem functioning. Adaptation mechanisms, in particular those associated with species interactions including facilitation and predation, may provide better explanations.     

A tale of four stories: soil ecology, theory, evolution and the publication system

Background

Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals.

Findings

We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals.

Conclusion

This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate “particularity” (empirical observations) and “generality” (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary.     

The soil quality concept as a framework to assess management practices in vulnerable agroecosystems: A case study in Mediterranean vineyards

Land management aiming to sustain ecosystem services is an important issue, especially in biodiversity hot spots such as found in Mediterranean areas. In Mediterranean areas, viticulture is an important land use. Vineyards are frequently found on inherently poor soils and are submitted to intensive management practices, which threaten soil functioning and associated ecosystem services. To encourage winegrowers and stakeholders to be reflective and adapt their vineyard practices, we evaluated the effects of three soil management practices (inter row plant cover duration, weeding and fertilization strategies) on soil functioning in 146 commercial plots distributed in Southern France, by a complementary set of biological and physico-chemical indicators. We used the concept of soil dynamic quality to evaluate some soil management practices on soil functioning. The influence of inherent soil properties derived from pedogenesis on soil dynamic indicator response was accounted for by considering the response of soil indicators for three soil groups differing in their stoniness and Ca carbonate content. The three soil management practices systematically influenced some nematode-based indicators, whereas other indicators were ascribable to a specific soil type or practice. We demonstrated that the potential of soil management practices to enhance soil functioning is restricted by soil type. In particular for calcareous soils, the soil functioning is very stable limiting effects of soil management practices. The presence of a cover crop, even temporary, in the inter row, is the only practice which benefits soil functioning whatever the soil type whereas organic fertilization and chemical weeding exhibit contrasting results on soil functioning.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

Carbon isotopes in functional soil ecology

Soil is an integral part of terrestrial ecosystems. Many soil ecologists interested in soil ecosystem functioning rely, to some degree, on stable isotope methodologies. The study of the natural abundance of carbon isotopes, especially (13)C but also (14)C, in the environment and the use of stable carbon isotope tracers have proved very useful in investigating the soil carbon cycle and soil trophic relationships. Recent methodological and technical advances have greatly extended the possibilities for the application of stable carbon isotopes to terrestrial ecology and have vastly improved our knowledge of belowground ecosystem functioning and will continue to do so. A better understanding of soil processes is invaluable in predicting the future impacts of global environmental change on terrestrial ecosystems.     

Biodiversity and ecosystem functioning in naturally assembled communities

Approximately 25 years ago, ecologists became increasingly interested in the question of whether ongoing biodiversity loss matters for the functioning of ecosystems. As such, a new ecological subfield on Biodiversity and Ecosystem Functioning (BEF) was born. This subfield was initially dominated by theoretical studies and by experiments in which biodiversity was manipulated, and responses of ecosystem functions such as biomass production, decomposition rates, carbon sequestration, trophic interactions and pollination were assessed. More recently, an increasing number of studies have investigated BEF relationships in non‐manipulated ecosystems, but reviews synthesizing our knowledge on the importance of real‐world biodiversity are still largely missing. I performed a systematic review in order to assess how biodiversity drives ecosystem functioning in both terrestrial and aquatic, naturally assembled communities, and on how important biodiversity is compared to other factors, including other aspects of community composition and abiotic conditions. The outcomes of 258 published studies, which reported 726 BEF relationships, revealed that in many cases, biodiversity promotes average biomass production and its temporal stability, and pollination success. For decomposition rates and ecosystem multifunctionality, positive effects of biodiversity outnumbered negative effects, but neutral relationships were even more common. Similarly, negative effects of prey biodiversity on pathogen and herbivore damage outnumbered positive effects, but were less common than neutral relationships. Finally, there was no evidence that biodiversity is related to soil carbon storage. Most BEF studies focused on the effects of taxonomic diversity, however, metrics of functional diversity were generally stronger predictors of ecosystem functioning. Furthermore, in most studies, abiotic factors and functional composition (e.g. the presence of a certain functional group) were stronger drivers of ecosystem functioning than biodiversity per se. While experiments suggest that positive biodiversity effects become stronger at larger spatial scales, in naturally assembled communities this idea is too poorly studied to draw general conclusions. In summary, a high biodiversity in naturally assembled communities positively drives various ecosystem functions. At the same time, the strength and direction of these effects vary highly among studies, and factors other than biodiversity can be even more important in driving ecosystem functioning. Thus, to promote those ecosystem functions that underpin human well‐being, conservation should not only promote biodiversity per se, but also the abiotic conditions favouring species with suitable trait combinations.     

Assessing the functional implications of soil biodiversity in ecosystems

Soil communities are among the most species-rich components of terrestrial ecosystems. A major challenge for soil ecologists is to formulate feasible research strategies that will preserve and capitalize on the biodiversity resources of the soil. This article considers the role of soil organism diversity by concentrating on: (i) the relationship between soil biodiversity and ecosystem function; (ii) what issues need to be explored; (iii) studies carried out in the Ecotron controlled environment facility; and (iv) how stable isotope techniques can improve our understanding of the relationship between soil biodiversity and ecosystem function. It is advocated that: (i) the objective of any soil biodiversity study should always be the generation of general concepts, rather than local, system-specific observations; and (ii) any empirical study can be properly interpreted only within a quantitative ecological framework.     

Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance

Analysing the consequences of the decrease in biodiversity for ecosystem functioning and stability has been a major concern in ecology. However, the impact of decline in soil microbial diversity on ecosystem sustainability remains largely unknown. This has been assessed for decomposition, which is insured by a large proportion of the soil microbial community, but not for more specialized and less diverse microbial groups. We determined the impact of a decrease in soil microbial diversity on the stability (i.e. resistance and resilience following disturbance) of two more specialized bacterial functional groups: denitrifiers and nitrite oxidizers. Soil microbial diversity was reduced using serial dilutions of a suspension obtained from a non-sterile soil that led to loss of species with low cell abundance, inoculation of microcosms of the same sterile soil with these serial dilutions, and subsequent incubation to enable establishment of similar cell abundances between treatments. The structure, cell abundance and activity of denitrifying and nitrite-oxidizing communities were characterized after incubation. Increasing dilution led to a progressive decrease in community diversity as assessed by the number of denaturating gradient gel electrophoresis (DGGE) bands, while community functioning was not impaired when cell abundance recovered after incubation. The microcosms were then subjected to a model disturbance: heating to 42 degrees C for 24 h. Abundance, structure and activity of each community were measured 3 h after completion of the disturbance to assess resistance, and after incubation of microcosms for 1 month to assess resilience. Resistance and resilience to the disturbance differed between the two communities, nitrite oxidizers being more affected. However, reducing the diversity of the two microbial functional groups did not impair either their resistance or their resilience following the disturbance. These results demonstrate the low sensitivity of the resistance and resilience of both microbial groups to diversity decline provided that cell abundance is similar between treatments.     

Time for a change: dynamic urban ecology

Contemporary cities are expanding rapidly in a spatially complex, non-linear manner. However, this form of expansion is rarely taken into account in the way that urbanization is classically assessed in ecological studies. An explicit consideration of the temporal dynamics, although frequently missing, is crucial in order to understand the effects of urbanization on biodiversity and ecosystem functioning in rapidly urbanizing landscapes. In particular, a temporal perspective highlights the importance of land-use legacies and transient dynamics in the response of biodiversity to environmental change. Here, we outline the essential elements of an emerging framework for urban ecology that incorporates the characteristics of contemporary urbanization and thus empowers ecologists to understand and intervene in the planning and management of cities.     

The influence of biotic interactions on soil biodiversity

Belowground communities usually support a much greater diversity of organisms than do corresponding aboveground ones, and while the factors that regulate their diversity are far less well understood, a growing number of recent studies have presented data relevant to understanding how these factors operate. This review considers how biotic factors influence community diversity within major groups of soil organisms across a broad spectrum of spatial scales, and addresses the mechanisms involved. At the most local scale, soil biodiversity may potentially be affected by interactions within trophic levels or by direct trophic interactions. Within the soil, larger bodied invertebrates can also influence diversity of smaller sized organisms by promoting dispersal and through modification of the soil habitat. At larger scales, individual plant species effects, vegetation composition, plant species diversity, mixing of plant litter types, and aboveground trophic interactions, all impact on soil biodiversity. Further, at the landscape scale, soil diversity also responds to vegetation change and succession. This review also considers how a conceptual understanding of the biotic drivers of soil biodiversity may assist our knowledge of key topics in community and ecosystem ecology, such as aboveground–belowground interactions, and the relationship between biodiversity and ecosystem functioning. It is concluded that an improved understanding of what drives the diversity of life in the soil, incorporated within appropriate conceptual frameworks, should significantly aid our understanding of the structure and functioning of terrestrial communities.