From peds to paradoxes: Linkages between soil biota and their influences on ecological processes

Soils and their biota have been studied by a variety of observational and experimental methods that have allowed biologists to infer their structural and functional interactions. Viewing progress made over the last 10 years, it is apparent that an increasing diversity of analytical and chemical methods are providing much more detailed information about feeding preferences and niche overlaps of speciose groups such as oribatid mites.Other topics in which considerable progress has been made include new advances in knowledge of root and mycorrhiza production and turnover and their impacts on soil ecosystems; soil biota, exudations and secretions and soil aggregation phenomena; the biology of invasive species in soils; soil biodiversity, legacies and linkages to soil processes; and soil biodiversity and ecosystem functional responses. Throughout the review I suggest ways for new progress to be made in future research.     

Positive relationship between herbaceous layer diversity and the performance of soil biota in a temperate forest

The current decline in biodiversity is particularly pronounced in the herbaceous layer of forest ecosystems. We explored the relationship between a naturally occurring plant diversity gradient in the understory vegetation of a deciduous forest and several above-and belowground ecosystem processes. We show that particularly soil microbial parameters and microarthropod densities are positively correlated with plant species richness. These results confirm recent findings in grassland ecosystems and highlight the intimate interconnectance between the diversity and functioning of above-and belowground compartments. We conclude that irrespective of a potential causal relationship between plant species richness and belowground processes, it is essential to consider the performance of soil biota in order to understand the relationship between herbaceous layer composition and ecosystem function.     

The role of soil fauna in ecosystems: A historical review

The research development in this review is divided into successive periods: (1) “From Darwin to Satchell”, covering the “pre-experimental” decades dealing with the functions of earthworms, (2) “Litterbag Studies”, characterized by field experiments on the faunal influence on litter decomposition, (3) “The Time of IBP”, concentrating on community energetics, (4) “The Microcosm Era”, laboratory studies that started with simple systems, followed by increasing complexity of experimental setup and community of organisms, including living plants, and ending to laboratory-scale “ecosystems”, (5) the recent “Biodiversity Boom”, analysing the relations between soil biodiversity and ecosystem functions, and (6) the current “Holistic View” that tends to link the diversity and functions of aboveground and belowground communities. These “periods” started roughly in this order, but are largely overlapping, since the early techniques are in continuing use together with the modern ones. The current knowledge on the role of soil biota, their diversity and various components has accumulated mainly during the last 30 years, resulting in the modern view of soil fauna as a part of the ecosystem.     

Functional aspects of soil animal diversity in agricultural grasslands

There has been recent interest in the characterization of soil biodiversity and its function in agricultural grasslands. Much of the interest has come from the need to develop grassland management strategies directed at manipulating the soil biota to encourage a greater reliance on ecosystem self-regulation. This review summarises information on selected groups of soil animals in grasslands, the factors influencing their abundance, diversity and community structure and their relationships to the functioning and stability of grassland ecosystems. Observations on the impacts of agricultural managements on populations and communities of soil fauna and their interactions confirm that high input, intensively managed systems tend to promote low diversity while lower input systems conserve diversity. It is also evident that high input systems favour bacterial-pathways of decomposition, dominated by labile substrates and opportunistic, bacterial-feeding fauna. In contrast, low-input systems favour fungal-pathways with a more heterogeneous habitat and resource leading to domination by more persistent fungal-feeding fauna. In view of this, we suggest that low input grassland farming systems are optimal for increasing soil biotic diversity and hence self-regulation of ecosystem function. Research is needed to test the hypothesis that soil biodiversity is positively associated with stability, and to elucidate relationships between productivity, community integrity and functioning of soil biotic communities.     

植物多样性对土壤动物影响的研究进展

生物多样性与生态系统功能一直是生态学研究的一个热点。近些年来的研究表明,植物多样性除了影响陆地生态系统地上部分的初级生产力等生态系统功能,还会间接影响地下生物多样性及土壤生态系统过程。本文概述了植物多样性对土壤动物的影响及其主要机制,归纳了植物多样性通过改变输入土壤中的资源数量与资源多样性、微生境结构、土壤环境因子等影响土壤动物的途径。目前关于土壤动物群落对植物多样性的响应仍存在很多问题和争议,本文总结了需要进一步深入研究的方向,特别指出了要加强研究影响植物多样性与土壤动物关系的生物与非生物因子、后续的生态效应和反馈、不同机制和途径的贡献定量化等。     

Long-term management effects on organic C and N pools and activities of C-transforming enzymes in prairie soils

Changes in soil microbial and biochemical properties in response to management practices reflect changes in the functional capacity of soil ecosystems. The objectives were to evaluate effects of long-term management practices on different soil organic C and N pools and activities of glycoside hydrolases, including α- and β-glucosidases, α- and β-galactosidases, cellulase, and invertase, in semiarid prairie soils. Soils were sampled from five long-term management systems including: undisturbed, abandoned from cultivation, moderately grazed, heavily grazed, and cultivated with winter wheat (Triticum aestivum L.). Activities of C-transforming enzymes were sensitive in discriminating soil ecosystems under various land uses and can be used as indicators for detecting impact of soil management practices on the soil capacity to cycle C. Long-term cultivation (more than 30 yr) decreased total organic C and N, microbial biomass, and activities of C-transforming enzymes, and led to development of a microbial community with enhanced metabolic activity. Grazing, especially at moderate intensity, did not lessen soil capacity to support microbial life and cycle C. The intermediate status of the chemical, microbial, and biochemical properties in the abandoned from cultivation soils suggested that through secondary succession the soil ecosystem is restoring its capacity to sequester C and support microbial life.     

Terrestrial ecosystem processes of Victoria Land, Antarctica

Terrestrial environments of Victoria Land, Antarctica are ideal systems to test hypotheses about the sensitivity of ecosystem processes to climate variability, and the relationships between soil biodiversity and ecosystem functioning because of their high sensitivity to climate change and their limited diversity. This region is also considered among the most pristine of ecosystems, and therefore may serve as an indicator for detecting the response of other ecosystems to global environmental change. Rates and controls over key ecosystem processes remain poorly documented over much of Victoria Land, but it is generally held that the distribution and functioning of soil communities are most limited by the availability of liquid water and organic carbon. Here we review examples of ecosystem processes from several sites in North and South Victoria Land and develop a regional synthesis accounting for variation in the availability of soil resources (i.e. liquid water, organic matter, inorganic nutrients). Variation in soil microclimate, organic matter, moisture and salinity encountered over gradients of coastal to interior sites, latitude, and soil chronosequences are the primary controls over the structure of soil communities and their functioning. Imbalanced stoichiometric nutrient ratios frequently encountered in Victoria Land ecosystems also contribute to limited distribution of soil biota, and where they occur these elemental imbalances indicate lower biological activity and little biotic control over bulk element ratios in soils. Priorities and future directions of Victoria Land soil and ecosystem research are also discussed.     

Biological crusts as a model system for examining the biodiversity-ecosystem function relationship in soils

Despite that soils may be the greatest repository of biodiversity on Earth, and that most terrestrial ecosystem functions occur in the soil, research on the role of soil biodiversity in ecosystem function has lagged behind corresponding research on aboveground organisms. Soil organisms pose special problems to biodiversity-function research, including the fact that we usually do not know their identity nor what they do in soil ecosystems, cannot easily estimate their biodiversity, and cannot culture the majority of the organisms for use in manipulative experiments. We propose here that biological soil crusts (BSCs) of deserts and many other ecosystems may serve as a useful model system for diversity-function research because the species concept is relatively well-defined within BSC organisms, their functional attributes are relatively well-known, and estimation and manipulation of biodiversity in experiments are feasible, at least within some groups of BSC biota. In spite of these features, there is a pronounced lack of research on biodiversity-function using these organisms. At least two complementary approaches are possible: experiments using artificially-constructed BSCs, and observational studies which statistically control for the effects of other factors which are likely to covary with biodiversity. We applied the latter to four observational datasets collected at multiple spatial scales in Spain and the United States using structural equation models or path analysis using ecosystem function indicators relating to hydrology, trapping and retention of soil resources, and nutrient cycling. We found that, even when total BSC abundance and key environmental gradients are controlled for, direct and approximately linear relationships between species richness and/or evenness and indicators of ecosystem functioning were common. Such relationships appear to vary independently of region or spatial scale, but their strength seems to differ in every dataset. Functional group richness did not seem to adequately capture biodiversity-function relationships, suggesting that bryophyte and lichen components of BSC may exhibit low redundancy. More research employing the multi-trophic, multi-functional, and manipulable BSC system may enable more rapid understanding of the consequences of biodiversity loss in soils, and help enable a biodiversity-function theory that is pertinent to the numerous ecosystem services provided by soil organisms.     

Soil fertility and bacterial community composition in a semiarid Mediterranean agricultural soil under long-term tillage management

This research attempted to investigate a part of the United Nations sustainable development goal 15, dealing with preventing land degradation and halting the loss of microorganisms’ diversity. Since soil deterioration and biodiversity loss in the Mediterranean area are occurring because of intensive management, we evaluated some biochemical and microbiological parameters and bacterial biodiversity under long-term conventional tillage (CT) and no-tillage (NT) practices, in Basilicata, a typical Region of Southern Italy, characterized by a semiarid ecosystem. The highest biological fertility index (BFI) (composed of soil organic matter, microbial biomass C, cumulative microbial respiration during 25 days of incubation, basal respiration, metabolic quotient and mineralization quotient) was determined for the 0–20 cm of NT soil (class V, high biological fertility level). The analysis of the taxonomic composition at the phylum level revealed the higher relative abundance of copiotrophic bacteria such as Proteobacteria, Actinobacteria and Bacteroidetes in the NT soil samples as compared to the CT soil. These copiotrophic phyla, more important decomposers of soil organic matter (SOM) than oligotrophic phyla, are responsible of a higher microbial C use efficiency (CUE) in tilled soil, being microbial community composition, C substrates content and CUE closely linked. The higher Chao1 and Shannon indices, under the NT management, also supported the hypothesis that the bacterial diversity and richness increased in the no-till soils. In conclusion, we can assume that the long-term no-tillage can preserve an agricultural soil in a semiarid ecosystem, enhancing soil biological fertility level and bacterial diversity.     

Crop rotation complexity regulates the decomposition of high and low quality residues

While many ecosystem processes depend on biodiversity, the relationships between agricultural plant diversity and soil carbon (C) and nitrogen (N) dynamics remains controversial. Our objective was to examine how temporal plant diversity (i.e. crop rotation) influences residue decomposition, a key ecosystem function that regulates nutrient cycling, greenhouse gas emissions, and soil organic matter formation. We incubated soils from five long-term crop rotations, located at W.K. Kellogg Biological Station LTER in southwestern Michigan, USA, with and without four chemically diverse crop residues. Increasing crop biodiversity increased soil potentially mineralizable C by 125%, increased hydrolytic enzyme activity by 46%, but decreased oxidative enzyme activity by 20% in soils before residue was added. After residue additions, soils from more diverse cropping systems decomposed all residues more rapidly (0.2–8.3% greater mass loss) compared to monoculture corn. The fast-cycling, ‘Active C’ pool and microbial biomass N increased with higher cropping diversity, but the differences among rotations in Active C pools was higher for the most recalcitrant residues. Further, the ratio of the cellulose degrading enzyme (β-glucosidase) to the lignin degrading enzyme (phenol oxidase) was highest in the two most diverse crop rotations regardless of residue additions, providing additional evidence of enhanced microbial activity and substrate acquisition in more diverse rotations. Our study shows that crop diversity over time influences the processing of newly-added residues, microbial dynamics, and nutrient cycling. Diversifying crop rotations has the potential to enhance soil ecosystem functions and is critical to maintaining soil services in agricultural systems.     

Soil biodiversity and DNA barcodes: opportunities and challenges

Soils encompass a huge diversity of organisms which mostly remains to be characterized due to a number of methodological and logistical issues. Nonetheless, remarkable progress has been made in recent years toward developing strategies to characterize and describe soil biodiversity, especially thanks to the development of molecular approaches relying on direct DNA extraction from the soil matrix.Metabarcoding can be applied to DNA from any environment or organism, and is gaining increasing prominence in biodiversity studies. This approach is already commonly used to characterize soil microbial communities and its application is now being extended to other soil organisms, i.e. meso- and macro-fauna.These developments offer unprecedented scientific and operational opportunities in order to better understand soil biodiversity distribution and dynamics, and to propose tools and strategies for biodiversity diagnosis. However, these opportunities also come with challenges that the scientific community must face. Such challenges are related to i) clarification of terminology, (ii) standardisation of methods and further methodological development for additional taxonomic groups, (iii) development of a common database, and (iv) ways to avoid waste of information and data derived from metabarcoding. In order to facilitate common application of metabarcoding in soil biodiversity assessment, we discuss these opportunities and challenges and propose solutions towards a more homogeneous framework.     

基于土壤生物空间异质性分析的空间土壤生态学研究

土壤生物以不同的方式改变着土壤的物理、化学和生物学特性。了解土壤生物的空间异质性是很关键的。土壤生态学和空间生态学结合的新的研究领域─空间土壤生态学关注空间在土壤生物种群结构及动态中的重要性。本文通过对土壤生物空间异质性的分析,内容包括空间土壤生态学的提出、土壤生物空间异质性研究的意义、研究方法,重点综述了影响土壤生物分布格局的因素、尺度,土壤生物空间分布对植被-土壤系统的影响,土壤生物空间异质性的作用,其中包括土壤生物空间异质性与多样性的关系、土壤生物对局部干扰的响应、土壤生物空间格局对植被的影响。     

稻鸭共作对稻田水体底栖动物生物多样性的影响

在水稻不同生育时期对稻鸭共作稻田和常规稻田的土壤取样,研究不同稻田生态系统水体底栖动物的生物多样性。结果表明：与常规稻田相比,稻鸭共作使水体底栖动物的种类数减少。水稻生育前期,稻鸭共作使底栖动物的个体总数减少较大,后期与常规稻田差异较小。水稻各生育时期常规稻田和稻鸭共作稻田底栖动物的Shannon-Wiener多样性指数、Simpson多样性指数和Pielou均匀度指数变化趋势相似,均为水稻生育前期稻鸭共作稻田的生物多样性指数和均匀度指数高于常规稻田,而后期低于常规稻田。研究结果为规范稻鸭共作稻田水分管理和稻鸭共作技术提供理论指导,促进稻鸭共作技术的推广和应用。     

Interactive effects of warming, soil humidity and plant diversity on litter decomposition and microbial activity

Human activity has induced a multitude of global changes that are likely to affect the functioning of ecosystems. Although these changes act in concert, studies on interactive effects are scarce. Here, we conducted a laboratory microcosm experiment to explore the impacts of temperature (9, 12 and 15 °C), changes in soil humidity (moist, dry) and plant diversity (1, 4, 16 species) on soil microbial activity and litter decomposition.We found that changes in litter decomposition did not mirror impacts on microbial measures indicating that the duration of the experiment (22 weeks) may not have been sufficient to determine the full magnitude of global change effects. However and notably, changes in temperature, humidity and plant litter diversity/composition affected in a non-additive way the microbial parameters investigated. For instance, microbial metabolic efficiency increased with plant diversity in the high moisture treatment but remained unaffected in low moisture treatment suggesting that climate changes may mask beneficial effects of biodiversity on ecosystem functioning. Moreover, litter decomposition was unaffected by plant litter diversity/composition but increased with increasing temperature in the high moisture treatment, and decreased with increasing temperature in the low moisture treatment.We conclude that it is inevitable to perform complex experiments considering multiple global change agents in order to realistically predict future changes in ecosystem functioning. Non-additive interactions highlight the context-dependency of impacts of single global change agents.     

土壤微生物多样性实验研究方法概述

对有关土壤微生物多样性,包括微生物类群多样性、群落结构多样性、功能多样性以及基因多样性等的描述与表征方法进行了探讨,同时,对当前国内外土壤微生物多样性的一些实验研究方法,包括土壤微生物分离培养方法、Biolog 微平板方法、FAME 分析方法和分子生物学方法等进行了介绍和评述。并指出在土壤微生物多样性研究中,如果可能的话,需要将各种方法结合起来使用,方可得到有关土壤生物多样性的较为全面的信息和理解。     

Soil microbial communities resistant to changes in plant functional group composition

The soil community is an often ignored part of research which links plant biodiversity and ecosystem functioning despite their influence on numerous functions such as decomposition and nutrient cycling. Few consistent patterns have been detected that link plant and soil community composition. We used a removal experiment in a northern Canadian grassland to examine the effects of plant functional group identity on soil microbial community structure and function. Plant functional groups (graminoids, legumes and forbs) were removed independently from plots for five growing seasons (2003-2007) and in the fifth year effects on the soil microbial community were examined using substrate-induced respiration (SIR - a measure of metabolic diversity) and phospholipid fatty acid analysis (PLFA - a measure of microbial community composition). Removal treatments were also crossed with both a fertilizer treatment and a fungicide treatment to determine if effects of functional group identity on the soil community were context dependent. Plant functional group identity had almost no effect on the soil microbial community as measured by either SIR or PLFA. Likewise, soil properties including total carbon, pH, moisture and nutrients showed a limited response to plant removals in the fifth year after removals. We found a direct effect of fertilizer on the soil community, with fertilized plots having decreased metabolic diversity, with a decreased ability to metabolize amino acids and a phenolic acid, but there was no direct soil microbial response to fungicide. We show that in this northern Canadian grassland the soil microbial community is relatively insensitive to changes in plant functional group composition, and suggest that in northern ecosystems, where plant material is only slowly incorporated into the soil, five growing seasons may be insufficient to detect the impact of a changing plant community on the soil microbes.     

Bacterial Biodiversity in Soil with an Emphasis on Chemically-Contaminated Soils

Microorganisms isolated from soil are sources of known and new microorganisms and genetic material. This review examines general principles of soil bacterial biodiversity, limitations in sampling soils, and examples of bacterial diversity in chemically-contaminated soils. Both conventional and molecular methods used to assess microbial biodiversity in soils will be addressed as well as selected examples of the effects of organic and inorganic pollutants on soil microbial diversity.     

Relationships between microbial biomass and dissipation of 2,4-D and dicamba in soil

A study was conducted to evaluate relationships between microbial biomass and the dissipation of 2,4-D (2,4-dichlorophenoxy acetic acid) and dicamba (2-methoxy-3,6-dichlorobenzoic acid) in soil. We hypothesized that the size of the microbial biomass should be a strong predictor of the pesticide degradation capacity of a particular soil. Soils with a high microbial biomass should have relatively high levels of general microbial activity and should support a diversity of degradation pathways. In this study, we quantified the degradation of 2,4-D and dicamba in a range of soils with different concentrations of microbial biomass. The herbicides 2,4-D and dicamba were added to similar soils collected from five different land use types (home lawn, cornfield, upland hardwood forest, wetland forest, and aquifer material) and incubated for 80 days under laboratory conditions. Herbicide residue and microbial biomass (C and N) analyses were performed 5, 10, 20, 40, and 80 days following herbicide application. Microbial biomass-C and -N and soil organic matter content were positively correlated with dissipation of 2,4-D and dicamba. The results suggest that there are relationships between the size of the soil microbial biomass and the herbicide degradation capacity of an ecosystem. These relationships may be useful for developing approaches for evaluating and predicting the fate of pesticides in different ecosystems.     

Benefactor and allelopathic shrub species have different effects on the soil microbial community along an environmental severity gradient

Patches where shrubs have either positive or negative effects on their understory plant community are common in arid ecosystems. The intensity and balance of these effects change along environmental severity gradients but, despite the major role of soil microbes in plant interactions, little is known about the differences among soil microbial communities under these species and their possible influence on such contrasting shrub effects. We hypothesized that microbial communities associated to benefactor and allelopathic shrubs would differ among them and that differences would increase with environmental severity. To test these hypotheses we characterized soil microbial biomass, activity and community composition under a benefactor shrub species, Retama sphaerocarpa, an allelopathic shrub species, Thymus hyemalis, and in bare soil among plants (gaps) at three sites along an environmental severity gradient. Shrubs promoted an increase in soil bacterial diversity, being bacterial communities associated to benefactor shrubs, allelopathic shrubs and gaps different in composition. Microbial enzymatic activity and biomass increased under shrubs and under more mesic conditions; nonetheless, they were highest under benefactor shrubs at the most arid site and under allelopathic shrubs at the less severe site. Compared to gaps, the presence of shrubs induced changes in microbial activity and community composition that were larger at the most severe site than at the less severe site. Along the gradient, benefactor shrubs enhanced the abundance of bacterial groups involved in organic matter decomposition and N fixation as well as plant pathogens, which could contribute to Retama's outstanding positive effects on understory plant biomass and diversity. Plant patches mitigate the effects of extreme conditions on associated plant and soil microbial communities and promote soil biodiversity and ecosystem functioning in arid ecosystems, with shrubs actively selecting for specific microbial groups in their understory.     

Relationships between microbial biomass and dissipation of 2,4-D and dicamba in soil

A study was conducted to evaluate relationships between microbial biomass and the dissipation of 2,4-D (2,4-dichlorophenoxy acetic acid) and dicamba (2-methoxy-3,6-dichlorobenzoic acid) in soil. We hypothesized that the size of the microbial biomass should be a strong predictor of the pesticide degradation capacity of a particular soil. Soils with a high microbial biomass should have relatively high levels of general microbial activity and should support a diversity of degradation pathways. In this study, we quantified the degradation of 2,4-D and dicamba in a range of soils with different concentrations of microbial biomass. The herbicides 2,4-D and dicamba were added to similar soils collected from five different land use types (home lawn, cornfield, upland hardwood forest, wetland forest, and aquifer material) and incubated for 80 days under laboratory conditions. Herbicide residue and microbial biomass (C and N) analyses were performed 5, 10, 20, 40, and 80 days following herbicide application. Microbial biomass-C and -N and soil organic matter content were positively correlated with dissipation of 2,4-D and dicamba. The results suggest that there are relationships between the size of the soil microbial biomass and the herbicide degradation capacity of an ecosystem. These relationships may be useful for developing approaches for evaluating and predicting the fate of pesticides in different ecosystems.