The interaction of soil biota and soil structure under global change

The structural framework of soil mediates all soil processes, at all relevant scales. The spatio-temporal heterogeneity prevalent in most soils underpins the majority of biological diversity in soil, providing refuge sites for prey against predator, flow paths for biota to move, or be moved, and localized pools of substrate for biota to multiply. Just as importantly, soil biota play a crucial role in mediating soil structure: bacteria and fungi aggregate and stabilize structure at small scales (μm–cm) and earthworms and termites stabilize and create larger-scale structures (mm–m). The stability of this two-way interaction of structure and biota relations is crucial to the sustainability of the ecosystem. Soil is constantly reacting to changes in microclimates, and many of the soil–plant–microbe processes rely on the functioning of subtle chemical and physical gradients. The effect of global change on soil structure–biota interactions may be significant, through alterations in precipitation, temperature events, or land-use. Nonetheless, because of the complexity and the ubiquitous heterogeneity of these interactions, it is difficult to extrapolate from general qualitative predictions of the effects of perturbations to specific reactions. This paper reviews some of the main soil structure–biota interactions, particularly focusing on soil stability, and the role of biota mediating soil structures. The effect of alterations in climate and land-use on these interactions is investigated. Several case studies of the effect of land-use change are presented.     

Phage-host interactions in soil

Abstract Phages are abundant and ubiquitous in nature, and are therefore important components of microbial communities. They can impact on host populations in several ways, including predation and alteration of host phenotype by genetic interactions. The dynamic survival of phage populations in soil requires infective interactions with host populations which must be undergoing growth. Hence survival is limited by the activity of soil bacteria, and phage populations must adopt strategies to overcome periods of inactivity. One of the most effective strategies is the lysogenic cycle of temperate phages. It is argued here that lysogeny in soil has a distinct advantage over virulence for phage and host survival, as opposed to aquatic ecosystems where virulence seems a more successful strategy for phage populations.     

Structure and evolution of Streptomyces interaction networks in soil and in silico

Soil grains harbor an astonishing diversity of Streptomyces strains producing diverse secondary metabolites. However, it is not understood how this genotypic and chemical diversity is ecologically maintained. While secondary metabolites are known to mediate signaling and warfare among strains, no systematic measurement of the resulting interaction networks has been available. We developed a high-throughput platform to measure all pairwise interactions among 64 Streptomyces strains isolated from several individual grains of soil. We acquired more than 10,000 time-lapse movies of colony development of each isolate on media containing compounds produced by each of the other isolates. We observed a rich set of such sender-receiver interactions, including inhibition and promotion of growth and aerial mycelium formation. The probability that two random isolates interact is balanced; it is neither close to zero nor one. The interactions are not random: the distribution of the number of interactions per sender is bimodal and there is enrichment for reciprocity--if strain A inhibits or promotes B, it is likely that B also inhibits or promotes A. Such reciprocity is further enriched in strains derived from the same soil grain, suggesting that it may be a property of coexisting communities. Interactions appear to evolve rapidly: isolates with identical 16S rRNA sequences can have very different interaction patterns. A simple eco-evolutionary model of bacteria interacting through antibiotic production shows how fast evolution of production and resistance can lead to the observed statistical properties of the network. In the model, communities are evolutionarily unstable--they are constantly being invaded by strains with new sets of interactions. This combination of experimental and theoretical observations suggests that diverse Streptomyces communities do not represent a stable ecological state but an intrinsically dynamic eco-evolutionary phenomenon.     

Climate change and multitrophic interactions in soil: the primacy of plants and functional domains

Soil multitrophic interactions transfer energy from plants as the predominant primary producer to communities of organisms that occupy different positions in the food chain and are linked by multiple ecological networks, which is the soil food web. Soil food web sequesters carbon, cycles nutrients, maintains soil health to suppress pathogens, helps plants tolerate abiotic and biotic stress, and maintains ecosystem resilience and sustainability. Understanding the influence of climate change on soil multitrophic interactions is necessary to maintain these essential ecosystem services. But summarising this influence is a daunting task due to a paucity of knowledge and a lack of clarity on the ecological networks that constitute these interactions. The scant literature is fragmented along disciplinary lines, often reporting inconsistent findings that are context and scale‐dependent. We argue for the differentiation of soil multitrophic interactions along functional and spatial domains to capture cross‐disciplinary knowledge and mechanistically link all ecological networks to reproduce full functionalities of the soil food web. Distinct from litter mediated interactions in detritosphere or elsewhere in the soil, the proposed ‘pathogen suppression’ and ‘stress tolerance’ interactions operate in the rhizosphere. A review of the literature suggests that climate change will influence the relative importance, frequency and composition of functional groups, their trophic interactions and processes controlling these interactions. Specific climate change factors generally have a beneficial influence on pathogen suppression and stress tolerance, but findings on the overall soil food web are inconsistent due to a high level of uncertainty. In addition to an overall improvement in the understanding of soil multitrophic interactions using empirical and modelling approaches, we recommend linking biodiversity to function, understanding influence of combinations of climatic factors on multitrophic interactions and the evolutionary ecology of multitrophic interactions in a changing climate as areas that deserve most attention.     

Interactions between soil and tree roots accelerate long-term soil carbon decomposition

Decomposition of soil organic carbon (SOC) is the main process governing the release of CO₂ into the atmosphere from terrestrial systems. Although the importance of soil–root interactions for SOC decomposition has increasingly been recognized, their long-term effect on SOC decomposition remains poorly understood. Here we provide experimental evidence for a rhizosphere priming effect, in which interactions between soil and tree roots substantially accelerate SOC decomposition. In a 395-day greenhouse study with Ponderosa pine and Fremont cottonwood trees grown in three different soils, SOC decomposition in the planted treatments was significantly greater (up to 225%) than in soil incubations alone. This rhizosphere priming effect persisted throughout the experiment, until well after initial soil disturbance, and increased with a greater amount of root-derived SOC formed during the experiment. Loss of old SOC was greater than the formation of new C, suggesting that increased C inputs from roots could result in net soil C loss.     

Single introductions of soil biota and plants generate long‐term legacies in soil and plant community assembly

Recent demonstrations of the role of plant–soil biota interactions have challenged the conventional view that vegetation changes are mainly driven by changing abiotic conditions. However, while this concept has been validated under natural conditions, our understanding of the long‐term consequences of plant–soil interactions for above‐belowground community assembly is restricted to mathematical and conceptual model projections. Here, we demonstrate experimentally that one‐time additions of soil biota and plant seeds alter soil‐borne nematode and plant community composition in semi‐natural grassland for 20 years. Over time, aboveground and belowground community composition became increasingly correlated, suggesting an increasing connectedness of soil biota and plants. We conclude that the initial composition of not only plant communities, but also soil communities has a long‐lasting impact on the trajectory of community assembly.     

Biological interactions in soil

Book Review

Biological interactions in soilC.A. Edwards, B.R. Stinner, D. Stinner and S. Rabatin (Eds.), Amsterdam: Elsevier, 1988. vi+380 pages. US$144.75/Dfl. 275.00. ISBN 0-44-87154-3     

Effects of changes in soil moisture and precipitation patterns on plant-mediated biotic interactions in terrestrial ecosystems

Due to climate change, the amount, frequency, and intensity of precipitation worldwide are changing. There is increasing evidence that hydrological change severely affects species interactions and that these effects might overrule direct autecological responses, although this is currently understudied. Here, I synthesize published data on 405 interactions to show how changes in soil moisture affect the frequency or strength of plant-mediated biotic interactions. Despite substantial variation among published responses, general patterns have emerged. A recurrent finding in the synthesized studies is that dryness impedes beneficial interactions between plants and other organisms (decreased mycorrhization and infection with other symbiotic endophytes, less pollinator visits, less active decomposers) and increases detrimental interactions (increased performance of sucking insects, pathogen infection and competition between functionally similar plants). For increased wetness, which is far less studied, stress intensity seems to matter: Slightly increased precipitation often benefits plants and thereby associated interaction partners (increased mycorrhization and infection with symbiotic endophytes, increased herbivore performance), while extreme waterlogging or flooding impedes many interactions (decreased decomposer activity and mycorrhization). Legacy effects of changed soil moisture on plant community composition can amplify or reverse short-term effects on interactions. Although some concepts acknowledge the role of stress intensity (mild versus severe) and stress type (permanent versus pulsed) empirical research testing-related hypotheses is largely lacking, as is research on the role of soil moisture legacies for interactions.     

Causes and consequences of biological diversity in soil

There is a vast diversity of organisms that live in the soil, and the activities of the total soil biota, together with the diverse forms and functions of plant roots, have critical roles in soil functioning. In this paper I discuss the likely determinants of soil diversity and also comment on recent studies that have explored whether or not there is a relationship between soil organism diversity and ecosystem function. There is little evidence to suggest that soil diversity is regulated in a predicable fashion by competition or disturbance; rather it is attributed to the nature of the soil environment, in that soil offers an extremely heterogeneous habitat, both spatially and temporally, proving unrivalled potential for niche partitioning, or resource or habitat specialisation, thereby enabling co-existence of species. Most evidence that is available suggests that there is no predictable relationship between diversity and function in soils, and that ecosystem properties are governed more by individual traits of dominant species, and by the extraordinary complexity of biotic interactions that occur between components of soil food webs. There is evidence of redundancy in soil communities with respect to soil functions, but the scale of effect of changes in soil diversity on process rates depends on which species are removed from the community and the degree to which remaining species can compensate. As in aboveground communities, therefore, it would appear that species traits and changes in species composition, and alterations in the nature of the many important species interactions that occur in soil, are likely to be the main biotic control of ecosystem function. In view of this, consideration of these important biotic interactions and their sensitivity to environmental change must be a key priority for future research.     

Interactions between arbuscular mycorrhizal fungi and soil bacteria

The soil environment is interesting and complicated. There are so many interactions taking place in the soil, which determine the properties of soil as a medium for the growth and activities of plants and soil microorganisms. The soil fungi, arbuscular mycorrhiza (AM), are in mutual and beneficial symbiosis with most of the terrestrial plants. AM fungi are continuously interactive with a wide range of soil microorganisms including nonbacterial soil microorganisms, plant growth promoting rhizobacteria, mycorrhiza helper bacteria and deleterious bacteria. Their interactions can have important implications in agriculture. There are some interesting interactions between the AM fungi and soil bacteria including the binding of soil bacteria to the fungal spore, the injection of molecules by bacteria into the fungal spore, the production of volatiles by bacteria and the degradation of fungal cellular wall. Such mechanisms can affect the expression of genes in AM fungi and hence their performance and ecosystem productivity. Hence, consideration of such interactive behavior is of significance. In this review, some of the most important findings regarding the interactions between AM fungi and soil bacteria with some new insights for future research are presented.     

Variation in plant–soil interactions among temperate forest herbs

Plant Ecology - Antagonistic interactions between plants and soil biota promote species diversity in many plant communities but little is known about how these plant–soil interactions...     

Mycorrhizosphere interactions to improve plant fitness and soil quality

Arbuscular mycorrhizal fungi are key components of soil microbiota and obviously interact with other microorganisms in the rhizosphere, i.e. the zone of influence of plant roots on microbial populations and other soil constituents. Mycorrhiza formation changes several aspects of plant physiology and some nutritional and physical properties of the rhizospheric soil. These effects modify the colonization patterns of the root or mycorrhizas (mycorrhizosphere) by soil microorganisms. The rhizosphere of mycorrhizal plants, in practice a mycorrhizosphere, harbors a great array of microbial activities responsible for several key ecosystem processes. This paper summarizes the main conceptual principles and accepted statements on the microbial interactions between mycorrhizal fungi and other members of rhizosphere microbiota and discusses current developments and future trends concerning the following topics: (i) effect of soil microorganisms on mycorrhiza formation; (ii) mycorrhizosphere establishment; (iii) interactions involved in nutrient cycling and plant growth; (iv) interactions involved in the biological control of plant pathogens; and (v) interactions to improve soil quality. The main conclusion is that microbial interactions in the rhizosphere of mycorrhizal plants improve plant fitness and soil quality, critical issues for a sustainable agricultural development and ecosystem functioning. This revised version was published online in August 2006 with corrections to the Cover Date.     

Belowground volatiles facilitate interactions between plant roots and soil organisms

Many interactions between organisms are based on the emission and perception of volatiles. The principle of using volatile metabolites as communication signals for chemo-attractant or repellent for species-specific interactions or mediators for cell-to-cell recognition does not stop at an apparently unsuitable or inappropriate environment. These infochemicals do not only diffuse through the atmosphere to process their actions aboveground, but belowground volatile interactions are similarly complex. This review summarizes various eucaryotes (e.g., plant (roots), invertebrates, fungi) and procaryotes (e.g., rhizobacteria) which are involved in these volatile-mediated interactions. The soil volatiles cannot be neglected anymore, but have to be considered in the future as valuable infochemicals to understand the entire integrity of the ecosystems.     

Interactions between mycorrhizal fungi and other soil organisms

Mycorrhizal fungi interact with a wide range of other soil organisms, in the root, in the rhizosphere and in the bulk soil. These interactions may be inhibitory or stimulatory; some are clearly competitive, others may be mutualistic. Effects can be seen at all stages of the mycorrhizal fungal life-cycle, from spore population dynamics (predation, dispersal and germination) through root colonization to external hyphal growth. Two areas that seem likely to be of particular importance to the functioning of the symbiosis are the role of bacteria in promoting mycorrhiza formation and of soil animals in grazing the external mycelium. Mycorrhizal fungi also modify the interactions of plants with other soil organisms, both pathogens, such as root-inhabiting nematodes and fungi, and mutualists, notably nitrogen-fixing bacteria. These interactions are probably important both in natural ecosystems, where pathogens are increasingly recognized as playing controlling roles, and in agricultural systems, where mycorrhizas may be valuable in designing integrated systems of pest control and growth stimulation.     

Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.Subject terms: Soil microbiology, Ecology     

The effect of arbuscular mycorrhizal fungi Rhizophagus intraradices and soil microbial community on a model plant community in a post-mining soil

Plant Ecology - The aim of this study was to assess the effect of arbuscular mycorrhizal fungi Rhizophagus intraradices and soil microbial groups and their interactions on a simple plant community...     

Microbe-mediated plant–soil feedback and its roles in a changing world

Plants affect soil conditions, which in turn alter plant growth and interspecific competition, forming plant?Csoil feedback (PSF) systems. PSF is a good example of bidirectional interactions between biomes and the non-living environments, acting as a major driving force of community structure and ecosystem function. Among the major types of PSF mediated by various soil components, there are many holes in our knowledge of the interactions between PSF mediated by plant species-specific litter and PSF mediated by soil microbes. Here I discuss the role of the functional diversity of microbial decomposers in litter-mediated PSF and also propose new hypotheses on the role of microbial diversity in PSF mediated by pathogenic and mutualistic soil microbes. I also review how PSF interacts with human-induced environmental change, i.e., direct drivers of change in the ecosystem (e.g. climate change and the invasion of alien species). Many authors have suggested that the impact of alien plant species on ecosystems is mediated by PSF, which also interacts with other direct drivers, such as climate change. Using a simple model of litter-mediated PSF with microbial decomposers, I confirm that the interactions between PSF and other direct drivers affect the invasion process of alien species. The model also demonstrates that the functional diversity of microbial decomposers accelerates or decelerates the speed of the invasion depending on the environmental change scenarios. Further theoretical and empirical studies are needed to derive general predictions on how exogenous environmental change induced by human activities alters communities and ecosystems through disturbance or modification of endogenous community?Cecosystem interactions, such as the functioning of PSF.     

Negative plant–soil feedback and species coexistence

Different mechanisms, including equilibrium and non-equilibrium processes, have been taken into account as possible theoretical explanations of species coexistence. Despite the ample evidence on the existence of negative plant–soil feedback in both agriculture and natural vegetation, the role of these processes in the organization and dynamics of plant communities has so far been neglected. In this study, simulations by an individual-based competition model show how the intensity of negative feedback on individual plant performance can produce faster successional dynamics and allow species coexistence in two- and multi-species systems. The results show that even low levels of negative plant–soil feedback can enable species coexistence and often produce cyclic population dynamics. Moreover, the model highlights how negative feedback can generate positive reciprocal interspecific interactions at the population level, despite the fact that only competitive interactions is present between individual plants. In fact, competitive effects occur on a short-term scale, but positive reciprocal species interactions emerge only if negative feedback affects all species and if longer periods of simulation, more than the species life span, are considered. An important outcome of the model is the evidence that the effects at population level are timescale-dependent, thus showing the limitation of short-term species removal experiments used in traditional competition studies.     

Seed in soil,with an epigenetic view

It is becoming increasingly evident that discrete genetic alterations in neoplastic cells alone cannot explain multistep carcinogenesis whereby tumor cells are able to express diverse phenotypes during the complex phases of tumor development and progression. The epigenetic model posits that the host microenvironment exerts an initial, inhibitory constraint on tumor growth that is followed by acceleration of tumor progression through complex cell–matrix interactions. This review emphasizes the epigenetic aspects of breast cancer development in light of such interactions between epithelial cells (“seed”) and the tumor microenvironment (“soil”). Our recent research findings suggest that epigenetic perturbations induced by the tumor microenvironment may play a causal role in promoting breast cancer development. It is believed that abrogation of these initiators could offer a promising therapeutic strategy.     

Hyphal interactions among some soil fungi

Summary Hyphal interactions amongRhizopus oryzae, a dominant soil inhabiting fungus and soil fungi with potential antagonistic characters, were studiedin vitro. Results depict that diameter of the hyphae of interacting fungi plays an important role in hyperparasitic interactions. None of the hyphae with wide diam. could penetrate inside and coil around the hyphae ofR. oryzae, while most of the hyphae with narrow diam. did so.