Trophic interaction modifications: an empirical and theoretical framework

Cd indirectly affects the structure and function of plankton ecosystems by affecting trophic interactions at environmental concentrations

The toxic effects of potentially toxic elements have been observed at low concentrations; however, many studies have focused on single-species toxicity testing. Consequently, it is imperative to quantify toxicity at the community level at environmental concentrations. A microcosm approach was employed in conjunction with the Lotka-Volterra model to ascertain the impact of environmentally relevant concentrations of cadmium (Cd) on plankton abundance, community function, and stability. The results demonstrated that Cd led to a reduction in the abundance of Daphnia magna, yet unexpectedly resulted in an increase in the abundance of Brachionus calyciflorus and Paramecium caudatum. Additionally, Cd was observed to impede primary productivity, metabolic capacity and the stability of the planktonic community. Further model analyses revealed that the environmental concentration of Cd directly reduced intrinsic growth rates and intraspecific interactions. In particular, we found that the predation effects of Daphnia magna on Brachionus calyciflorus were significantly weakened. The findings of this study offer quantitative evidence that Cd exposure exerts an indirect influence on the structure and functioning of plankton ecosystems, mediated by alterations in trophic interactions. The findings indicate that the impact of environmental concentrations of potentially toxic elements may be underestimated in single-species experiments.

Dynamic Trait Distribution as a Source for Shifts in Interaction Strength and Population Density

AbstractIntraspecific trait variation has been increasingly recognized as an important factor in determining species interactions and diversity. Eco-evolutionary models have studied the distribution of trait values within a population that changes over the generations as a result of selection and heritability. Nonheritable traits that can change within the lifetime, such as behavior, can cause trait-mediated indirect effects, often studied by modeling the dynamics of a homogeneous trait. Complementary to these approaches, we study the distribution of traits within a population and its dynamics on short timescales due to ecological processes. We consider several mechanisms by which the trait distribution can shift dynamically: phenotypic plasticity within each individual, differential growth among individuals, and preferential consumption by the predator. Through a simple predator-prey model that explicitly tracks the trait distribution within the prey, we identify the density and trait effects from the predator. We show that the dynamic shift of the trait distribution can lead to the modification of interaction strength between species and result in otherwise unexpected consequences. A particular example is the emergent promotion of the prey by the predator, where the introduction of the predator causes the prey population to increase rather than decrease.

Food web context modifies predator foraging and weakens trophic interaction strength

Trophic interaction modifications (TIM) are widespread in natural systems and occur when a third species indirectly alters the strength of a trophic interaction. Past studies have focused on documenting the existence and magnitude of TIMs; however, the underlying processes and long-term consequences remain elusive. To address this gap, we experimentally quantified the density-dependent effect of a third species on a predator's functional response. We conducted short-term experiments with ciliate communities composed of a predator, prey and non-consumable 'modifier' species. In both communities, increasing modifier density weakened the trophic interaction strength, due to a negative effect on the predator's space clearance rate. Simulated long-term dynamics indicate quantitative differences between models that account for TIMs or include only pairwise interactions. Our study demonstrates that TIMs are important to understand and predict community dynamics and highlights the need to move beyond focal species pairs to understand the consequences of species interactions in communities.

Combination of direct boiling and glass beads increases the purity and accuracy of bacterial DNA extraction

Extraction of DNA is a key step in molecular biology experiments and important for counting tiny microbial individuals. Direct boiling and mechanical cell lysis like glass beads are two independent physical extraction methods, thus crossing the barriers of thresholds of magnitude in popular reagent kits or traditional spread plate method when non-equilibrium phenomenon is ongoing. The two approaches above were combined to generate a new one. In three typical microbial species, direct boiling with glass beads significantly increased the purity of DNA solution compared with some other methods (p < 0.05). The qPCR results of them were closer to direct microscopy counting than some other methods. Therefore, it provides a new choice in extracting bacterial DNA for specific circumstances.

Connecting higher-order interactions with ecological stability in experimental aquatic food webs

Community ecology is built on theories that represent the strength of interactions between species as pairwise links. Higher-order interactions (HOIs) occur when a species changes the pairwise interaction between a focal pair. Recent theoretical work has highlighted the stabilizing role of HOIs for large, simulated communities, yet it remains unclear how important higher-order effects are in real communities. Here, we used experimental communities of aquatic protists to examine the relationship between HOIs and stability (as measured by the persistence of a species in a community). We cultured a focal pair of consumers in the presence of additional competitors and a predator and collected time series data of their abundances. We then fitted competition models with and without HOIs to measure interaction strength between the focal pair across different community compositions. We used survival analysis to measure the persistence of individual species. We found evidence that additional species positively affected persistence of the focal species and that HOIs were present in most of our communities. However, persistence was only linked to HOIs for one of the focal species. Our results vindicate community ecology theory positing that species interactions may deviate from assumptions of pairwise interactions, opening avenues to consider possible consequences for coexistence and stability.

Surprising effects of cascading higher order interactions

Most species are embedded in multi-interaction networks. Consequently, theories focusing on simple pair-wise interactions cannot predict ecological and/or evolutionary outcomes. This study explores how cascading higher-order interactions (HOIs) would affect the population dynamics of a focal species. Employing a system that involves a myrmecophylic beetle, a parasitic wasp that attacks the beetle, an ant, and a parasitic fly that attacks the ant, the study explores how none, one, and two HOIs affect the parasitism and the sex ratio of the beetle. We conducted mesocosm experiments to examine these HOIs on beetle survival and sex ratio and found that the 1st degree HOI does not change the beetle's survival rate or sex ratio. However, the 2nd degree HOI significantly reduces the beetle's survival rate and changes its sex ratio from even to strongly female-biased. We applied Bayes' theorem to analyze the per capita survival probability of female vs. male beetles and suggested that the unexpected results might arise from complex eco-evolutionary dynamics involved with the 1st and 2nd degree HOIs. Field data suggested the HOIs significantly regulate the sex ratio of the beetle. As the same structure of HOIs appears in other systems, we believe the complexity associated with the 2nd degree HOI would be more common than known and deserve more scientific attention.

Beyond body size—new traits for new heights in trait-based modelling of predator-prey dynamics

Food webs map feeding interactions among species, providing a valuable tool for understanding and predicting community dynamics. Using species’ body sizes is a promising avenue for parameterizing food-web models, but such approaches have not yet been able to fully recover observed community dynamics. Such discrepancies suggest that traits other than body size also play important roles. For example, differences in species’ use of microhabitat or non-consumptive effects of intraguild predators may affect dynamics in ways not captured by body size. In Laubmeier et al. (2018), we developed a dynamic food-web model incorporating microhabitat and non-consumptive predator effects in addition to body size, and used simulations to suggest an optimal sampling design of a mesocosm experiment to test the model. Here, we perform the mesocosm experiment to generate empirical time-series of insect herbivore and predator abundance dynamics. We minimize least squares error between the model and time-series to determine parameter values of four alternative models, which differ in terms of including vs excluding microhabitat use and non-consumptive predator-predator effects. We use both statistical and expert-knowledge criteria to compare the models and find including both microhabitat use and non-consumptive predator-predator effects best explains observed aphid and predator population dynamics, followed by the model including microhabitat alone. This ranking suggests that microhabitat plays a larger role in driving population dynamics than non-consumptive predator-predator effects, although both are clearly important. Our results illustrate the importance of additional traits alongside body size in driving trophic interactions. They also point to the need to consider trophic interactions and population dynamics in a wider community context, where non-trophic impacts can dramatically modify the interplay between multiple predators and prey. Overall, we demonstrate the potential for utilizing traits beyond body size to improve trait-based models and the value of iterative cycling between theory, data and experiment to hone current insights into how traits affect food-web dynamics.

Associational Effects and Indirect Interactions-The Dynamical Effects of Consumer and Resource Traits on Generalist-Resource Interactions

Trophic interaction modifications occur in food webs when the direct or indirect interaction between two species is affected by a third species. These behavioral modification effects are often referred to as associational effects. Changes in focal resource availability and consumption by a generalist herbivore can affect a range of outcomes from resource exclusion to multiple resources coexisting with the focal plant species. Here, we investigate the indirect interaction between a focal and alternative resource mediated by a generalist consumer. Using theoretical approaches we analyse the conceptual link between associational effects (both resistance and susceptibility) and the theory of apparent competition and resource switching. We find that changes in focal resource traits have the potential to affect the long-term outcome of indirect interactions. Inclusion of density-dependence expands generalist life-histories and broadens the range where, through associational effects, the availability of alternative resources positively influence a focal resource. We conclude that different forms of associational effects could, in the long-term, lead to a range of indirect interaction dynamics, including apparent competition and apparent mutualism. Our work aims to connects the theoretical body of work on indirect interactions to the concepts of associational effects. The indirect interactions between multiple resources need more thorough investigation to appreciate the range of associational effects that could result from the dynamical interaction between a generalist consumers and its focal and alternative resources.

Predator interference and complexity-stability in food webs

It is predicted that ecological communities will become unstable with increasing species numbers and subsequent interspecific interactions; however, this is contrary to how natural ecosystems with diverse species respond to changes in species numbers. This contradiction has steered ecologists toward exploring what underlying processes allow complex communities to stabilize even through varying pressures. In this study, a food web model is used to show an overlooked role of interference among multiple predator species in solving this complexity–stability problem. Predator interference in large communities weakens species interactions due to a reduction in consumption rates by prey-sharing species in the presence of predators in response to territorial and aggressive behavior, thereby playing a key stabilizing role in communities. Especially when interspecific interference is strong and a community has diverse species and dense species interactions, stabilization is likely to work and creates a positive complexity–stability relationship within a community. The clear positive effect of complexity on community stability is not reflected by/intraspecific interference, emphasizing the key role of interspecific interference among multiple predator species in maintaining larger systems.

Vector-borne plant pathogens modify top-down and bottom-up effects on insect herbivores

Ecological theory predicts that host-plant traits affect herbivore population growth rates, which in turn modulates predator-prey interactions. However, while vector-borne plant pathogens often alter traits of both host plants and vectors, a few studies have assessed how pathogens may act as interaction modifiers within tri-trophic food webs. By applying a food web motif framework, we assessed how a vector-borne plant pathogen (Pea-enation mosaic virus, PEMV) modified both bottom-up (plant-herbivore) and top-down (predator-prey) interactions. Specifically, we assessed trophic interactions with PEMV-infectious Acyrthosiphon pisum (pea aphid) vectors compared to non-infectious aphids in a factorial experiment that manipulated predator and plant communities. We show that PEMV altered bi-trophic relationships, whereby on certain plant species, PEMV reduced vector performance but also increased their susceptibility to predators. However, on other plant species, PEMV weakened top-down control or increased vector performance. Our results suggest that vector-borne plant pathogens are important interaction modifiers for plant-herbivore-predator dynamics: host-plant response to viruses can decrease herbivore abundance by reducing herbivore performance, but also increase herbivore abundance by weakening top-down control. Broadly speaking, trophic interactions that regulate herbivore outbreaks appear to be modified for herbivores actively transmitting viruses to host plants. Consequently, management and monitoring of outbreaking herbivores should consider the infection status of focal populations.

Building clone-consistent ecosystem models

Many ecological studies employ general models that can feature an arbitrary number of populations. A critical requirement imposed on such models is clone consistency: If the individuals from two populations are indistinguishable, joining these populations into one shall not affect the outcome of the model. Otherwise a model produces different outcomes for the same scenario. Using functional analysis, we comprehensively characterize all clone-consistent models: We prove that they are necessarily composed from basic building blocks, namely linear combinations of parameters and abundances. These strong constraints enable a straightforward validation of model consistency. Although clone consistency can always be achieved with sufficient assumptions, we argue that it is important to explicitly name and consider the assumptions made: They may not be justified or limit the applicability of models and the generality of the results obtained with them. Moreover, our insights facilitate building new clone-consistent models, which we illustrate for a data-driven model of microbial communities. Finally, our insights point to new relevant forms of general models for theoretical ecology. Our framework thus provides a systematic way of comprehending ecological models, which can guide a wide range of studies.

Converting Ecological Currencies: Energy, Material, and Information Flows

Understanding how the three currencies of life - energy, material, and information - interact is a key step towards synthesis in ecology and evolution. However, current theory focuses on the role of matter as a resource and energy, and typically ignores how the same matter can have other important effects as a carrier of information or modifier of the environment. Here we present the hypothesis that the dynamic conversion of matter by organisms among its three currencies mediates the structure and function of ecosystems, and that these effects can even supersede the effects of matter as a resource. Humans are changing the information in the environment and this is altering species interactions and flows of matter within and among ecosystems.

Higher order interactions and species coexistence

Higher order interactions (HOIs) have been suggested to stabilize diverse ecological communities. However, their role in maintaining species coexistence from the perspective of modern coexistence theory is not known. Here, using generalized Lotka-Volterra model, we derive a general rule for species coexistence modulated by HOIs. We show that where pairwise species interactions fail to promote species coexistence in regions of extreme fitness differences, negative HOIs that intensify pairwise competition, however, can promote coexistence provided that HOIs strengthen intraspecific competition more than interspecific competition. In contrast, positive HOIs that alleviate pairwise competition can stabilize coexistence across a wide range of fitness differences, irrespective of differences in strength of inter- and intraspecific competition. In addition, we extend our three-species analytical result to multispecies communities and show, using simulations, that multispecies coexistence is possible provided that strength of negative intraspecific HOIs is higher than interspecific HOIs. Our work sheds light on the underlying mechanisms through which HOIs can maintain species diversity.

Finding missing links in interaction networks

Documenting which species interact within ecological communities is challenging and labor intensive. As a result, many interactions remain unrecorded, potentially distorting our understanding of network structure and dynamics. We test the utility of four structural models and a new coverage-deficit model for predicting missing links in both simulated and empirical bipartite networks. We find they can perform well, although the predictive power of structural models varies with the underlying network structure. The accuracy of predictions can be improved by ensembling multiple models. Augmenting observed networks with most-likely missing links improves estimates of qualitative network metrics. Tools to identify likely missing links can be simple to implement, allowing the prioritization of research effort and more robust assessment of network properties.

Can an herbivore affect where a top predator kills its prey by modifying woody vegetation structure?

In large mammal communities, little is known about modification of interspecific interactions through habitat structure changes. We assessed the effects of African elephants (Loxodonta africana) on features of woody habitat structure that can affect predator-prey interactions. We then explored how this can influence where African lions (Panthera leo) kill their prey. Indeed, lions are stalk-and-ambush predators and habitat structure and concealment opportunities are assumed to influence their hunting success. During 2 years, in Hwange National Park, Zimbabwe, kill sites (n = 167) of GPS-collared lions were characterized (visibility distance for large mammals, distance to a potential ambush site and presence of elephant impacts). We compared characteristics of lion kill sites with characteristics of random sites (1) at a large scale (i.e. in areas intensively used by lions, n = 418) and (2) at the microhabitat scale (i.e. in the direct surrounding available habitat, < 150 m, n = 167). Elephant-impacted sites had a slightly higher visibility and a longer distance to a potential ambush site than non-impacted sites, but these relationships were characterized by a high variability. At large scale, kill sites were characterized by higher levels of elephant impacts compared to random sites. At microhabitat scale, compared to the direct nearby available habitat, kill sites were characterized by a reduced distance to a potential ambush site. We suggest a conceptual framework whereby the relative importance of habitat features and prey abundance could change upon the scale considered.

Towards a Probabilistic Understanding About the Context-Dependency of Species Interactions

Observational and experimental studies have shown that an interaction class between two species (be it mutualistic, competitive, antagonistic, or neutral) may switch to a different class, depending on the biotic and abiotic factors within which species are observed. This complexity arising from the evidence of context-dependencies has underscored a difficulty in establishing a systematic analysis about the extent to which species interactions are expected to switch in nature and experiments. Here, we propose an overarching theoretical framework, by integrating probabilistic and structural approaches, to establish null expectations about switches of interaction classes across environmental contexts. This integration provides a systematic platform upon which it is possible to establish new hypotheses, clear predictions, and quantifiable expectations about the context-dependency of species interactions.

Trait-mediated indirect interactions: Moose browsing increases sawfly fecundity through plant-induced responses

Induced responses in plants, initiated by herbivory, create potential for trait-mediated indirect interactions among herbivores. Responses to an initial herbivore may change a number of plant traits that subsequently alter ecological processes with additional herbivores. Although common, indirect interactions between taxonomically distant herbivores, such as mammals and insects, are less studied than between taxonomically related species (i.e., insect-insect). In terms of mammal-insect interactions, effects on insect numbers (e.g., density) are relatively well studied, whereas effects on performance (e.g., fecundity) are rarely explored. Moreover, few studies have explored mammal-insect interactions on coniferous plants.The aim of this study was to investigate the effect of mammalian induced responses on insect performance. We specifically investigated the effect of moose (Alces alces) browsing on Scots pine (Pinus sylvestris) and subsequent effects on sawfly (Neodiprion sertifer) performance.Sawfly larvae were reared on browsed, clipped, and unbrowsed control pine trees in a controlled field experiment. Afterward, cocoon weight was measured. Needle C:N ratio and di-terpene content were measured in response to browsing.Sawfly performance was enhanced on trees browsed by moose. Cocoon weight (proxy for fecundity) was 9 and 13% higher on browsed and clipped trees compared to unbrowsed trees. Cocoon weight was weakly related to needle C:N ratio, and browsed trees had lower a C:N ratio compared to unbrowsed trees. Needle di-terpene content, known to affect sawfly performance, was neither affected by the browsing treatments nor did it correlate with sawfly weight.We conclude that mammalian herbivory can affect insect herbivore performance, with potential consequences for ecological communities and with particular importance for insect population dynamics. The measured plant variables could not fully explain the effect on sawfly performance providing a starting point for the consideration of additional plant responses induced by mammalian browsing affecting insect performance.

Predation risk influences food-web structure by constraining species diet choice

The foraging behaviour of species determines their diet and, therefore, also emergent food-web structure. Optimal foraging theory (OFT) has previously been applied to understand the emergence of food-web structure through a consumer-centric consideration of diet choice. However, the resource-centric viewpoint, where species adjust their behaviour to reduce the risk of predation, has not been considered. We develop a mechanistic model that merges metabolic theory with OFT to incorporate the effect of predation risk on diet choice to assemble food webs. This 'predation-risk-compromise' (PR) model better captures the nestedness and modularity of empirical food webs relative to the classical optimal foraging model. Specifically, compared with optimal foraging alone, risk-mitigated foraging leads to more-nested but less-modular webs by broadening the diet of consumers at intermediate trophic levels. Thus, predation risk significantly affects food-web structure by constraining species' ability to forage optimally, and needs to be considered in future work.

Interaction modifications lead to greater robustness than pairwise non-trophic effects in food webs

Considerable emphasis has been placed recently on the importance of incorporating non-trophic effects into our understanding of ecological networks. Interaction modifications are well-established as generating strong non-trophic impacts by modulating the strength of interspecific interactions. For simplicity and comparison with direct interactions within a network context, the consequences of interaction modifications have often been described as direct pairwise interactions. The consequences of this assumption have not been examined in non-equilibrium settings where unexpected consequences of interaction modifications are most likely. To test the distinct dynamic nature of these "higher-order" effects, we directly compare, using dynamic simulations, the robustness to extinctions under perturbation of systems where interaction modifications are either explicitly modelled or represented by corresponding equivalent pairwise non-trophic interactions. Full, multi-species representations of interaction modifications resulted in a greater robustness to extinctions compared to equivalent pairwise effects. Explanations for this increased stability despite apparent greater dynamic complexity can be found in additional routes for dynamic feedbacks. Furthermore, interaction modifications changed the relative vulnerability of species to extinction from those trophically connected close to the perturbed species towards those receiving a large number of modifications. Future empirical and theoretical research into non-trophic effects should distinguish interaction modifications from direct pairwise effects in order to maximize information about the system dynamics. Interaction modifications have the potential to shift expectations of species vulnerability based exclusively on trophic networks.

The mechanistic basis for higher-order interactions and non-additivity in competitive communities

Motivated by both analytical tractability and empirical practicality, community ecologists have long treated the species pair as the fundamental unit of study. This notwithstanding, the challenge of understanding more complex systems has repeatedly generated interest in the role of so-called higher-order interactions (HOIs) imposed by species beyond the focal pair. Here we argue that HOIs - defined as non-additive effects of density on per capita growth - are best interpreted as emergent properties of phenomenological models (e.g. Lotka-Volterra competition) rather than as distinct 'ecological processes' in their own right. Using simulations of consumer-resource models, we explore the mechanisms and system properties that give rise to HOIs in observational data. We demonstrate that HOIs emerge under all but the most restrictive of assumptions, and that incorporating non-additivity into phenomenological models improves the quantitative and qualitative accuracy of model predictions. Notably, we also observe that HOIs derive primarily from mechanisms and system properties that apply equally to single-species or pairwise systems as they do to more diverse communities. Consequently, there exists a strong mandate for further recognition of non-additive effects in both theoretical and empirical research.

Three-species competition with non-deterministic outcomes

Theoretical and experimental research studies have shown that ecosystems governed by non-transitive competition networks tend to maintain high levels of biodiversity. The theoretical body of work, however, has mainly focused on competition networks in which the outcomes of competition events are predetermined and hence deterministic, and where all species are identical up to their competitive relationships, an assumption that may limit the applicability of theoretical results to real-life situations. In this paper, we aim to probe the robustness of the link between biodiversity and non-transitive competition by introducing a three-dimensional winning probability parameter space, making the outcomes of competition events in a three-species in silico ecosystem uncertain. While two degenerate points in this parameter space have been the subject of previous studies, we investigate the remaining settings, which equip the species with distinct competitive abilities. We find that the impact of this modification depends on the spatial dimension of the system. When the system is well mixed, it collapses to monoculture, as is also the case in the non-transitive deterministic setting. In one dimension, chaotic patterns emerge, which tend to maintain biodiversity, and a power law relates the time that species manage to coexist to the degree of uncertainty regarding competition event outcomes. In two dimensions, the formation of spiral wave patterns ensures that biodiversity is maintained for moderate degrees of uncertainty, while considerable deviations from the non-transitive deterministic setting have strong negative effects on species coexistence. It can hence be concluded that non-transitive competition can still produce coexistence when the assumption of deterministic competition is abandoned. When the system collapses to monoculture, one observes a "survival of the strongest" law, as the species that has the highest probability of defeating its competitors has the best odds to become the sole survivor.

Energy Flux: The Link between Multitrophic Biodiversity and Ecosystem Functioning

Relating biodiversity to ecosystem functioning in natural communities has become a paramount challenge as links between trophic complexity and multiple ecosystem functions become increasingly apparent. Yet, there is still no generalised approach to address such complexity in biodiversity-ecosystem functioning (BEF) studies. Energy flux dynamics in ecological networks provide the theoretical underpinning of multitrophic BEF relationships. Accordingly, we propose the quantification of energy fluxes in food webs as a powerful, universal tool for understanding ecosystem functioning in multitrophic systems spanning different ecological scales. Although the concept of energy flux in food webs is not novel, its application to BEF research remains virtually untapped, providing a framework to foster new discoveries into the determinants of ecosystem functioning in complex systems.