Induced defenses within food webs: The role of community trade-offs, delayed responses, and defense specificity

Differences in alternative splicing events in the adaptive strategies of two Daphnia galeata genotypes induced by fish kairomones

BACKGROUND

Daphnia galeata is a suitable model organism for investigating predator-induced defense. Genes and pathways exhibiting differential expression between fish kairomone-treated and untreated groups in D. galeata have been identified. However, understanding of the significance of alternative splicing, a crucial process of the regulation of gene expression in eukaryotes, to this mechanism remains limited. This study measured life-history traits and conducted short-read RNA sequencing and long-read isoform sequencing of two Korean D. galeata genotypes (KB1 and KE2) to uncover the genetic mechanism underlying their phenotypic plasticity under predation stress.

RESULTS

KB1 exhibited strategies to enhance fertility and decrease body length when exposed to fish kairomones, while KE2 deployed an adaptive strategy to increase body length. Full-length transcriptomes from KB1 and KE2 yielded 65,736 and 57,437 transcripts, respectively, of which 32 differentially expressed transcripts (DETs) were shared under predation stress across both genotypes. Prominent DETs common to both genotypes were related to energy metabolism and the immune system. Additionally, differential alternative splicing (DAS) events were detected in both genotypes in response to fish kairomones. DAS genes shared between both genotypes may indicate their significant role in the post-transcriptional stress response to fish predation. Calpain-3, involved in digestion and nutrient absorption, was identified as a DAS gene in both genotypes when exposed to fish kairomones. In addition, the gene encoding thymosin beta, which is related to growth, was found to be a statistically significant DAS only in KB1, while that encoding ultraspiracle protein, also associated with growth, was only identified in KE2. Moreover, transcripts encoding proteins such as EGF-like domain-containing protein, vitellogenin fused with superoxide dismutase, and others were identified overlapping between DAS events and DETs and potentially elucidating their association with the observed phenotypic variation in each genotype.

CONCLUSIONS

Our findings highlight the crucial role of alternative splicing in modulating transcriptome landscape under predation stress in D. galeata, emphasizing the requirement for integrating gene expression and splicing analyses in evolutionary adaptation studies.

Comparative transcriptome analysis of two Daphnia galeata genotypes displaying contrasting phenotypic variation induced by fish kairomones in the same environment of the Han River, Korea

BACKGROUND

Phenotypic plasticity is a crucial adaptive mechanism that enables organisms to modify their traits in response to changes in their environment. Predator-induced defenses are an example of phenotypic plasticity observed across a wide range of organisms, from single-celled organisms to vertebrates. In addition to morphology and behavior, these responses also affect life-history traits. The crustacean Daphnia galeata is a suitable model organism for studying predator-induced defenses, as it exhibits life-history traits changes under predation risk. To get a better overview of their phenotypic plasticity under predation stress, we conducted RNA sequencing on the transcriptomes of two Korean Daphnia galeata genotypes, KE1, and KB11, collected in the same environment.

RESULTS

When exposed to fish kairomones, the two genotypes exhibited phenotypic variations related to reproduction and growth, with opposite patterns in growth-related phenotypic variation. From both genotypes, a total of 135,611 unigenes were analyzed, of which 194 differentially expressed transcripts (DETs) were shared among the two genotypes under predation stress, which showed consistent, or inconsistent expression patterns in both genotypes. Prominent DETs were related to digestion and reproduction and consistently up-regulated in both genotypes, thus associated with changes in life-history traits. Among the inconsistent DETs, transcripts encode vinculin (VINC) and protein obstructor-E (OBST-E), which are associated with growth; these may explain the differences in life-history traits between the two genotypes. In addition, genotype-specific DETs could explain the variation in growth-related life-history traits between genotypes, and could be associated with the increased body length of genotype KE1.

CONCLUSIONS

The current study allows for a better understanding of the adaptation mechanisms related to reproduction and growth of two Korean D. galeata genotypes induced by predation stress. However, further research is necessary to better understand the specific mechanisms by which the uncovered DETs are related with the observed phenotypic variation in each genotype. In the future, we aim to unravel the precise adaptive mechanisms underlying predator-induced responses.

Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model

Ecological communities are undeniably diverse, both in terms of the species that compose them as well as the type of interactions that link species to each other. Despite this long recognition of the coexistence of multiple interaction types in nature, little is known about the consequences of this diversity for community functioning. In the ongoing context of global change and increasing species extinction rates, it seems crucial to improve our understanding of the drivers of the relationship between species diversity and ecosystem functioning. Here, using a multispecies dynamical model of ecological communities including various interaction types (e.g. competition for space, predator interference, recruitment facilitation in addition to feeding), we studied the role of the presence and the intensity of these interactions for species diversity, community functioning (biomass and production) and the relationship between diversity and functioning.Taken jointly, the diverse interactions have significant effects on species diversity, whose amplitude and sign depend on the type of interactions involved and their relative abundance. They however consistently increase the slope of the relationship between diversity and functioning, suggesting that species losses might have stronger effects on community functioning than expected when ignoring the diversity of interaction types and focusing on feeding interactions only.

The question of how species diversity contributes to the functioning of ecological communities has intrigued ecologists for decades, and is especially relevant in the current context of species extinctions. Ecological communities are not only diverse in terms of the species that compose them but also in terms of the way they interact with each other: for example, species compete for space and for food, eat and facilitate each other. The diversity of ways species interact has rarely been taken into account in the study of ecological communities, although widely acknowledged. Here we show that the diversity of interaction types matters: it affects species diversity, community functioning and the relationship between them by strengthening this relationship. This means that when the diversity of interaction types is taken into account, species losses have stronger impacts on the functioning of ecological communities. Our results therefore suggest that species loss may have more important consequences than expected based on classical models that do not take the diversity of interaction types into account.

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.

Effects of Predator Avoidance Behavior on the Coexistence of Competing Prey

Predator avoidance behavior, in which prey limit foraging activities in the presence of predation threats, affects the dynamics of many ecological communities. Despite the growing theoretical appreciation of the role predation plays in coexistence, predator avoidance behavior has yet to be incorporated into the theory in a general way. We introduce adaptive avoidance behavior to a consumer-resource model with three trophic levels to ask whether the ability of prey-the middle trophic level-to avoid predators alters their ability to coexist. We determine the characteristics of cases in which predator avoidance behavior changes prey coexistence or the order of competitive dominance. The mechanism underlying such changes is the weakening of apparent competition relative to resource competition in determining niche overlap, even with resource intake costs. Avoidance behavior thus generally promotes coexistence if prey partition resources but not predators, whereas it undermines coexistence if prey partition predators but not resources. For any given case, the changes in the average fitness difference between two species resulting from avoidance behavior interact with changes in niche overlap to determine coexistence. These results connect the substantial body of theoretical work on avoidance behavior and population dynamics with the body of theory on competitive coexistence.

Trophic interaction modifications: an empirical and theoretical framework

Consumer-resource interactions are often influenced by other species in the community. At present these 'trophic interaction modifications' are rarely included in ecological models despite demonstrations that they can drive system dynamics. Here, we advocate and extend an approach that has the potential to unite and represent this key group of non-trophic interactions by emphasising the change to trophic interactions induced by modifying species. We highlight the opportunities this approach brings in comparison to frameworks that coerce trophic interaction modifications into pairwise relationships. To establish common frames of reference and explore the value of the approach, we set out a range of metrics for the 'strength' of an interaction modification which incorporate increasing levels of contextual information about the system. Through demonstrations in three-species model systems, we establish that these metrics capture complimentary aspects of interaction modifications. We show how the approach can be used in a range of empirical contexts; we identify as specific gaps in current understanding experiments with multiple levels of modifier species and the distributions of modifications in networks. The trophic interaction modification approach we propose can motivate and unite empirical and theoretical studies of system dynamics, providing a route to confront ecological complexity.

Environmentally relevant approaches to assess nanoparticles ecotoxicity: a review

Despite the increasing production and use of nanoparticles (NPs), there is a lack of knowledge about their environmental fate and ecotoxicity. Studies in environmentally relevant conditions are necessary to better assess these parameters, but such studies are rather rare. The present work represents first time that studies on engineered NPs using environmentally relevant exposure methods have been reviewed. These exposure methods differ from standardized protocols and can be classified into three groups: experimental trophic chains that allow study of the trophic route, multi-species exposures under laboratory conditions that allow for complex but controlled exposure and outdoor exposures that are more similar to environmentally realistic conditions. The majority of studies of micro- or mesocosms have focused on NP partitioning and bioaccumulation. The other major parameter that has been studied is NP ecotoxicity, which has been assessed in single species, in single species via the trophic route, and at the community level. The induction of biochemical defense systems, immunomodulation, effects on growth and reproduction, behavioral alterations and mortality have been used as indicators of major toxicity, depending on the species studied. The major effects of NPs on both microbial and algal communities include modifications of community compositions and diversities, decreased biomass and changes in community activities.