Biotic interactions affect the elevational ranges of high‐latitude plant species

Ecological theory suggests that positive plant–plant interactions can extend species distributions into areas that would otherwise be unfavourable. However, few studies have tested this hypothesis, and none have explicitly examined the associated prediction that inter‐specific interactions between plants may broaden species altitudinal distributions. Here we test this prediction, using fine‐scale species distribution data for 156 bryophytes, lichens and vascular plants spanning a 900 m elevational gradient in north‐western Finland and Norway, analysed with a niche modelling approach. Species altitudinal ranges of all three groups of plants were more accurately predicted when including the cover of any of the 24 most wide‐spread and abundant species (‘dominants’) than when using abiotic variables alone, emphasizing the importance of including relevant biotic predictors in species distribution models. Half of the models showed that species had very low probabilities of occurrence under high cover of dominants, suggesting a strong negative impact of dominant species. Similarly, for species that are predicted to occur irrespective of dominant species cover, 62% of models showed narrower species altitudinal distributions when occurring under high dominant cover, with contractions of species’ lower and upper elevational limits being common. Nonetheless, high cover of dominant species was associated with upslope range extension in 43 species, and a net range expansion in nearly 10% of all models. Species distributional responses to dominants were only weakly related to species traits, with larger range contractions associated with arctic‐alpine dominants. Therefore, dominant species appear to exert a strong influence on the elevational distribution of other species in high latitude environments.     

Community‐wide impacts of herbivore‐induced plant regrowth on arthropods in a multi‐willow species system

It has been widely accepted that herbivory induces morphological, phenological, and chemical changes in a wide variety of terrestrial plants. There is an increasing appreciation that herbivore‐induced plant responses affect the performance and abundance of other arthropods. However, we still have a poor understanding of the effects of induced plant responses on community structures of arthropods. We examined the community‐level effects of willow regrowth in response to damage by larvae of swift moth Endoclita excrescence (Lepidoptera: Hepialidae) on herbivorous and predaceous arthropods on three willow species, Salix gilgiana, S. eriocarpa and S. serissaefolia. The leaves of sprouting lateral shoots induced by moth‐boring had a low C:N ratio. The overall abundance and species richness of herbivorous insects on the lateral shoots were increased on all three willow species. Densities of specialist chewers and sap‐feeders, and leaf miners increased on the newly emerged lateral shoots. In contrast, the densities of generalist chewers and sap‐feeders, and gall makers did not increase. Furthermore, ant and spider densities, and the overall abundance and species richness of predaceous arthropods increased on the lateral shoots on S. gilgiana and S. eriocarpa, but not S. serissaefolia. In addition to finding that effects of moth‐boring on arthropod abundance and species richness varied among willow species, we also found that moth‐boring, willow species, and their interaction differentially affected community composition. Our findings suggest that moth‐boring has community‐wide impacts on arthropod assemblages across three trophic levels via induced shoot regrowth and increase arthropod species diversity in this three willow species system.     

Spatial determinants of infection risk in a multi‐species avian malaria system

Spatially‐variable processes can be an important element of host–parasite interactions, but their longer term demographic and evolutionary effects depend on the magnitude of variation in space, the scale at which variation occurs and the degree to which such processes are temporally stable. Here, we use multiple years of data from a study of two closely related tit species (Paridae), infected with two congeneric species of avian malaria (Plasmodium), to evaluate the roles of extrinsic and intrinsic factors in driving spatial heterogeneity in infection risk, and to address questions of scale and temporal stability in these vector‐driven host–parasite interactions. We show that the two malaria parasite species exhibit markedly different spatial epidemiology: P. relictum infections are effectively randomly distributed in space, with no temporal consistency, whereas P. circumflexum infections exhibit pronounced spatial structuring that is stable over the six years of this study and similar in both host species. We show that both conspecific and heterospecific host density contribute to elevated infection risk, but that the main determinants of elevated risk of P. circumflexum infection risk are habitat features probably associated with vector distribution and abundance. We discuss the implications of these findings, both for our understanding of the epidemiology of malaria in the wild, but also in terms of the longer‐term evolutionary and demographic consequences that spatially variable parasite‐mediated selection may have on host populations.     

Nitric oxide‐mediated dispersal in single‐ and multi‐species biofilms of clinically and industrially relevant microorganisms

Strategies to induce biofilm dispersal are of interest due to their potential to prevent biofilm formation and biofilm‐related infections. Nitric oxide (NO), an important messenger molecule in biological systems, was previously identified as a signal for dispersal in biofilms of the model organism Pseudomonas aeruginosa. In the present study, the use of NO as an anti‐biofilm agent more broadly was assessed. Various NO donors, at concentrations estimated to generate NO levels in the picomolar and low nanomolar range, were tested on single‐species biofilms of relevant microorganisms and on multi‐species biofilms from water distribution and treatment systems. Nitric oxide‐induced dispersal was observed in all biofilms assessed, and the average reduction of total biofilm surface was 63%. Moreover, biofilms exposed to low doses of NO were more susceptible to antimicrobial treatments than untreated biofilms. For example, the efficacy of conventional chlorine treatments at removing multi‐species biofilms from water systems was increased by 20‐fold in biofilms treated with NO compared with untreated biofilms. These data suggest that combined treatments with NO may allow for novel and improved strategies to control biofilms and have widespread applications in many environmental, industrial and clinical settings.     

Development of oligonucleotide microarrays for simultaneous multi‐species identification of Phellinus tree‐pathogenic fungi

Polyporoid Phellinus fungi are ubiquitously present in the environment and play an important role in shaping forest ecology. Several species of Phellinus are notorious pathogens that can affect a broad variety of tree species in forest, plantation, orchard and urban habitats; however, current detection methods are overly complex and lack the sensitivity required to identify these pathogens at the species level in a timely fashion for effective infestation control. Here, we describe eight oligonucleotide microarray platforms for the simultaneous and specific detection of 17 important Phellinus species, using probes generated from the internal transcribed spacer regions unique to each species. The sensitivity, robustness and efficiency of this Phellinus microarray system was subsequently confirmed against template DNA from two key Phellinus species, as well as field samples collected from tree roots, trunks and surrounding soil. This system can provide early, specific and convenient detection of Phellinus species for forestry, arboriculture and quarantine inspection, and could potentially help to mitigate the environmental and economic impact of Phellinus‐related diseases.     

Specific non-monotonous interactions increase persistence of ecological networks

The relationship between stability and biodiversity has long been debated in ecology due to opposing empirical observations and theoretical predictions. Species interaction strength is often assumed to be monotonically related to population density, but the effects on stability of ecological networks of non-monotonous interactions that change signs have not been investigated previously. We demonstrate that for four kinds of non-monotonous interactions, shifting signs to negative or neutral interactions at high population density increases persistence (a measure of stability) of ecological networks, while for the other two kinds of non-monotonous interactions shifting signs to positive interactions at high population density decreases persistence of networks. Our results reveal a novel mechanism of network stabilization caused by specific non-monotonous interaction types through either increasing stable equilibrium points or reducing unstable equilibrium points (or both). These specific non-monotonous interactions may be important in maintaining stable and complex ecological networks, as well as other networks such as genes, neurons, the internet and human societies.     

Forecasting the future of biodiversity: a test of single‐ and multi‐species models for ants in North America

The geographic distributions of many taxonomic groups remain mostly unknown, hindering attempts to investigate the response of the majority of species on Earth to climate change using species distributions models (SDMs). Multi‐species models can incorporate data for rare or poorly‐sampled species, but their application to forecasting climate change impacts on biodiversity has been limited. Here we compare forecasts of changes in patterns of ant biodiversity in North America derived from ensembles of single‐species models to those from a multi‐species modeling approach, Generalized Dissimilarity Modeling (GDM). We found that both single‐ and multi‐species models forecasted large changes in ant community composition in relatively warm environments. GDM predicted higher turnover than SDMs and across a larger contiguous area, including the southern third of North America and notably Central America, where the proportion of ants with relatively small ranges is high and where data limitations are most likely to impede the application of SDMs. Differences between approaches were also influenced by assumptions regarding dispersal, with forecasts being more similar if no‐dispersal was assumed. When full‐dispersal was assumed, SDMs predicted higher turnover in southern Canada than did GDM. Taken together, our results suggest that 1) warm rather than cold regions potentially could experience the greatest changes in ant fauna under climate change and that 2) multi‐species models may represent an important complement to SDMs, particularly in analyses involving large numbers of rare or poorly‐sampled species. Comparisons of the ability of single‐ and multi‐species models to predict observed changes in community composition are needed in order to draw definitive conclusions regarding their application to investigating climate change impacts on biodiversity.     

Partitioning the effects of species loss on community variability using multi‐level selection theory

The temporal variability of ecological communities may depend on species richness and composition due to a variety of statistical and ecological mechanisms. However, ecologists currently lack a general, unified theoretical framework within which to compare the effects of these mechanisms. Developing such a framework is difficult because community variability depends not just on how species vary, but also how they covary, making it unclear how to isolate the contributions of individual species to community variability. Here I develop such a theoretical framework using the multi‐level Price equation, originally developed in evolutionary biology to partition the effects of group selection and individual selection. I show how the variability of a community can be related to the properties of the individual species comprising it, just as the properties of an evolving group can be related to the properties of the individual organisms comprising it. I show that effects of species loss on community variability can be partitioned into effects of species richness (random loss of species), effects of species composition (non‐random loss of species with respect to their variances and covariances), and effects of context dependence (post‐loss changes in species’ variances and covariances). I illustrate the application of this framework using data from the Biodiversity II experiment, and show that it leads to new conceptual and empirical insights. For instance, effects of species richness on community variability necessarily occur, but often are swamped by other effects, particularly context dependence.     

Engineered single‐ and multi‐cell chemotaxis pathways in E. coli

We have engineered the chemotaxis system of Escherichia coli to respond to molecules that are not attractants for wild‐type cells. The system depends on an artificially introduced enzymatic activity that converts the target molecule into a ligand for an E. coli chemoreceptor, thereby enabling the cells to respond to the new attractant. Two systems were designed, and both showed robust chemotactic responses in semisolid and liquid media. The first incorporates an asparaginase enzyme and the native E. coli aspartate receptor to produce a response to asparagine; the second uses penicillin acylase and an engineered chemoreceptor for phenylacetic acid to produce a response to phenylacetyl glycine. In addition, by taking advantage of a ‘hitchhiker’ effect in which cells producing the ligand can induce chemotaxis of neighboring cells lacking enzymatic activity, we were able to design a more complex system that functions as a simple microbial consortium. The result effectively introduces a logical ‘AND’ into the system so that the population only swims towards the combined gradients of two attractants.     

A spectrum of modularity in multi‐functional gene circuits

A major challenge in systems biology is to understand the relationship between a circuit's structure and its function, but how is this relationship affected if the circuit must perform multiple distinct functions within the same organism? In particular, to what extent do multi‐functional circuits contain modules which reflect the different functions? Here, we computationally survey a range of bi‐functional circuits which show no simple structural modularity: They can switch between two qualitatively distinct functions, while both functions depend on all genes of the circuit. Our analysis reveals two distinct classes: hybrid circuits which overlay two simpler mono‐functional sub‐circuits within their circuitry, and emergent circuits, which do not. In this second class, the bi‐functionality emerges from more complex designs which are not fully decomposable into distinct modules and are consequently less intuitive to predict or understand. These non‐intuitive emergent circuits are just as robust as their hybrid counterparts, and we therefore suggest that the common bias toward studying modular systems may hinder our understanding of real biological circuits.     

Systems‐level interactions between insulin–EGF networks amplify mitogenic signaling

Crosstalk mechanisms have not been studied as thoroughly as individual signaling pathways. We exploit experimental and computational approaches to reveal how a concordant interplay between the insulin and epidermal growth factor (EGF) signaling networks can potentiate mitogenic signaling. In HEK293 cells, insulin is a poor activator of the Ras/ERK (extracellular signal‐regulated kinase) cascade, yet it enhances ERK activation by low EGF doses. We find that major crosstalk mechanisms that amplify ERK signaling are localized upstream of Ras and at the Ras/Raf level. Computational modeling unveils how critical network nodes, the adaptor proteins GAB1 and insulin receptor substrate (IRS), Src kinase, and phosphatase SHP2, convert insulin‐induced increase in the phosphatidylinositol‐3,4,5‐triphosphate (PIP₃) concentration into enhanced Ras/ERK activity. The model predicts and experiments confirm that insulin‐induced amplification of mitogenic signaling is abolished by disrupting PIP₃‐mediated positive feedback via GAB1 and IRS. We demonstrate that GAB1 behaves as a non‐linear amplifier of mitogenic responses and insulin endows EGF signaling with robustness to GAB1 suppression. Our results show the feasibility of using computational models to identify key target combinations and predict complex cellular responses to a mixture of external cues.     

Geography,topography, and history affect realized‐to‐potential tree species richness patterns in Europe

Environmental conditions and biotic interactions are generally thought to influence local species richness. However, immigration and the evolutionary and historical factors that shape regional species pools should also contribute to determining local species richness because local communities arise by assembly from regional species pools. Using the European tree flora as our study system, we implemented a novel approach to assess the relative importance of local and regional mechanisms that control local species richness. We first identified species pools that tolerate particular local environments and quantified the proportion of the pool that is present locally, i.e. the realized/potential (R/P) richness ratio. Because no consensus exists on how to estimate potential richness, we estimated it using three different approaches. Using these three estimates separately and in a combined ensemble estimate, we then analyzed the effects of potential drivers on R/P richness ratios. We predicted that the R/P richness ratio would 1) increase with decreasing distance from glacial refugia (accessibility), 2) and be generally low in geographically fragmented southern Europe because of dispersal limitation; 3) increase with actual evapotranspiration because greater availability of water and energy promotes local population persistence; and 4) increase with topographic heterogeneity because it promotes local species coexistence and facilitates long‐term species survival. There was considerable variation among the three R/P richness ratio estimates, but we found consistent support for a negative effect of regional geographic fragmentation and a positive topographic effect. We also identified fairly broad support for the predicted effect of accessibility. We conclude that local tree assemblages in Europe often fail to realize a large proportion of the potential richness held in the regional species pool, partially reflecting their geographical, historical, and environmental circumstances. The dispersal‐related effects of geographic fragmentation and accessibility exemplify regional controls that combine with local ecological sorting to determine local species richness.     

A modular toolbox for Golden‐Gate‐based plasmid assembly streamlines the generation of Ralstonia solanacearum species complex knockout strains and multi‐cassette complementation constructs

Members of the Ralstonia solanacearum species complex (Rssc) cause bacterial wilt, a devastating plant disease that affects numerous economically important crops. Like other bacterial pests, Rssc injects a cocktail of effector proteins via the bacterial type III secretion system into host cells that collectively promote disease. Given their functional relevance in disease, the identification of Rssc effectors and the investigation of their in planta function are likely to provide clues on how to generate pest‐resistant crop plants. Accordingly, molecular analysis of effector function is a focus of Rssc research. The elucidation of effector function requires corresponding gene knockout strains or strains that express the desired effector variants. The cloning of DNA constructs that facilitate the generation of such strains has hindered the investigation of Rssc effectors. To overcome these limitations, we have designed, generated and functionally validated a toolkit consisting of DNA modules that can be assembled via Golden‐Gate (GG) cloning into either desired gene knockout constructs or multi‐cassette expression constructs. The Ralstonia‐GG‐kit is compatible with a previously established toolkit that facilitates the generation of DNA constructs for in planta expression. Accordingly, cloned modules, encoding effectors of interest, can be transferred to vectors for expression in Rssc strains and plant cells. As many effector genes have been cloned in the past as GATEWAY entry vectors, we have also established a conversion vector that allows the implementation of GATEWAY entry vectors into the Ralstonia‐GG‐kit. In summary, the Ralstonia‐GG‐kit provides a valuable tool for the genetic investigation of genes encoding effectors and other Rssc genes.     

Interspecific interactions affect species and community responses to climate shifts

The response of individual species to climate change may alter the composition and dynamics of communities. Here, we show that the impacts of environmental change on communities can depend on the nature of the interspecific interactions: mutualistic communities typically respond differently than commensalistic or parasitic communities. We model and analyse the geographic range shifting of metapopulations of two interacting species – a host and an obligate species. Different types of interspecific interactions are implemented by modifying local extinction rates according to the presence/absence of the other species. We distinguish and compare three fundamentally different community types: mutualism, commensalism and parasitism. We find that community dynamics during geographic range shifting critically depends on the type of interspecific interactions. Parasitic interactions exacerbate the negative effect of environmental change whereas mutualistic interactions only partly compensate it. Commensalistic interactions exhibit an intermediate response. Based on these model outcomes, we predict that parasitic species interactions may be more vulnerable to geographic range shifting than commensalistic or mutualistic ones. However, we observe that when climate stabilises following a period of change, the rate of community recovery is largely independent of the type of interspecific interactions. These results emphasize that communities respond delicately to environmental change, and that local interspecific interactions can affect range shifting communities at large spatial scales.     

Competition hierarchies among ants and predation by birds jointly determine the strength of multi‐species ant–aphid mutualisms

Protection mutualisms often involve multiple species of protector that vary in quality as mutualists. Because protectors may compete for access to mutualists, concordance between competitive ability and degree of benefit will determine the overall strength of multi‐species mutualisms. We compared the abilities of two similarly sized congener ants as competitors for, and mutualists of pine‐feeding aphids, and how insectivorous birds affected each ant–aphid mutualism. Formica planipilis and F. podzolica were indistinguishable in forager abundance, but the former was 13‐fold more abundant at competition baits and provided 11‐fold more benefits to aphids. These results highlight how, in a single environment, a great ecological distance can exist between two congener ants of similar size. Insectivorous birds disrupted the two mutualisms to a similar extent, reducing aphid and ant abundance by 91% and 39% respectively. Nevertheless, birds had an important influence on the relative benefits of the two ants to aphids: where F. planipilis consistently benefited aphids, F. podzolica only did so in the absence of birds. Consequently, the presence of insectivorous birds and ant species identity jointly determined whether ant–aphid mutualisms occurred in pine canopies and the strength of such interactions. Our study highlights the inter‐relatedness of competition, predation and mutualism, and how competition can serve to strengthen mutualism by filtering inferior mutualists.