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.     

Long‐term successional forest dynamics: species and community responses to climatic variability

Question: Are trees sensitive to climatic variability, and do tree species differ in their responses to climatic variability? Does sensitivity of forest communities to climatic variability depend on stand composition? Location: Mixed young forest at Walker Branch Watershed near Oak Ridge, East Tennessee, USA. Methods: Using a long‐term dataset (1967–2006), we analyzed temporal forest dynamics at the tree and species level, and community dynamics for forest stands that differed in initial species composition (i.e., chestnut oak, oak–hickory, pine, and yellow poplar stands). Using summer drought and growing season temperature as defined climate drivers, we evaluated relationships between forest dynamics and climate across levels of organization. Results: Over the four‐decade study period, forest communities underwent successional change and substantially increased in biomass. Variation in summer drought and growing season temperature contributed to temporal biomass dynamics for some tree species, but not for others. Stand‐level responses to climatic variability were related to the responses of component species, except in pine stands. Pinus echinata, the dominant species in pine stands, decreased over time due to periodic outbreaks of pine bark beetle (Dendroctonus frontalis). These outbreaks at Walker Branch could not be directly related to climatic conditions. Conclusions: The results indicate that sensitivity of developing forests to climatic variability is stand type‐dependent, and hence is a function of species composition. However, in the long term, direct effects of climatic variability on forest dynamics may be small relative to autogenic successional processes or climate‐related insect outbreaks. Empirical studies testing for interactions between forest succession and climatic variability are needed.     

Population fluctuations affect inference in ecological networks of multi‐species interactions

Local abundance and population fluctuations are key factors affecting the realized interaction frequencies in biotic interactions, but they are commonly ignored when network metrics are calculated over aggregated sets of observations. Here we studied how abundance fluctuations (i.e. demographic and stochastic population dynamics in one of the trophic levels) may affect derived network‐level inferences in bipartite ecological networks. Variation at both the species and network level in network indices (d’, Dependence, Fisher's alpha diversity for both levels, H₂’, weighted NODF) were strongly correlated with the extent of abundance fluctuations, with a strong effect of environmental stochasticity on all indices except NODF; this was the only index for which considerable variation was caused by varying carrying capacities among species. Binary connectance, in turn, does not take interaction frequency (and thus abundance) into account and was only influenced by abundance fluctuations at low population sizes if this led to non‐occurrence of ‘true’ interactions. Overall, abundance and population dynamics are likely to play an important role in determining what is commonly observed and summarized into ecological networks. We suggest that ecological network inference should account for underlying population dynamics and uncertainty in what is observed as interaction frequencies, modelling mechanisms at operative organisational levels below the network rather than using aggregated data of observations. Modelling population dynamics may be a valuable tool in this field to conceptualize and tease apart different sources of variation and express uncertainty in our inference from small samples.     

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.     

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.     

Community‐level vs species‐specific approaches to model selection

A topic of particular current interest is community‐level approaches to species distribution modelling (SDM), i.e. approaches that simultaneously analyse distributional data for multiple species. Previous studies have looked at the advantages of community‐level approaches for parameter estimation, but not for model selection – the process of choosing which model (and in particular, which subset of environmental variables) to fit to data. We compared the predictive performance of models using the same modelling method (generalised linear models) but choosing the subset of variables to include in the model either simultaneously across all species (community‐level model selection) or separately for each species (species‐specific model selection). Our results across two large presence/absence tree community datasets were inconclusive as to whether there was an overall difference in predictive performance between models fitted via species‐specific vs community‐level model selection. However, we found some evidence that a community approach was best suited to modelling rare species, and its performance decayed with increasing prevalence. That is, when data were sparse there was more opportunity for gains from “borrowing strength” across species via a community‐level approach. Interestingly, we also found that the community‐level approach tended to work better when the model selection problem was more difficult, and more reliably detected “noise” variables that should be excluded from the model.     

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.     

Quantification of protein mixture in chromatographic separation using multi‐wavelength UV spectra

In therapeutic protein production, the protein purification with chromatographic processes is of high importance in separating the qualified proteins from the impurities for consistent product quality. Therefore, to aid real‐time monitoring of the protein purification processes, various kinds of methodologies have been proposed until now. However, the majority of them still rely on the use of a single ultraviolet (UV) absorbance or the utilization of expensive and time‐consuming instruments, thus requiring a simple, fast, and cost‐effective methodology for protein quantification. In this study, the feasibility of using multiwavelength UV spectroscopy was investigated as an alternative tool for the real‐time monitoring of the protein mixtures in protein purification. To this end, three different proteins were selected as a model system for the protein mixture, and the multivariate UV spectra were analyzed to construct the reliable quantification models for different proteins of interest. By using various chemometrics tools, such as partial least squares (PLS), the validity of estimating the protein concentration from the UV spectra of the mixture samples was rigorously analyzed with their prediction performance, and the results indicated that the multiwavelength UV spectra had sufficient sensitivity and accuracy to estimate the protein concentrations in mixture, demonstrating its usefulness for the rapid quantification of the protein mixtures in protein purification. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:664–671, 2013     

The effects of multilocus balancing selection on neutral variability

We studied the effect of multilocus balancing selection on neutral nucleotide variability at linked sites by simulating a model where diallelic polymorphisms are maintained at an arbitrary number of selected loci by means of symmetric overdominance. Different combinations of alleles define different genetic backgrounds that subdivide the population and strongly affect variability. Several multilocus fitness regimes with different degrees of epistasis and gametic disequilibrium are allowed. Analytical results based on a multilocus extension of the structured coalescent predict that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. Our simulation results show that although variability increases with the number of genetic backgrounds that are maintained in the population, it is reduced by random fluctuations in the frequencies of those backgrounds and does not reach high levels even in very large populations. We also show that previous results on balancing selection in single-locus systems do not extend to the multilocus scenario in a straightforward way. Different patterns of linkage disequilibrium and of the frequency spectrum of neutral mutations are expected under different degrees of epistasis. Interestingly, the power to detect balancing selection using deviations from a neutral distribution of allele frequencies seems to be diminished under the fitness regime that leads to the largest increase of variability over the neutral case. This and other results are discussed in the light of data from the Mhc.     

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.     

CFD of mixing of multi‐phase flow in a bioreactor using population balance model

Mixing in bioreactors is known to be crucial for achieving efficient mass and heat transfer, both of which thereby impact not only growth of cells but also product quality. In a typical bioreactor, the rate of transport of oxygen from air is the limiting factor. While higher impeller speeds can enhance mixing, they can also cause severe cell damage. Hence, it is crucial to understand the hydrodynamics in a bioreactor to achieve optimal performance. This article presents a novel approach involving use of computational fluid dynamics (CFD) to model the hydrodynamics of an aerated stirred bioreactor for production of a monoclonal antibody therapeutic via mammalian cell culture. This is achieved by estimating the volume averaged mass transfer coefficient (k_La) under varying conditions of the process parameters. The process parameters that have been examined include the impeller rotational speed and the flow rate of the incoming gas through the sparger inlet. To undermine the two‐phase flow and turbulence, an Eulerian‐Eulerian multiphase model and k‐ε turbulence model have been used, respectively. These have further been coupled with population balance model to incorporate the various interphase interactions that lead to coalescence and breakage of bubbles. We have successfully demonstrated the utility of CFD as a tool to predict size distribution of bubbles as a function of process parameters and an efficient approach for obtaining optimized mixing conditions in the reactor. The proposed approach is significantly time and resource efficient when compared to the hit and trial, all experimental approach that is presently used. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:613–628, 2016     

Stressed but stable: canopy loss decreased species synchrony and metabolic variability in an intertidal hard-bottom community

The temporal stability of aggregate community properties depends on the dynamics of the component species. Since species growth can compensate for the decline of other species, synchronous species dynamics can maintain stability (i.e. invariability) in aggregate properties such as community abundance and metabolism. In field experiments we tested the separate and interactive effects of two stressors associated with storminess--loss of a canopy-forming species and mechanical disturbances--on species synchrony and community respiration of intertidal hard-bottom communities on Helgoland Island, NE Atlantic. Treatments consisted of regular removal of the canopy-forming seaweed Fucus serratus and a mechanical disturbance applied once at the onset of the experiment in March 2006. The level of synchrony in species abundances was assessed from estimates of species percentage cover every three months until September 2007. Experiments at two sites consistently showed that canopy loss significantly reduced species synchrony. Mechanical disturbance had neither separate nor interactive effects on species synchrony. Accordingly, in situ measurements of CO(2)-fluxes showed that canopy loss, but not mechanical disturbances, significantly reduced net primary productivity and temporal variation in community respiration during emersion periods. Our results support the idea that compensatory dynamics may stabilise aggregate properties. They further suggest that the ecological consequences of the loss of a single structurally important species may be stronger than those derived from smaller-scale mechanical disturbances in natural ecosystems.     

Gel‐free species identification using melt‐curve analysis

DNA‐based identification of organisms is an important tool in biosecurity, ecological monitoring and wildlife forensics. Current methods usually involve post‐polymerase chain reaction (PCR) manipulations (e.g. restriction digest, gel electrophoresis), which add to the expense and time required for processing samples, and may introduce error. We developed a method of species identification that uses species‐specific primers and melt‐curve analysis, and avoids post‐PCR manipulation of samples. The method was highly accurate when trialled on DNA from six large carnivore species from Tasmania, Australia. Because of its flexibility and cost‐effectiveness, this method should find wide use in many areas of applied biological science.     

An evolutionary theory of large‐scale human warfare: Group‐structured cultural selection

When humans wage war, it is not unusual for battlefields to be strewn with dead warriors. These warriors typically were men in their reproductive prime who, had they not died in battle, might have gone on to father more children. Typically, they are also genetically unrelated to one another. We know of no other animal species in which reproductively capable, genetically unrelated individuals risk their lives in this manner. Because the immense private costs borne by individual warriors create benefits that are shared widely by others in their group, warfare is a stark evolutionary puzzle that is difficult to explain. Although several scholars have posited models of the evolution of human warfare, 1 - 6 these models do not adequately explain how humans solve the problem of collective action in warfare at the evolutionarily novel scale of hundreds of genetically unrelated individuals. We propose that group‐structured cultural selection explains this phenomenon.     

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.     

Low‐level effects of inert sediments on temperate stream invertebrates

1. The delivery, entrainment and deposition of inert fine sediments are among the most significant contributors to stream and river impairment worldwide. Associated ecological effects have been observed frequently, but specific experiments to identify sensitivity and avoidance behaviour in stream organisms are few, particularly in headwaters. 2. In a field‐experiment, we added fine sand at low levels (c. 4–5 kg m^?2) to 10 m reaches of two replicate headwater streams in the Usk catchment (Wales, U.K.) over two periods (autumn and summer). Upstream reaches were used as control in a classic before‐after‐control‐impact design. Invertebrate drift and benthic composition were measured for 2 days before and 1 day after sediment impact. 3. Sediment addition significantly increased overall drift density (by 45%) and propensity (by 200%), with effects largest on the night following addition rather than immediately (i.e. within 9 h). The mayflies Baetis rhodani, B. muticus and Ecdyonurus spp., simuliid and chironomid dipterans, and helodid beetles were the strongest contributors. 4. There were no marked effects on benthic composition, but density declined in treated reaches by 30–60%, particularly in B. rhodani, Ecdyonurus spp. and Leuctra hippopus + L. moselyi. 5. All effects were consistent between both seasons and streams. 6. These data show how even low‐level, short‐term, increases in fine sediment loading to upland, stony streams can reduce overall benthic density through increased drift. We suggest that the likely cause of the delayed drift response was a change in habitat quality which prompted avoidance behaviour. Longer‐term experiments are required to assess whether these effects reduce fitness or explain the losses of some types of organisms observed recently in sediment‐impaired reaches of this and other catchments.     

Partitioning the effects of algal species identity and richness on benthic marine primary production

Influential research in terrestrial habitats indicates that several ecosystem processes are related to plant biodiversity, yet these links remain poorly studied in marine ecosystems. We conducted one field and one mesocosm experiment to quantify the relative effects of macroalgal species identity and richness on primary production in coral reef macroalgal communities off the north coast of Jamaica. We measured production as the net accumulation of algal biomass in the absence of consumers and as photosynthetic rate using oxygen probes in sealed aquaria. We used two recently developed techniques to attribute deviations in expected relative yield to components associated with species identity or diversity and then to further partition diversity effects into mechanistic components based on dominance, trait-dependent complementarity, and trait-independent complementarity. Our results indicate that algal identity had far greater effects on absolute net growth and photosynthesis than richness. The most diverse mixture of macroalgae did not outperform the most productive monoculture or the average monoculture in either measure of primary production (i.e. we did not find evidence of either transgressive or non-transgressive overyielding). Trait-independent complementarity effects were positive but dominance and trait-dependent complementarity were both negative and became stronger when richness was increased. Thus the potentially positive influence of species interactions and niche partitioning on production were negated by dominance and other negative selection effects. These results demonstrate that the counteracting influence of component effects can diminish the net richness effects on production. This could explain frequently observed weak net richness effects in other aquatic and terrestrial systems and suggests that life history tradeoffs greatly reduce the potential for ecologically relevant plant biodiversity effects on ecosystem properties.     

Analyzing the effects of species gain and loss on ecosystem function using the extended Price equation partition

In nature species richness and composition, as well as the functioning of individual species, all covary along environmental gradients, making it difficult to tease apart their effects on ecosystem function. Here we use a novel extension of the Price equation to partition the causes of functional variation between any two sites sharing at least one species in common. We use the extension to separate effects of species loss from those of species gain; species gain is analogous to migration in evolution. Previous theoretical and empirical studies of biodiversity and ecosystem function fail to distinguish effects of species gain from those of species loss, and so are conceptually incomplete. Application of this approach to data on total plant biomass along an experimental N enrichment gradient leads to novel empirical insights and reveals subtle effects. For instance, effects of species gain are non‐negligible even though enrichment leads to loss of many species and gain of few, and non‐random gain of high‐biomass species reduces the biomass of the persisting species. We also discuss the interpretation of this new approach, which provides a highly‐general partitioning of the factors affecting ecosystem function.