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Biological invasions are a major threat to biodiversity and as such understanding their impacts is a research priority. Ecological networks provide a valuable tool to explore such impacts at the community level, and can be particularly insightful for planning and monitoring biocontrol programmes, including the potential for their seldom evaluated indirect non-target effects. Acacia longifolia is among the worst invasive species in Portugal, and has been recently targeted for biocontrol by a highly specific gall-wasp. Here we use an ambitious replicated network approach to: (1) identify the mechanisms by which direct and indirect impacts of A. longifolia can cascade from plants to higher trophic levels, including gallers, their parasitoids and inquilines; (2) reveal the structure of the interaction networks between plants, gallers, parasitoids and inquilines before the biocontrol; and (3) explore the potential for indirect interactions among gallers, including those established with the biocontrol agent, via apparent competition. Over a 15-month period, we collected 31,737 galls from native plants and identified all emerging insects, quantifying the interactions between 219 plant-, 49 galler-, 65 parasitoid- and 87 inquiline-species—one of the largest ecological networks to date. No galls were found on any of the 16 alien plant species. Invasion by A. longifolia caused an alarming simplification of plant communities, with cascading effects to higher trophic levels, namely: a decline of overall gall biomass, and on the richness, abundance and biomass of galler insects, their parasitoids, and inquilines. Correspondingly, we detected a significant decline in the richness of interactions between plants and galls. The invasion tended to increase overall interaction evenness by promoting the local extinction of the native plants that sustained more gall species. However, highly idiosyncratic responses hindered the detection of further consistent changes in network topology. Predictions of indirect effects of the biocontrol on native gallers via apparent competition ranged from negligible to highly significant. Such scenarios are incredibly hard to predict, but even if there are risks of indirect effects it is critical to weigh them carefully against the consequences of inaction and invasive species spread.

A large array of species distribution model (SDM) approaches has been developed for explaining and predicting the occurrences of individual species or species assemblages. Given the wealth of existing models, it is unclear which models perform best for interpolation or extrapolation of existing data sets, particularly when one is concerned with species assemblages. We compared the predictive performance of 33 variants of 15 widely applied and recently emerged SDMs in the context of multispecies data, including both joint SDMs that model multiple species together, and stacked SDMs that model each species individually combining the predictions afterward. We offer a comprehensive evaluation of these SDM approaches by examining their performance in predicting withheld empirical validation data of different sizes representing five different taxonomic groups, and for prediction tasks related to both interpolation and extrapolation. We measure predictive performance by 12 measures of accuracy, discrimination power, calibration, and precision of predictions, for the biological levels of species occurrence, species richness, and community composition. Our results show large variation among the models in their predictive performance, especially for communities comprising many species that are rare. The results do not reveal any major trade‐offs among measures of model performance; the same models performed generally well in terms of accuracy, discrimination, and calibration, and for the biological levels of individual species, species richness, and community composition. In contrast, the models that gave the most precise predictions were not well calibrated, suggesting that poorly performing models can make overconfident predictions. However, none of the models performed well for all prediction tasks. As a general strategy, we therefore propose that researchers fit a small set of models showing complementary performance, and then apply a cross‐validation procedure involving separate data to establish which of these models performs best for the goal of the study.

Background Host–pathogen interactions are important in a wide range of research fields. Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions. However, the validity of this method remains unclear because of the various explanations presented and the influence of potentially confounding factors that have thus far been neglected. Results We re-evaluated the importance of the reverse ecology method for evaluating host–pathogen interactions while statistically controlling for confounding effects using oxygen requirement, genome, metabolic network, and phylogeny data. Our data analyses showed that host–pathogen interactions were more strongly influenced by genome size, primary network parameters (e.g., number of edges), oxygen requirement, and phylogeny than the reserve ecology-based measures. Conclusion These results indicate the limitations of the reverse ecology method; however, they do not discount the importance of adopting reverse ecology approaches altogether. Rather, we highlight the need for developing more suitable methods for inferring host–pathogen interactions and conducting more careful examinations of the relationships between metabolic networks and host–pathogen interactions.

Dietary specialization in insect herbivores has long been hypothesized to predict tolerance of plant defences, with more specialized herbivores being highly tolerant of and sometimes sequestering plant secondary compounds. Plant variation in secondary compounds should thus play an important and predictable role in shaping the performance and distribution of insect communities. We compared the performance of four naturally co‐occurring aphid species on twenty genotypes of the common milkweed Asclepias syriaca. Genotypes of milkweed consistently differed in functional traits, including concentrations of toxic cardenolides, while the diet breadths of the four aphids ranged from broadly generalized to monophagous. The two more generalized species had the highest population growth rate overall, while growth rates decreased with increasing specialization. In contrast, honeydew exudation as a measure of phloem consumption increased with specialization; thus, resource‐use efficiency was lower in specialist aphids. The two more generalized aphids grew best on genotypes with the highest plant growth rate (as an approximation for resource availability), while specialist aphids were not affected by plant growth. All four species contained apolar cardenolides in their bodies and excreted polar cardenolides, but only the most specialized aphid Myzocallis asclepiadis was negatively affected by increasing cardenolide concentrations of the host plant. Sequestration of cardenolides increased with diet specialization, with M. asclepiadis accumulating twice as much as any other species, perhaps explaining its susceptibility to plant cardenolides. Heritable plant traits differentially impacted co‐occurring insect herbivores within the same guild. Generalist aphids were susceptible to variation in plant vigour but not defensive compounds. Increased host specialization resulted in lower resource‐use efficiency, increased phloem throughput and ultimately higher cardenolide sequestration. Variation in these traits is thus likely to determine the relative distribution of generalist and specialist herbivores on plants in natural communities.

Abstract Streptococcus pneumoniae and Haemophilus influenzae are both commensals of the human nasopharynx with an ability to migrate to other niches within the human body to cause various diseases of the upper respiratory tract such as pneumonia, otitis media and bronchitis. They have long been detected together in a multispecies biofilm in infected tissue. However, an understanding of their interplay is a recent field of study, and while over recent years, there has been research that has identified many specific elements important in these biofilms, to date, it remains questionable whether the relationship between H. influenzae and S. pneumoniae is competitive or cooperative. Additionally, the factors that govern the nature of the interspecies interaction are still undefined. This review aims to collate the information that has emerged on the cocolonization and co-infection by S. pneumoniae and nontypeable H. influenzae (NTHi) and their formation of a multispecies biofilm. Bacterial opportunists including Haemophilus influenzae and Streptococcus pneumoniae frequently reside in the nasopharynx of healthy children from where it can migrate to cause severe infections involving lungs middle ear and the brain. It is now clear that biofilms promote bacterial persistence during many of these infections. This MiniReview nicely summarizes a large amount of work on Haemophilus and pneumococcus in biofilms alone and in co-culture.

1. Certain non-native invaders reduce the species diversity and alter the structure of natural communities by displacing native species with differing life histories, successional roles or resource requirements. Few studies have tested the potential for these 'strong invaders' to exert multiple mechanisms of control on natives that differ in these traits. 2. We assessed the mechanisms by which bohemian knotweed (Polygonum × bohemicum) regulates seedling growth and survival among early-, mid- and late-seral tree species in a riparian forest ecosystem in western North America. We used general linear mixed models to compare seedling performance (survival, height and diameter growth, biomass allocation and ectomycorrhizal colonization of root systems) over two growing seasons in paired experimental plots from which knotweed was either removed or retained (controls). Seedling performance was assessed relative to the effects of knotweed on light and soil resources and the traits of the native species. 3. Results from paired t-tests suggest that knotweed had a significant effect on light availability ( > 85% reduction), but small, mostly non-significant effects on measured soil properties. Knotweed imposed strong controls on growth and survival of all three tree species. The apparent mechanisms of interaction varied in a manner consistent with species' ecophysiologies. Reduced survival of early- and mid-seral species was correlated with light limitation beneath knotweed (≤ 7% of ambient levels): light transmittance was significantly higher (79%) above surviving seedlings. Knotweed also exerted strong controls on the late-seral species, reducing survival by 24% and height and diameter growth by 91—122% and 37—55%. These effects were not correlated with reductions in light. Instead, in the presence of knotweed, ectomycorrhizal colonization was significantly reduced (64%) and root/shoot ratio was significantly increased, suggesting a disruption of soil mutualisms. 4. Synthesis. We demonstrate that strong invaders can displace co-occurring native species through multiple mechanisms that are consistent with the functional traits of native species. To our knowledge, this is the first study to relate community-level impacts of an invader to the combined effects of resource exploitation and interference of below-ground mutualisms. Where invaders have the ability to displace early- to late-seral dominants, the consequences for community structure and ecosystem functioning can be profound.

Biotic signalling refers to species or phylogenetic-clade-specific signals that elicit adaptive and acceptable responses within and among organisms. It is not only the molecular basis of the ecological relationships among different species, such as parasitism, symbiosis and predation, but also serves as ideal targets that can be used to manipulate these ecological relationships. This concept was proposed by a group of scientists from the Chinese Academy of Sciences (CAS) and actively pursued in a five-year research project in 2014 funded by the CAS ($40 million), entitled ‘Decoding biotic interactions and mechanism for target management of agricultural pests'. The multi-disciplinary project aimed at a systematic investigation of the intra-species and inter-species and interactions via biotic signalling, with the ultimate goal being the development of novel methods to manage the pest insects and diseases. We hereby propose a topic ‘Biotic signalling sheds light on smart pest control’ as a theme issue for the Philosophical Transactions of the Royal Society B . It contains a total of 18 reviews and research articles under the topic of signalling manipulation for pest management. Unravelling these complex interactions among plants, microbial pathogens and insects holds promise for developing novel strategies to protect crop plants without compromising agricultural productivity and environmental health. This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.

Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphapro teobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.

Summary Droughts are a rising concern for terrestrial ecosystems, particularly for forests where drought‐induced reductions in tree growth and survival are reported. Biodiversity has long been acknowledged as an important component modulating ecosystem functions, including mitigating their vulnerability to climate‐related stresses. Yet the impact of tree diversity on forest vulnerability to drought is unclear. In this review, consistent mechanisms are identified by which tree diversity could reduce vulnerability to drought and emerging evidence is revealed that tree diversity is not systematically positively related to drought resistance in forests. A path is suggested to further increase our knowledge on this subject in the face of climate change, proposing standardization of methods to quantitatively establish diversity impacts on the drought resistance of forests. Charlotte Grossiord is an honourably mentioned finalist of the 2018 New Phytologist Tansley Medal competition for excellence in plant science. See Lennon & Dolan, in this issue of New Phytologist (2020, 228: 5) for more details.

Phenology—the timing of biological events—is highly sensitive to climate change. However, our general understanding of how phenology responds to climate change is based almost solely on incomplete assessments of phenology (such as first date of flowering) rather than on entire phenological distributions. Using a uniquely comprehensive 39-y flowering phenology dataset from the Colorado Rocky Mountains that contains more than 2 million flower counts, we reveal a diversity of species-level phenological shifts that bring into question the accuracy of previous estimates of long-term phenological change. For 60 species, we show that first, peak, and last flowering rarely shift uniformly and instead usually shift independently of one another, resulting in a diversity of phenological changes through time. Shifts in the timing of first flowering on average overestimate the magnitude of shifts in the timing of peak flowering, fail to predict shifts in the timing of last flowering, and underrepresent the number of species changing phenology in this plant community. Ultimately, this diversity of species-level phenological shifts contributes to altered coflowering patterns within the community, a redistribution of floral abundance across the season, and an expansion of the flowering season by more than I mo during the course of our study period. These results demonstrate the substantial reshaping of ecological communities that can be attributed to shifts in phenology.