Explore the vast range of titles available.

Symbiotic microbial communities may interact with infectious pathogens sharing a common host. The microbiome may limit pathogen infection or, conversely, an invading pathogen can disturb the microbiome. Documentation of such relationships during naturally occurring disease outbreaks is rare, and identifying causal links from field observations is difficult. This study documented the effects of an amphibian skin pathogen of global conservation concern [the chytrid fungus Batrachochytrium dendrobatidis (Bd)] on the skin-associated bacterial microbiome of the endangered frog, Rana sierrae , using a combination of population surveys and laboratory experiments. We examined covariation of pathogen infection and bacterial microbiome composition in wild frogs, demonstrating a strong and consistent correlation between Bd infection load and bacterial community composition in multiple R. sierrae populations. Despite the correlation between Bd infection load and bacterial community composition, we observed 100% mortality of postmetamorphic frogs during a Bd epizootic, suggesting that the relationship between Bd and bacterial communities was not linked to variation in resistance to mortal disease and that Bd infection altered bacterial communities. In a controlled experiment, Bd infection significantly altered the R. sierrae microbiome, demonstrating a causal relationship. The response of microbial communities to Bd infection was remarkably consistent: Several bacterial taxa showed the same response to Bd infection across multiple field populations and the laboratory experiment, indicating a somewhat predictable interaction between Bd and the microbiome. The laboratory experiment demonstrates that Bd infection causes changes to amphibian skin bacterial communities, whereas the laboratory and field results together strongly support Bd disturbance as a driver of bacterial community change during natural disease dynamics. Significance Animals are inhabited by communities of microbes (the microbiome) that potentially interact with pathogens. Detailed studies of microbiome–pathogen interactions in nature are rare, and even when correlations are observed, determining causal relationships is challenging. The microbiome–pathogen relationship is of particular interest in the case of Batrachochytrium dendrobatidis , a chytrid fungus that infects the skin of amphibians and is causing amphibian declines worldwide. We documented a strong correlation between pathogen load and skin bacterial communities of frogs during natural disease episodes. We then showed experimentally that infection alters the microbiome, with similar bacteria responding in both laboratory and field. The results indicate that the chytrid pathogen drives changes in the amphibian skin microbiome during disease episodes in wild frogs.

Pathogenic fungi are increasingly contributing to the global emerging disease burden, threatening biodiversity and imposing increasing costs on ecosystem health, hence steps must be taken to tighten biosecurity worldwide to reduce the rate of fungal disease emergence. The threat from emerging pathogenic fungi Fungal infections have caused widespread damage in crops and dramatic decline in populations of amphibians and bats. In recent years newly emerged pathogenic fungi have been reported in corals, bees and many plant species. In this Review, Matthew Fisher and colleagues warn that human activity is intensifying fungal-disease dispersal by modifying natural ecosystems and creating new opportunities for evolution. Unless steps are taken to reduce the risk of these infectious diseases spreading globally, the authors suggest, fungal infections will cause increasing attrition of biodiversity, with wider implications for human and ecosystem health. The authors' recommendations include better monitoring of emerging diseases, stringent biosecurity controls on international trade and intensified research on the interactions between hosts, pathogens and the environment. The past two decades have seen an increasing number of virulent infectious diseases in natural populations and managed landscapes. In both animals and plants, an unprecedented number of fungal and fungal-like diseases have recently caused some of the most severe die-offs and extinctions ever witnessed in wild species, and are jeopardizing food security. Human activity is intensifying fungal disease dispersal by modifying natural environments and thus creating new opportunities for evolution. We argue that nascent fungal infections will cause increasing attrition of biodiversity, with wider implications for human and ecosystem health, unless steps are taken to tighten biosecurity worldwide.

Despite often violent fluctuations in nature, species extinction is rare. California red scale, a potentially devastating pest of citrus, has been suppressed for fifty years in California to extremely low yet stable densities by its controlling parasitoid. Some larch budmoth populations undergo extreme cycles; others never cycle. In Consumer-Resource Dynamics, William Murdoch, Cherie Briggs, and Roger Nisbet use these and numerous other biological examples to lay the groundwork for a unifying theory applicable to predator-prey, parasitoid-host, and other consumer-resource interactions. Throughout, the focus is on how the properties of real organisms affect population dynamics. The core of the book synthesizes and extends the authors' own models involving insect parasitoids and their hosts, and explores in depth how consumer species compete for a dynamic resource. The emerging general consumer-resource theory accounts for how consumers respond to differences among individuals in the resource population. From here the authors move to other models of consumer-resource dynamics and population dynamics in general. Consideration of empirical examples, key concepts, and a necessary review of simple models is followed by examination of spatial processes affecting dynamics, and of implications for biological control of pest organisms. The book establishes the coherence and broad applicability of consumer-resource theory and connects it to single-species dynamics. It closes by stressing the theory's value as a hierarchy of models that allows both generality and testability in the field.

Epidemiological theory generally suggests that pathogens will not cause host extinctions because the pathogen should fade out when the host population is driven below some threshold density. An emerging infectious disease, chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd) is directly linked to the recent extinction or serious decline of hundreds of amphibian species. Despite continued spread of this pathogen into uninfected areas, the dynamics of the host-pathogen interaction remain unknown. We use fine-scale spatiotemporal data to describe (i) the invasion and spread of Bd through three lake basins, each containing multiple populations of the mountain yellow-legged frog, and (ii) the accompanying host-pathogen dynamics. Despite intensive sampling, Bd was not detected on frogs in study basins until just before epidemics began. Following Bd arrival in a basin, the disease spread to neighboring populations at [almost equal to]700 m/yr in a wave-like pattern until all populations were infected. Within a population, infection prevalence rapidly reached 100% and infection intensity on individual frogs increased in parallel. Frog mass mortality began only when infection intensity reached a critical threshold and repeatedly led to extinction of populations. Our results indicate that the high growth rate and virulence of Bd allow the near-simultaneous infection and buildup of high infection intensities in all host individuals; subsequent host population crashes therefore occur before Bd is limited by density-dependent factors. Preventing infection intensities in host populations from reaching this threshold could provide an effective strategy to avoid the extinction of susceptible amphibian species in the wild.

Chytridiomycosis, the disease caused by the chytrid fungus, Batrachochytrium dendrobatidis (Bd), has contributed to amphibian population declines and extinctions worldwide. The impact of this pathogen, however, varies markedly among amphibian species and populations. Following invasion into some areas of California's Sierra Nevada, Bd leads to rapid declines and local extinctions of frog populations (Rana muscosa, R. sierrae). In other areas, infected populations of the same frog species have declined but persisted at low host densities for many years. We present results of a 5-year study showing that infected adult frogs in persistent populations have low fungal loads, are surviving between years, and frequently lose and regain the infection. Here we put forward the hypothesis that fungal load dynamics can explain the different population-level outcomes of Bd observed in different areas of the Sierra Nevada and possibly throughout the world. We develop a model that incorporates the biological details of the Bd-host interaction. Importantly, model results suggest that host persistence versus extinction does not require differences in host susceptibility, pathogen virulence, or environmental conditions, and may be just epidemic and endemic population dynamics of the same host-pathogen system. The different disease outcomes seen in natural populations may result solely from density-dependent host-pathogen dynamics. The model also shows that persistence of Bd is enhanced by the long-lived tadpole stage that characterize these two frog species, and by nonhost Bd reservoirs.

Tropical reefs often undergo acute disturbances that result in landscape-scale loss of coral. Due to increasing threats to coral reefs from climate change and anthropogenic perturbations, it is critical to understand mechanisms that drive recovery of these ecosystems. We explored this issue on the fore reef of Moorea, French Polynesia, following a crown-of-thorns seastar outbreak and cyclone that dramatically reduced cover of coral. During the five-years following the disturbances, the rate of re-establishment of coral cover differed systematically around the triangular-shaped island; coral cover returned most rapidly at sites where the least amount of live coral remained after the disturbances. Although sites differed greatly in the rate of return of coral, all showed at least some evidence of re-assembly to their pre-disturbance community structure in terms of relative abundance of coral taxa and other benthic space holders. The primary driver of spatial variation in recovery was recruitment of sexually-produced corals; subsequent growth and survivorship were less important in shaping the spatial pattern. Our findings suggest that, although the coral community has been resilient, some areas are unlikely to attain the coral cover and taxonomic structure they had prior to the most recent disturbances before the advent of another landscape-scale perturbation.

The fungal pathogen Batrachochytrium dendrobatidis (Bd) causes the disease amphibian chytridiomycosis, which has contributed to population declines in many species of amphibians throughout the world. Previous observational studies have shown that nematodes, waterfowl, lizards, other dipterans, and crayfish have properties which may allow them to harbor and spread Bd; therefore, we sought to determine the carrier capabilities of invertebrates to a further extent in a laboratory setting. We use the insect Drosophila melanogaster as a model organism to quantify the potential relationship between insects and Bd. Our findings show that D. melanogaster can test positive for Bd for up to five days post-exposure and can transmit Bd to conspecifics without suffering mortality. Insects of various types interact with the amphibian habitat and amphibians themselves, making this a potentially important route of transmission between amphibians and of dispersal across the environment.

Coral reef systems can undergo rapid transitions from coral-dominated to macroalgae-dominated states following disturbances, and models indicate that these may sometimes represent shifts between alternative stable states. While several mechanisms may lead to alternate stable states on coral reefs, only a few have been investigated theoretically. We explore a model that illustrates that reduced vulnerability of macroalgae to herbivory as macroalgae grow and mature could be an important mechanism: when macroalgae are palatable to herbivores as juveniles, but resistant as adults, coral-dominated and algae-dominated states are bistable across a wide range of parameter space. We compare two approaches to global sensitivity analysis to rank the relative importance of the model parameters in determining the presence and magnitude of alternative stable states, and find that the two most influential parameters are the death rate of coral and the rate of maturation of algae out of the vulnerable stage. The Random Forest approach for global sensitivity analysis, recently adopted by ecologists, provides a more efficient method for ranking the relative importance of parameters than a variance-based approach that has been used frequently by computer scientists and engineers. Our results suggest that managing reefs to reduce chronic stressors that cause coral mortality and/or enhance the growth rates of algae can help prevent reefs from becoming locked in a macroalgae-dominated state.

Understanding the evolutionary history of microbial pathogens is critical for mitigating the impacts of emerging infectious diseases on economically and ecologically important host species. We used a genome resequencing approach to resolve the evolutionary history of an important microbial pathogen, the chytrid Batrachochytrium dendrobatidis (Bd), which has been implicated in amphibian declines worldwide. We sequenced the genomes of 29 isolates of Bd from around the world, with an emphasis on North, Central, and South America because of the devastating effect that Bd has had on amphibian populations in the New World. We found a substantial amount of evolutionary complexity in Bd with deep phylogenetic diversity that predates observed global amphibian declines. By investigating the entire genome, we found that even the most recently evolved Bd clade (termed the global panzootic lineage) contained more genetic variation than previously reported. We also found dramatic differences among isolates and among genomic regions in chromosomal copy number and patterns of heterozygosity, suggesting complex and heterogeneous genome dynamics. Finally, we report evidence for selection acting on the Bd genome, supporting the hypothesis that protease genes are important in evolutionary transitions in this group. Bd is considered an emerging pathogen because of its recent effects on amphibians, but our data indicate that it has a complex evolutionary history that predates recent disease outbreaks. Therefore, it is important to consider the contemporary effects of Bd in a broader evolutionary context and identify specific mechanisms that may have led to shifts in virulence in this system.

Changing climate has driven shifts in species phenology, influencing a range of ecological interactions from plant–pollinator to consumer–resource. Phenological changes in host–parasite systems have implications for pathogen transmission dynamics. The seasonal timing, or phenology, of peak larval and nymphal tick abundance is an important driver of tick‐borne pathogen prevalence through its effect on cohort‐to‐cohort transmission. Tick phenology is tightly linked to climatic factors such as temperature and humidity. Thus, variation in climate within and across regions could lead to differences in phenological patterns. These differences may explain regional variation in tick‐borne pathogen prevalence of the Lyme disease‐causing Borrelia bacteria in vector populations in the United States. For example, one factor thought to contribute to high Lyme disease prevalence in ticks in the eastern United States is the asynchronous phenology of ticks there, where potentially infected nymphal ticks emerge earlier in the season than uninfected larval ticks. This allows the infected nymphal ticks to transmit the pathogen to hosts that are subsequently fed upon by the next generation of larval ticks. In contrast, in the western United States where Lyme disease prevalence is generally much lower, tick phenology is thought to be more synchronous with uninfected larvae emerging slightly before, or at the same time as, potentially infected nymphs, reducing horizontal transmission potential. Sampling larval and nymphal ticks, and their host‐feeding phenology, both across large spatial gradients and through time, is challenging, which hampers attempts to conduct detailed studies of phenology to link it with pathogen prevalence. In this study, we demonstrate through intensive within‐season sampling that the relative abundance and seasonality of larval and nymphal ticks are highly variable along a latitudinal gradient and likely reflect the variable climate in the far western United States with potential consequences for pathogen transmission. We find that feeding patterns were variable and synchronous feeding of juvenile ticks on key blood meal hosts was associated with mean temperature. By characterizing within‐season phenological patterns of the Lyme disease vector throughout a climatically heterogeneous region, we can begin to identify areas with high potential for tick‐borne disease risk and underlying mechanisms at a finer scale.