Cheryl J. Briggs - US grants

9420286 Murdoch This research will develop theory for the population dynamics of insect host-parasitoid interactions for species with continuous reproduction and development. It will concentrate on mechanisms that depend on either the host developmental stage that is attacked (stage-structured processes) or the physiological state of the searching parasitoid (state-dependent processes), or on both. Only recently have modeling techniques advanced to the point that these types of mechanisms can be realistically incorporated into population dynamic models. The goals of the research are (1) to get insight into the dynamical effects of processes seen in stage-structured parasitoid-host systems, (2) to obtain generality by showing how apparently different mechanisms have similar dynamical consequences, (3) to incorporate into population dynamics recent evolutionary ideas about optimal parasitoid behavior, and (4) to explain observed dynamical patterns and alert us to potential new patterns. About 10% of all metazoan species are parasitoids. They are important in many natural communities and have been used in agriculture over the past 100 years as environmentally safe, and frequently highly effective, agents for controlling insect pests. The results will give insight into the processes and mechanisms driving the dynamics of such parasitoid-host systems. In addition, they will bring together population dynamics and recent ideas on, and insights into, the evolutionary basis for parasitoid behavior.

DESCRIPTION (provided by applicant): The newly identified fungal pathogen, Batrachochytrium, has recently been implicated as causing the decline of amphibians worldwide. We aim to determine the origin of chytridiomycosis (the disease caused by Batrachochytrium), and understand how anthropogenic environmental changes influence its prevalence and spread. Our research will focus specifically on the relationship between Batrachochytrium and the mountain yellow-legged frog (Rana muscosa), a once-common amphibian in California's Sierra Nevada mountains. R. muscosa is an ideal study host as it is still common enough despite population declines to be used in experiments, and populations are strongly influenced by chytridiomycosis infection. As with animal populations throughout the world, amphibians in the Sierra Nevada are being subjected to an increasing array of anthropogenic stressors including exotic species introductions, habitat fragmentation, and chemical contaminants and these may change the prevalence and spread of disease. Using a team with expertise in pathogenic fungi, epidemiology, amphibian ecology, population genetics, and statistical and mechanistic modeling, our specific objectives are to: 1) describe the origin of Batrachochytrium to determine whether its association with amphibians in the Sierra Nevada represents an old association or a recent expansion of the fungus into previously uninfected frogs; 2) describe the effect of infection and spread on frog population dynamics using temporal resurveys of sites identified from an existing database of 4,500 water bodies in the Sierra Nevada; 3) develop statistical models to describe the effect of nonnative fish, habitat fragmentation, and windborne agricultural contaminants on the distribution of frogs and chytridiomycosis; and 4) develop detailed mechanistic models to predict the likely effects of various biological mechanisms (both natural and anthropogenic) on the incidence, spatial distribution, and persistence of chytridiomycosis, and to predict the impact of this disease on the abundance and dynamics of R. muscosa. Given the paucity of studies of disease in animal populations in the wild, the results of our study will provide important insights into disease dynamics in other systems, and aid in efforts to protect biodiversity in the face of emerging infectious diseases.

Chytridiomycosis is an emerging infectious disease of amphibians caused by the fungal pathogen, Batrachochytrium dendrobatidis ("Bd") that has been implicated as a major cause of amphibian population declines and extinctions around the world. At the current rapid rate of global Bd spread, many amphibian populations will become infected within the next decade, and this will likely result in substantial numbers of species extinctions in this already-imperiled group of organisms. In California's Sierra Nevada mountains, Bd is rapidly spreading through previously uninfected amphibian populations. The mountain yellow-legged frog (Rana muscosa) is highly susceptible to chytridiomycosis, and has experienced hundreds of recent population extinctions due to Bd infection. Interestingly, although the majority of host populations are driven extinct following the arrival of Bd, a small fraction of populations persist with the pathogen, and disease dynamics in these persistent populations are fundamentally different from those during population crashes.

The goal of this research by researchers from University of California is to understand the mechanisms leading to these contrasting disease outcomes. The investigators hypothesize that population extinction versus persistence is the result of between-population differences in (1) density-dependent disease dynamics, (2) Bd virulence, (3) frog susceptibility, or (4) environmental conditions. A model of the R. muscosa- Bd interaction that includes within-host Bd dynamics and host stage-structure will be parameterized and tested. In addition, four non-mutually exclusive hypotheses that could account for different disease outcomes will be tested using field and laboratory experiments. A functional genomics approach that utilizes complete Bd and frog genome sequences will be used to describe the genetic basis of any observed differences in Bd virulence and/or frog susceptibility. The proposed research will contribute significantly to the ability to predict outcomes of future diseases on wildlife and human populations.

In terms of broader impacts, results from the research will be directly relevant to the conservation of amphibians worldwide that are threatened by disease, and will likely be broadly used to inform conservation strategies and policy initiatives. To ensure the rapid incorporation of results into such efforts, results will be communicated to policy makers via (i) continued participation by project researchers in an R. muscosa recovery working group, (ii) annual meetings with federal and state agencies charged with R. muscosa conservation (e.g., National Park Service, U. S. Fish and Wildlife Service, California Department of Fish and Game), and (iii) consultation with non-governmental organizations developing amphibian conservation programs worldwide. The project will promote teaching and training of a diverse group of students and postdoctoral researchers in modeling, genomics, molecular genetics, statistics, and laboratory and field methods through their direct involvement in the research. To provide Bd-specific training to a wider audience, three workshops targeted at federal and state agency biologists and private consultants will be hosted during the project in collaboration with the Amphibian Specialist Group (IUCN, World Conservation Union). Sampling protocols (in text and video formats) will also be provided online in both English and Spanish.

New diseases are emerging at an increasing rate, and in numerous cases are having devastating effects on wildlife species. The amphibian chytrid fungus (Batrachochytrium dendrobatidis; Bd) causes the disease chytridiomycosis that since its emergence has resulted in the extinction or serious decline of hundreds of amphibian species worldwide. In California?s Sierra Nevada, chytridiomycosis has caused the near-extinction of the once-common mountain yellow-legged frog. During summer 2012, the largest remaining mountain yellow-legged frog population will suffer a die-off event caused by the recent arrival of Bd in the area. In mountain yellow-legged frog populations the arrival of Bd in a previously uninfected population typically results in frog population extinction, and the goal of the proposed study is to change the outcome to long-term frog population persistence. This disease intervention will take the form of a field experiment implemented during the Bd-caused frog die-off. In this experiment the effectiveness of two treatments, (1) an antifungal drug, and (2) the augmentation of antifungal bacteria that occur naturally on frog skin, will be assessed at the scale of an entire frog population. This experiment will also provide an opportunity to describe the mechanisms underlying treatment effectiveness, including the role of the frog immune system, the microbial community present on the skin of frogs, and rapid evolution in frogs. Based on results from previous laboratory and small-scale field trials it is expected that antifungal drug and bacterial augmentation treatments will increase frog survival relative to frogs that are left untreated. Results from the proposed study will have important implications for conservation efforts aimed at wildlife species worldwide that are threatened by emerging diseases (e.g., amphibians, bats, apes). The study will also provide training opportunities for undergraduate and graduate students, with every effort made to include those from underrepresented groups to the maximum extent possible.

Project Summary: Symbiotic microflora (communities of microbes living on or in multicellular organisms) are important players in the health of multicellular organisms. Variation in the microbial species inhabiting the human body has been linked to differences in susceptibility to diseases from obesity to salmonellosis. In contrast, little is known about the microflora of non-human animals or plants. This study assesses how symbiotic microflora affect disease resistance in the mountain yellow-legged frog (Rana sierrae). Previous results show that differences in the microbial communities found on the skin of these frogs are linked to variation in the severity of chytridiomycosis, a disease of the skin that results from infection by the fungal pathogen, Batrachochytrium dendrobatidis. The current study investigates the causes responsible for these patterns by experimentally manipulating the microbial communities living on the skin of R. sierrae, subsequently exposing frogs to B. dendrobatidis, and measuring resulting disease progression. This experiment addresses three questions: (1) Which factors control the identity of microbes that make up the normal microflora? (2) Do differences in the species composition of the microflora affect the ability of the frogs to resist infection by B. dendrobatidis? (3) When infection by B. dendrobatidis does occur, does it disturb the symbiotic microbial community, leading to changes in the microbial species that make up the normal microflora? Results will advance fundamental understanding of the factors shaping symbiotic microbial communities and their importance in health and disease.

Broader impacts: Amphibians worldwide are undergoing mass declines and extinctions, and chytridiomycosis is one of the greatest threats to these animals. This study is relevant to the management of chytridiomycosis and the conservation of amphibians. Laboratory and field trials are currently underway to test the use of probiotic bacteria to protect amphibians from the disease, yet basic knowledge about the symbiotic communities naturally occurring on threatened amphibians and their function in disease resistance is limited. Such knowledge will be improved by this study. In addition, this project provides a critical training opportunity for the graduate student and for an undergraduate assistant who will gain research experience through integral participation in the study.

One of the fundamental challenges in contemporary disease ecology involves understanding infection dynamics within complex communities composed of multiple hosts and multiple pathogens. Hosts in nature are exposed to a 'cocktail' of different pathogens, therefore a central question concerns how interactions between co-occurring pathogens affect disease severity and pathogen transmission in host communities. Most research to date has been focused at a single level, examining either how multiple infections influence individual host pathology or using population surveys to identify correlations in pathogen co-occurrence within a host population. This focus on single scales (i.e., within-host vs. between- host) neglects a critically important question - namely, how do pathogen interactions within hosts 'scale up' to influence between- host processes, such as transmission and disease dynamics? The primary goal of this project is to understand how interactions among three virulent pathogens at different scales of biological complexity, including within hosts, between species, and among communities, combine to influence disease dynamics in amphibians, a group of globally threatened vertebrates. This project combines cross-sectional field surveys of wetland communities with controlled laboratory and mesocosm experiments to determine (1) how amphibian pathogens co-vary in occurrence and intensity across multiple spatial scales (individual hosts, host species, wetland communities), (2) the individual and combined effects of each pathogen on host pathology and pathogen infection success, and (3) the net effects of variation in host and pathogen community structure for pathogen transmission and host-pathogen dynamics. A stochastic, simulation-based modeling framework, uniquely focused on individual hosts, will be used to interpret experimental results and link field distributions of pathogens with underlying mechanisms. This project focuses on three pathogens that have been widely implicated in causing amphibian pathology: the chytrid fungus Batrachochytrium dendrobatidis, the trematode Ribeiroia ondatrae, and the viral genus Ranavirus.

One of the fundamental challenges in contemporary disease ecology involves understanding infection dynamics within complex communities composed of multiple hosts and multiple pathogens. Hosts in nature are exposed to a 'cocktail' of different pathogens, therefore a central question concerns how interactions between co-occurring pathogens affect disease severity and pathogen transmission in host communities. Most research to date has been focused at a single level, examining either how multiple infections influence individual host pathology or using population surveys to identify correlations in pathogen co-occurrence within a host population. This focus on single scales (i.e., within-host vs. between- host) neglects a critically important question - namely, how do pathogen interactions within hosts 'scale up' to influence between- host processes, such as transmission and disease dynamics? The primary goal of this project is to understand how interactions among three virulent pathogens at different scales of biological complexity, including within hosts, between species, and among communities, combine to influence disease dynamics in amphibians, a group of globally threatened vertebrates. This project combines cross-sectional field surveys of wetland communities with controlled laboratory and mesocosm experiments to determine (1) how amphibian pathogens co-vary in occurrence and intensity across multiple spatial scales (individual hosts, host species, wetland communities), (2) the individual and combined effects of each pathogen on host pathology and pathogen infection success, and (3) the net effects of variation in host and pathogen community structure for pathogen transmission and host-pathogen dynamics. A stochastic, simulation-based modeling framework, uniquely focused on individual hosts, will be used to interpret experimental results and link field distributions of pathogens with underlying mechanisms. This project focuses on three pathogens that have been widely implicated in causing amphibian pathology: the chytrid fungus Batrachochytrium dendrobatidis, the trematode Ribeiroia ondatrae, and the viral genus Ranavirus.

Animals have communities of microbes (bacteria, viruses, fungi) living in and on their bodies. These microbial communities are referred to as symbiotic microbial communities, or the microbiome. Symbiotic microbial communities are increasingly recognized as important players in the health of humans and animals. Symbiotic microbes may be important to animal (host) health by affecting host response to disease-causing organisms (pathogens). This project aims to understand how the microbiome affects disease resistance while studying chytridiomycosis, a devastating disease of amphibians (frogs, toads and salamanders) caused by the pathogen Batrachochytrium dendrobatidis (abbreviated Bd). Bd is a fungus that infects the skin of amphibians and can cause potentially-lethal chytridiomycosis. The Sierra Nevada yellow-legged frog (Rana sierrae) is in danger of extinction and Bd is one of the most serious threats to this frog. Bd has caused massive die-offs of entire populations of R. sierrae. However, certain populations of R. sierrae appear to be somewhat resistant to lethal chytridiomycosis. Understanding why these resistant populations are able to survive despite Bd infection may be critical for efforts to conserve the species. It is possible that the skin microbiome contributes to disease resistance, however definitive evidence is lacking. This project will address three core questions: (1) To what extent does the R. sierrae skin microbiome contribute to disease resistance? (2) Does microbiome composition (i.e., the microbial species that make up the microbiome) affect the stability of the microbiome when frogs become infected with Bd? This may be important to understanding continued functionality of the microbiome when the host is threatened by infectious diseases. (3) How do host and environmental differences affect microbiome assembly? In other words, what are the forces that lead to differences in the microbiome of different frogs or populations, or within an individual frog at different times? This may reveal underlying causes that shape functional variation attributed to the microbiome, such as differences in disease resistance. In summary, this work will advance understanding of how host and environment determine microbiome composition and how this in turn may shape microbiome function and stability. Understanding of these processes is relevant to strategies for protecting threatened amphibians. More broadly, understanding how the R. sierrae microbiome interacts with Bd can provide insights into microbiome-pathogen interactions and management of infectious disease in other animals and humans.

Symbiotic microbial communities are increasingly recognized as important players in the development and health of multicellular organisms. Several studies have found that disease caused by pathogenic microbes is associated with changes in the composition of the microbiome of the host compared with the microflora of healthy individuals, but it has often been difficult to determine cause and effect: the observed correlation may indicate that particular microbiome assemblages confer disease resistance, or that pathogen infection disrupts and alters the microbiome. This project aims to understand the role of the amphibian skin-associated bacterial community (skin microbiome) in mediating resistance to the fungal pathogen Batrachochytrium dendrobatidis. The project will test if microbiome differences exist between disease-resistant and -susceptible hosts, suggestive of a protective role in nature. Importantly, this work will further clarify the causal relationship between pathogen and microbiome by testing if experimental alteration of the microbiome leads to changes in disease resistance, or if instead pathogen infection alters the microbiome. This study also aims to understand what determines the phylogenetic and functional composition of the microbiome, a question that is fundamental to understanding the root of microbiome-associated differences in disease resistance. Field surveys will be used to quantify the degree to which host genetic variation and environmental factors are associated with the phylogenetic and functional composition of the skin microbiome sampled from wild frogs, while experimental manipulations will clearly show cause and effect in these relationships. Mathematical models will be developed to identify ecological mechanisms that potentially drive variation in microbial community composition. Finally, predictive models of microbial community dynamics under conditions of disturbance (such as pathogen infection) will be developed, integrating community assembly and disease resistance concepts.

Outbreaks of emerging infectious diseases are increasingly recognized as major threats to wildlife populations. The initial invasion of a novel pathogen into a susceptible host population can cause a disease outbreak resulting in high levels of mortality and declines in population size. When this happens, natural selection can occur on both the host and pathogen populations during the disease outbreak. This can result in evolutionary changes in the host's susceptibility and tolerance to infection by the pathogen. It can also change the pathogen's ability to damage the host (virulence). These changes can in turn determine whether the host population can persist and recover from the disease. Understanding these evolutionary processes is crucial in development of conservation strategies for threatened species. This project will examine these processes for the case of a fungal pathogen that causes the disease Chytridiomycosis in frogs and salamanders. This disease has had catastrophic effects on amphibians worldwide, with numerous species extinctions documented in recent decades and many more species at risk. The researchers will investigate the patterns of evolutionary change in both the pathogen and the host (mountain yellow-legged frogs), following the invasion of the disease into hundreds of high elevation lakes in the California Sierra Nevada. This project will contribute to the understanding of the role of infectious diseases, such as Chytridiomycosis, as agents of evolutionary change in natural populations. It will provide critical information to state and federal agencies. It will also train and educate numerous, undergraduates and graduate students as well as the general public.

This research builds on data from a long-term study of the population dynamics of mountain yellow-legged frogs (Rana sierrae and Rana muscosa) in the complex landscape of the California Sierra Nevada, and the impacts of Batrachochytrium dendrobatidis (Bd), as it has invaded and spread through hundreds of frog populations. In most cases, invasion of Bd results in outbreaks of the disease Chytridiomycosis, rapid frog population declines, and local extinctions. In some cases however long-term persistence of frog populations occurs with Bd in an enzootic state in which the impact of the pathogen is greatly reduced. The research will make use of recent advances in molecular approaches, and the extensive dataset and archive of samples from the R. sierrae/R. muscosa - Bd system, to investigate how populations of both host and pathogen change during the transition from pre-pathogen arrival, to disease outbreak, to enzootic disease, to potential recovery of the pre-disease host population abundances. This dataset will be used to investigate the genetic basis for differences in host resistance/tolerance and pathogen virulence. Cutting-edge genomic analysis of existing swab samples will be combined with continued surveys of field populations to identify new disease outbreaks and describe the transition from outbreak to enzootic state, collection of Bd cultures and frog mucosal samples from field populations, and laboratory experiments on Bd virulence and frog

Many fungal pathogens have broad host ranges, long-lived environmental stages, and the potential for saprotrophic growth. New models are needed for this type of pathogen, in order to improve our ability to understand the dynamics and impacts of this unique, diverse, and abundant group of pathogens. The overall aim of this project is to expand our understanding of the dynamics of emerging fungal pathogens both amongst and outside of their hosts. Laboratory and field experiments and field surveys will be conducted to develop and fit disease models, utilizing the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), as the primary model system. Recent evidence that Bd can infect a wide diversity of organisms (in addition to amphibians), and that Bd has the ability to form biofilms (which may enhance its potential for environmental persistence), makes this an ideal model system for this project. Fungal disease models will be developed and parameterized, including generalist pathogens, external pathogen reservoirs (including the possibility of incorporation of the pathogen into biofilms), and the potential for saprotrophic pathogen growth. The models will be used to explore the implications of these features of fungal pathogens on pathogen prevalence and disease severity in target host species, in the both the amphibian/Bd system and in other emerging fungal pathogen systems. Specifically, the research team will (1) perform an in-depth analysis of alternative hosts and environmental reservoirs where Bd may persist outside of the host, (2) test experimentally the role of these alternative hosts and environmental reservoirs on survival and reproduction of Bd, persistence of Bd in the environment, and in transmission of the pathogen to amphibians, (3) test how Bd biofilm formation affects Bd persistence and reproduction, (4) explore how Bd biofilms persist in extreme environments (i.e. temperatures) and if this affects the infectiousness of Bd using novel approaches (metagenomics, meta-transcriptomics, meta-proteomics), (5) improve the fungal-based disease model to include an ecosystem-centric approach using Bd as a case study, and (6) create an emerging fungal database, conduct a metanalysis, and fit our disease models to other emerging fungal diseases.