Ignazio Carbone

An important challenge for disease ecology is understanding how epidemics are driven by seasonality. As patterns of seasonality may shift in the future, this challenge is increasingly urgent. Predicting effects of seasonality on epidemics may require an understanding of the mechanisms linking them. For many parasites, a key mechanism may be ecological interactions, such as competition with other species of parasites. The strength of parasite interactions within host individuals and the timing of seasonal onset of parasite transmission (i.e. parasite phenology) can both link seasonality to epidemics. While strong tests of mechanism can be provided by experiments, the operation of these mechanisms has not been tested using experiments conducted in the field. The proposed project will advance our mechanistic understanding by leveraging an experimentally tractable system, fungal parasites infecting leaves of the widespread and agriculturally important grass species tall fescue, to investigate the roles of parasite interaction strength and parasite phenology in seasonally driven epidemics. Building on our work documenting strong interactions between parasite species that each have seasonal epidemics but that differ in phenology, we propose to develop a dynamical model that can incorporate both parasite phenology and seasonal variation in interaction strength, and use that model to integrate two field experiments and one large-scale field survey: ��� Aim 1: Experimentally quantify seasonal variation in parasite interaction strength within host individuals. ��� Aim 2: Quantify the effects of advancing parasite phenology on the size of experimental epidemics. ��� Aim 3: Quantify parasite epidemics on a geographic-scale elevational gradient in seasonality.

In the coming century, agricultural crop production and with it, civilization, will face great challenges. Two billion additional people will need to be fed by 2050, and together with the rise in global disposable income, the demand for food will increase by up to 50%. Despite constant increase in crop productivity since the first green revolution, the current rate of improvement is not sufficient to meet these needs. Filling this critical food security gap requires new approaches and initiatives that we do not currently use, which will lead to the next green revolution. Furthermore, any solutions to this food security challenge must be safe, sustainable and effective in the face of climate change and environmental pressures that will make crops more vulnerable. challenges of a changing world. From the strategic discussions begun at the 2018 Crop Resiliency Workshop and subsequent virtual and in-person project planning meetings held throughout the spring and early summer, three stand-alone, yet highly synergistic projects that aim to transform global agriculture and food security have been developed that will be briefly described in turn: 1) MATRIX, 2) InRoot, and 3) INTERACT (Figure 1). MATRIX (Microbiome Assisted Triticum Resilience In X-dimensions) will develop a scalable system-based strategy to harness the functional potential of plant microbiomes for improving crop resilience by focusing on experimental analyses and deep-learning modelling of the above-ground plant-associated microbial community (phyllosphere microbiome) of wheat (Triticum aestivum), one of the most important cereal food crops worldwide. Genomics, metabolomics, and phenomics will provide foundational data to build mechanistic models. These models will be iteratively tested with theoretical simulations and experimental validation to identify phyllosphere community members that are critical for productivity. Success for MATRIX will be yielding microbiome-assisted wheat culturing practice, resilient to ever-changing environmental stresses and resource limitations. InRoot (Molecular Mechanisms and Dynamics of Plant-Microbe Interactions at the Root-Soil Interface) will provide knowledge and tools for science-based development of new crop varieties and associated microbial interventions that will improve productivity, reduce the need for fertilizers and pesticides, and alleviate negative environmental impact. These critically important advances will be achieved by disentangling the effects of climate and soil type from the impact of root-microbe interactions, identifying key bacterial taxa governing the establishment of host-driven microbial networks in the rhizosphere, defining the plant genetic components that control infection of plant roots by ubiquitous and host-specific endophytes, understanding molecular mechanisms integrating root-microbe interactions into whole-plant physiology, and predicting plant performance as a function of plant and microbiota genotypes by building multiscale models. INTERACT will provide much needed insight into rhizosphere ecology with a goal to provide diagnostic chemical/biological signatures for agro-system stability. With this knowledge, we can rationally and strategically manipulate plant-associated microbial communities to support high plant productivity across challenging climatic and stress scenarios. These critical advances in our understanding of rhizosphere community structure and the chemical landscape that influences its formation and function will be achieved by using genomics, transcriptomics, metabolomics, in-field and greenhouse plant phenotyping, and network analysis/model construction for evaluating rhizosphere interactions for both wheat and the increasingly globally significant food, feed and energy crop, sorghum.

Our Vision is to provide a science-based platform for new agricultural practices enabling plant producers to manage their production ecosystems in a resource-efficient way with limited environmental footprint based on an in-depth understanding of key ecological functions in the soilplant interphase (rhizosphere). Our Motivation is to address the major research gaps in deciphering the complexity of microbemicrobe and microbe-plant interactions in the rhizosphere, and thereby provide new conceptual understanding on how these interactions influence plant performance. This motivation is timely due to recent developments in methodology and will enable us to provide the knowledge-base for unlocking the potential of the soil rhizobiota (microbes living on in the rhizosphere) as the key to development of sustainable and resilient plant production systems. Our Focus is to identify and quantify main determinants of microbial interactions and networks in the rhizosphere leading toward a resilient ecological unit, and thus reveal the importance and potential of microbial interactions and functions in the rhizosphere. The proposed research will take advantage of a multi-faceted, integrative and cross-disciplinary approach, which is fundamental for 1) achieving a deep understanding of the chemical and biological factors that control microbe-microbe and plantmicrobe interactions and functions under natural soil conditions, 2) establishing improved predictive models for microbial interactions in soil and 3) exploiting the microbial potential in plant-soil production systems for the benefit of plant growth and resilience. INTERACT will decode these important, yet often transient, microbial interactions in the complex soil matrix, in relation to soil biogeochemical status, water stress as well as pathogen attack, and the impact of these interactions on plant performance. We will challenge the currently accepted view among scientists that plants are the primary drivers for rhizobiome assembly. Hence, we will determine whether in fact soil microbes, largely through chemical communication and signaling, play a greater role in rhizobiome development and function than has been previously appreciated. INTERACT will provide critical insight into the rhizosphere ecology, as a basis for actively influencing the assembly of effective rhizosphere communities to support plant health and productivity, either through biotechnological or agronomic approaches.

Overview: As a unifying feature of living things, symbioses shape the phenotypes on which selection acts, influencing the form and function of biological units across the tree of life. Although all major biomes support and are influenced by symbioses, extreme environments are crucibles for symbiotic evolution, where strong selection can engage locally endemic partners with unique genomic architecture and potent functional roles. In turn, when such extreme environments undergo pervasive environmental change, resulting shifts in associations provide a real-time lens for characterizing novel and changing biodiversity of little-known symbiotic groups, defining the parameters of their ranges and community drivers, and exploring the factors that define important and complex biological affiliations. We propose to test hypotheses regarding shifts in the diversity, composition, and distributions of symbiotic fungi relevant to iconic plants and lichens across one of earth������������������s most drastically changing extreme environments, the terrestrial Arctic. Intellectual Merit: The over-arching goal of our proposed work is to document the biodiversity and characterize the temporal and spatial dynamics of little known but hyperdiverse fungal symbionts (endophytes) associated with plants and lichens across broad temporal and spatial scales in the vanishing biological landscape of the North American Arctic. In Aim 1 we will use newly validated methods that we have developed to screen herbarium specimens of preserved plants and lichens for endophytic fungi. Herbarium specimens represent snapshots of symbiotic communities and with careful quality control, we have successfully generated reliable data regarding endophyte diversity and composition via next-generation sequencing of dried plants and lichens collected well over 100 years ago. We have obtained permission to survey selected specimens of plants and lichens from 15 partner herbaria, with documented localities of origin, sufficient material to sample, and known collection dates up to 135 years ago. We will use those localities to define our survey sites for Aim 2, in which we will survey endophytes systematically via new field collections in the same host species and localities, establishing transects across all major Arctic subzones in both eastern and western North America. Here we will use culture-free and culture-based approaches to establish the current ranges, host use, diversity, and composition of endophyte communities, and compare them with historical data from herbarium specimens. In Aim 3 we will we will extend and share tools for biodiversity informatics to accelerate discovery and systematic treatments for fungal diversity from culture-based and next-generation studies. In doing so we will deliver robust multilocus reference trees for the most species-rich fungal phylum, Ascomycota, to the community; integrate genome-scale, ecological, and phylogenetic data to describe new taxa, especially in two clades (Coniochaeta and Daldinia) that are hyperdiverse in preliminary studies; and release novel biodiversity informatics tools for the community. Broader Impacts: The project will elucidate the dynamics and importance of symbioses while contributing new data, metadata, specimens, and tools for mycology, lichenology, botany, ecology, evolutionary biology, systematics, and bioinformatics relevant to the Arctic and beyond. Aims will be achieved via robust data-management and open-source data-sharing plans, facilitated by online portals and partnerships for sharing all products. The project will yield a large, publicly accessible, and novel culture library of endophytes (~13,500 cultures; >3000 fungal species); rapid online release of curated environmental and molecular���������������data (barcode, multilocus, ddRADseq, RNAseq, phenotypic, functional, and taxonomic); deposition of lichen and plant specimens to strengthen holdings at three US herbaria and multiple partner institutions; and the development and sharing���������������of new tools, protocols, and data to accelerate biodiversity discovery and

Plant disease outbreaks are increasing and threaten food security for the vulnerable in many areas of the world and in the US. Climate change is exacerbating weather events that affect crop production and food access for vulnerable areas. Now a global human pandemic is threatening the health of millions on our planet. A stable, nutritious food supply will be needed to lift people out of poverty and improve health outcomes. Plant diseases, both endemic and recently emerging, are spreading and exacerbated by climate change, transmission with global food trade networks, pathogen spillover and evolution of new pathogen genetic lineages. Prediction of plant disease pandemics is unreliable due to the lack of real-time detection, surveillance and data analytics to inform decisions and prevent spread. In order to tackle these grand challenges, a new set of predictive tools are needed. In the PIPP Phase I project, our multidisciplinary team will develop a pandemic prediction system called ����������������Plant Aid Database (PAdb)��������������� that links pathogen transmission biology, disease detection by in-situ and remote sensing, genomics of emerging pathogen strains and real-time spatial and temporal data analytics and predictive simulations to prevent pandemics. We plan to validate the PAdb using several model pathogens including novel and host resistance breaking strains of lineages of two Phytophthora species, Phytophthora infestans and P. ramorum and the cucurbit downy mildew pathogen Pseudoperonspora cubensis Adoption of new technologies and mitigation interventions to stop pandemics require acceptance by society. In our work, we will also characterize how human attitudes and social behavior impact disease transmission and adoption of surveillance and sensor technologies by engaging a broad group of stakeholders including growers, extension specialist, the USDA APHIS, Department of Homeland Security and the National Plant Diagnostic Network in a Biosecurity Preparedness workshop. This convergence science team will develop tools that help mitigate future plant disease pandemics using predictive intelligence. The tools and data can help stakeholders prevent spread from initial source populations before pandemics occur and are broadly applicable to animal and human pandemic research.

This proposal establishes a research and training partnership between scientists in the U.S. and East Africa to study the evolution of plant DNA viruses, which have emerged as leading pathogens and now threaten crops worldwide. Africa������������������s future depends on increasing food production to feed its growing population. There has been dramatic growth in the investments by governments, nongovernmental organizations, international donors and the private sector to develop the scientific expertise and infrastructure necessary to find solutions to the problems that limit African agriculture. The Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub in Kenya and the Mikocheni Agricultural Research Institute (MARI) in Tanzania were created to solve problems facing African farmers and limiting food security. A U.S.-East Africa partnership represents an excellent international opportunity for research synergy and training of U.S. students and early career scientists. Key features include the establishment of a research exchange program between laboratories in the U.S. and East Africa. Postdoctoral researchers, graduate students and undergraduates will be mentored by a strong international research team, which includes experts on viral population genetics, insect vector transmission and population dynamics, virus/vector/plant interactions, and STEM education. The multidisciplinary nature of the research will provide trainees experience in laboratory and field-based research as well as bioinformatics. This will prepare them to become globally engaged, independent scientists with a solid foundation in a range of research methodologies and environments and first-hand experience in international and multidisciplinary collaborations.

We propose to develop new methods for tracking the spread of plant pathogens through agricultural landscapes using population genetic data. Because plant pathogens spread across complex landscapes, our approach will build on network models from spatial epidemiology that provide the flexibility needed to track epidemic dynamics across multiple scales and locations. Network models will be combined with phylogenetic approaches for estimating spatial spread based on the genetic relatedness of pathogens sampled at different geographic locations. These methods will then be implemented in high-performance, user-friendly software for analysis and web-based visualization. We aplan to apply our approach to study the spatial epidemic dynamics to three crop pathogens of major economic importance: Barley yellow dwarf virus, the aflatoxin-producing mold Aspergillus flavus and the downy mildew Pseudoperonospora cubensis. By synthesizing advances in spatial epidemiology and population genetics, our approach will provide next-generation software tools that will help reveal the dominant pathways by which these pathogens spread and identify major geographic sources that future control strategies can target.

We propose to investigate whether and how interactions among parasites and mutualists within host individuals (i.e. within the microbiome) scale up to influence parasite transmission dynamics across the host population. We will leverage a growing ecological and evolutionary model system (the widespread grass tall fescue and its defensive mutualist Neotyphodium coenophialum, as well as three viruses and our main focal species: three fungal parasites) to take a mechanistic experimental approach that is not possible in most systems. Both the within-host interactions among these microbes, and the basic transmission pattern of each fungal parasite species, are well-characterized, which provides a strong platform for further work. The proposed work will characterize the linkage between the within-host microbial interactions and the transmission dynamics of the multi-parasite assemblage. We hypothesize that a key component of this linkage between the levels of host individuals and the host population is heterogeneity among parasite individuals. To quantify how such heterogeneity links within-host interactions to transmission rates, we will integrate diverse approaches ranging from field experimental manipulations of the species composition of the microbiome to transcriptomic analysis of parasite individuals. To execute this research agenda, we have assembled a multidisciplinary team with expertise in fungal biology, theoretical ecology, and computational evolutionary biology. Intellectual Merit : A long-term trajectory in disease ecology has been to incorporate increasing levels of complexity, from one-host/one-parasite dynamics to first including multiple host species, then multiple parasite species. A current frontier is the role of non-parasite symbionts of hosts, both commensals and mutualists. As the emergence of this frontier in disease ecology is coincident with broader scientific interest in the microbiome, one challenge for disease ecology is to take data on within-host interactions among parasites, commensals and mutualists from the rising tide of highly mechanistic biomedical studies, and use that data to predict transmission dynamics in host populations. We propose to pilot an approach to meet this challenge by leveraging a model system in which the mechanistic effects of a defensive mutualist on parasites have been studied for decades, and in which we can readily conduct experiments. Mathematical and statistical models will integrate the resulting data into a broader theoretical framework. Thus, the core intellectual merit of the proposed work will be to elucidate the linkage between within-host microbial interactions and population-level transmission dynamics in a way that is both theoretically grounded and mechanistic, and thus may inform dynamics in a wide range of systems. Broader Impacts : This research will develop a model system for the influence of the microbiome on parasite transmission, potentially improving the health of not only plants, but also humans, animals, and ecosystems. The focal parasites are of national agricultural significance, and tall fescue is a plant of national economic importance, so it may improve sustainable pest management. We will integrate this research into education, specifically our undergraduate courses. Also, we will build on our strong track records of broadly disseminating results, not only through journal articles, but by publicly distributing data and software tools. Furthermore, the PIs will leverage institutional programs to recruit personnel from underrepresented groups, and mentor them to achieve their educational and career goals. The capstone of this project������������������s broader impacts will be outreach. We will collaborate with the UNC Morehead Planetarium and Science Center to develop an interactive exhibit based on the project results. It will include multimedia and hands-on interactive components. Visitors������������������ understanding will be facilitated by trained, paid undergraduate students. Furthermore, Morehead will evaluate the exhibit������������������s impact by interviewing visitors before and after exploring the exhibit. We anticipate the exhibit will attract 22,000 K-12 visitors over one year. In addition to the main exhibit, we will host three interactive Meet-a-Scientist programs, each drawing about 40 people, resulting in a deeper dive into the content with 120 visitors.

North Carolina State University (Cooperator) and the Agricultural Research Service (ARS or Agency) desire to enter into this Agreement for the purpose of supporting research to be carried out at ARS and Cooperator facilities. ARS desires the Cooperator to provide goods and services necessary to carry out research of mutual interest within the Raleigh, North Carolina Location. The Agency Location is engaged in research addressing genetic improvement of small grains and characterization of pathogen populations. Under the authority of 7 USC 3319a, ARS desires to acquire goods and services from the Cooperator to further agricultural research supporting the independent interests of both parties.

North Carolina State Univ ersity (Cooperator) and the Agricultural Research Serv ice (ARS or Agency ) desire to enter into this Agreement f or the purpose of supporting research to be carried out at ARS and Cooperator f acilities. ARS desires the Cooperator to prov ide goods and serv ices necessary to carry out research of mutual interest within the Raleigh, North Carolina location. The Agency Location is engaged in research addressing Plant Genetic Resources, Genomics and Genetic Improv ement. Under the authority of 7 USC 3319a, ARS desires to acquire goods and serv ices f rom the Cooperator to f urther agricultural research supporting the independent interests of both parties.