Genomic tools to monitor and exploit microbial diversity for agricultural disease and aridland management

Fungi play important but underappreciated roles in the health of ecosystems impacting soils, plants, and water systems. Some of these microbes are potent diseases of agricultural systems that can are vectored by insects, can stay resident in soils for long periods, and can cause disease throughout the lifecycle of plants and postharvest products. Understanding the dynamics of populations of beneficial and plant disease-causing fungi will inform mitigation strategies, rapid detection of newly introduced pathogens or more virulent genotypes, and the monitoring of the emergence of fungicide resistance alleles that required changes in treatment strategies.This project takes a two-prong approach to study populations of fungi and bacteria. The first is a focus on characterizing beneficial microbes in aridland soils to understand their role in promoting and maintaining soil health in the presence of increased nitrification, salinity, and human disturbance. This work links to ANR Strategic Initiatives (SI) for Sustainable Natural Ecosystems (SNE) and Sustainable Food Systems (SFI). How microbial community diversity is changes as a consequence of disturbance can be important to evaluate human, livestock and climate change impact on soil health and productivity. Identifying changes in microbial communities will also inform restoration efforts. The reintroduction of endemic microbes into disturbed soils areas may contributed to increased rates of recovery. I will focus on cryptogamic soils or biological crusts (BSCs) which are collectives of bacteria, fungi, algae and other microbes and important components to SNE in arid and desert regions. These BSCs support the formation and maintenance of stable soils in aridlands and can be critical for dust reduction as these aggregates prevent movement of loose soil. Reduction of dust is important for improving human and livestock health. In addition, BSCs trap moisture, nutrients, and can contain nitrogen fixing bacteria which lead to improved soil health for plant growth. The promotion of biological crusts in marginal lands near agricultural fields or in the wake of human or livestock caused soil disturbance can assist in moisture trapping, reduction in erosion, and provide harbors of beneficial microbes that can contribute to soil health. This work focuses on the development of living culture collections of microbes, genomic sequencing and analyses of these isolates, and culture-independent surveys of soils to characterize the microbial community structure using amplicon sequencing and metabarcoding tools.The second focusis monitoring population diversity of new or existing fungal crop pathogens to understand introduction, dispersal, and emergence of fungicide resistance which will contribute to the SI of Endemic and Invasive Pests and Diseases (EIPD). Recently introduced tree disease pathogen Fusarium euwallaceae and Fus. kuroshino are an active threat to avocado in the state of California. These fungi are symbionts of the shot hole borer beetle, also recently introduced. A critical question in the management of the disease is the dispersal and introduction of strains of the fungus, whether there is recombination among strains which could lead to rapid spread of more virulent varieties, and the potential for acquired fungicide resistance. To provide better information towards disease management, I am developing and applying population genomics approaches to track fungi and their origins focused these newly introduced pathogens. The rise of fungicide resistance of foliar pathogens in vegetable and fruit crops are an additional area where whole genome approaches to detect, catalog the spread of resistant genotypes, and make predictions about future at risk areas can improve strategies to manage crop health. My work applies modern genomic approaches to analyzing genomes of isolates from populations of fungi with a focus on Fusarium dieback disease. Analytical and molecular techniques developed as part of this work will be applicable to multiple questions related to fungal disease, resistance to fungicides.Overall this work requires collecting of strains from environmental and agricultural origins, genomic sequencing and development of rapid diagnostic techniques, curation of databases of sequences of organisms and of resistance alleles. Detailed inventories of aridland microbes are limited and a comprehensive compilation of these data for bacteria, fungi, and algae will enable studies testing for the correlations with healthy or disturbed environments and in the development of mitigation strategies to amend soils with beneficial microbes. To support this work improved bioinformatics tools are needed to process increasingly larger genomic datasets and present useful summary and prediction information to stakeholders with foundational and applied research goals.The directions of this project work links to the AES-CE network. Improved understanding of healthy markers for aridlands soils is important in management of lands and in assessing potential for promoting and maintaining BSCs in areas near agriculture land use. Further characterizing the microbes that makeup BSCs can translate into methods to re-seed soils with native fungi or bacteria to jumpstart the growth of BSCs as part of efforts to reduce dust production in fallow or disturbed arid soils. These efforts are important for improving air quality in regions affected by dust pollution including the Salton Sea basin and Owens Lake, but also disturbed desert habitats that flank residential or agricultural lands. The curation of a living microbial culture collections will provide the reagents to develop these approaches.Measurements of the potential positive impact of BSCs near agricultural lands may provide new approaches to improving soil health by quantifying their effects and engaging in efforts to help farmers and farm advisors monitor and promoting these areas. Short term impacts of this work will be means to inventory soils to test for the presence of expected microbes from healthy BSCs which can suggest best practices for more protection of areas, while long term impacts will be the development of microbial amendments to improve soils and promote the processes of BSC formation.The research will also work to develop better tools for the application of genome sequencing to track introduction and spread of new genotypes of isolates including fungicide resistance. The research focus will be on Fusarium dieback disease affecting avocado crops in California but there are a broad range of tree hosts in Southern California which are susceptible. The technology in the form of software and analytic approaches will be broadly applicable to EIPD areas using genomic tools to track invasive microbes and be made as freely available resources. Short term impacts of this research will focus on tracking the spread of different strain genotypes of fungi with Fusarium dieback and evidence for sexual recombination to better understand the source of introductions and the changes in populations over time. In addition, the tools developed for this approach will support rapid comparative analyses of genomes to highlight variants that distinguish individuals or groups of strains to support development of diagnostic tools. Long term impacts from this work will be records of the changes in genetic makeup of invasive fungi, bioinformatics tools for automated assessment of genetic diversity and status of known fungicide resistant alleles in individuals.