Performing Department
Plant Science
Non Technical Summary
Ensuring agricultural productivity and sustainability in a rapidly changing world requires innovative linkages between fundamental research and novel applications. In the context of climate change, loss of soil fertility, loss of arable land, decreasing biodiversity resources, and increased reliance on core crops by a growing human population, creates a strong need for new strategies to enhance crop plant resiliency, productivity, and nutritional quality.Breeding and plant biotechnology provide extremely important tools for plant enhancement, but do not take full advantage of the immensely powerful but understudied toolkit embodied by microbes, and the diverse ways in which microorganisms positively and negatively interact with wild and domesticated plants. Recent advancements in microbial ecology, genomics, crop science, bioinformatics, and computation indicate that characterizing and translating plant microbiomes represents a particularly powerful tool for rapid enhancement of crop plants.In particular, evidence points to the importance of plant microbiomes in influencing plant productivity, protecting plants against environmental stresses, and transferring phenotypic traits -- such as drought-, salt-, or heat tolerance - rapidly and reliably from one host plant to another. In turn, recent advances in microbial ecology highlight the global uniqueness of Arizona's plant-microbiome resources, and advances in informatics and sequencing technologies now permit the rapid characterization and application of these resources in innovative ways. Desertification, land degradation, loss of fertility, drought stress, salinization, and soil loss together represent major challenges to agriculture both in the American West and globally, highlighting the need to discover and apply potentially beneficial microbes in the near term.Here, we posit that plants that flourish in arid, marginal, and degraded lands, and that are closely related to major crop plants (i.e., are congeners or confamilials), together represent promising and under-studied sources of agriculturally important microbes. We propose a study to take advantage of Arizona's uncommonly rich flora, which includes many close relatives of the top agricultural crops in our region (including Gossypium/cotton, Lactuca/lettuce, Medicago/alfalfa, Solanum/tomato), to characterize microbiomes (including bacteria and fungi from soil, plant surfaces, and plant interiors) of wild relatives of crop plants in degraded or marginal sites; to apply genomic and culture-based technologies to characterize beneficial traits these microbes confer to plants, with attention to stress tolerance, productivity, and nutrition; and to generate a network of collaborative researchers across the College of Agriculture and Life Sciences with an interest in crop enhancement through microbial symbioses and microbial products. In doing so we will engage students and stakeholders, train junior researchers, enhance courses for CALS students, contribute to CALS biodiversity collections, and increase connections between CALS and other campus units.
Animal Health Component
0%
Research Effort Categories
Basic
33%
Applied
33%
Developmental
34%
Goals / Objectives
We aim to characterize the composition, diversity, and potential applications of the microbial assemblages that colonize crop-related plants in stressful environments; to compare the microbiomes of focal crop plants with those of close, dryland-adapted relatives; to translate these findings to crop plant enhancement; to serve stakeholders, students, and junior scientists through engagement and mentorship; to interface with relevant commodity groups and industry partners; and to cultivate a broad collaborative network at the interface of microbiomes and crop improvement. Specifically, we aim to:1. Characterize the diverse and understudied microbiome of native and invasive arid-land plants in southern Arizona. Specifically, by synthesizing existing expertise in agricultural and wild settings, we will develop a comprehensive perspective on the structure and function of arid-land plant microbiomes. Focal research questions will include, but not be limited to: What microbial functions or groups are shared among drought-, salt-, and heat-adapted plants? What microbial symbionts enable growth of wild relatives of crop plants in marginal lands? What genomic traits of plants facilitate microbial enhancement? What is the relationship of microbiome taxonomy and function to yield and quality in major crops for Arizona, the Southwest, and arid- and arid-transitioning lands worldwide?2. Translate arid-land plant microbiomes for crop improvement in marginal, altered, and arid lands. Through innovative development of biodiversity informatics, genetic resources, microbial collections, and collaborations that leverage CALS infrastructure, we will test hypotheses regarding plant health and sustainability based on predictions from microbiome surveys and genomic analyses. Experiments will focus on enhancement of seed germination, drought tolerance, salt tolerance, and thermotolerance, carried out in field and controlled conditions3. Link microbiome characteristics to nutritional aspects of food plants through novel collaborations that will interface across CALS units, and develop related linkages with industry/growers groups, technology transfer, and as needed, patent protection4. Develop an infrastructure for intellectual and translational advancement of microbiome studies on campus and beyond, with the long-term goal of fostering research innovation, discovery, translational technologies, education, extension, outreach, and extramural funds.
Project Methods
Our methods include field surveys in collaboration with growers and in public lands in the Tucson basin, through which we will measure plant biomass and vigor, collect microbial associates via culture-based methods, and sequence microbial communities directly using next-generation sequencing. Resulting data will be integrated in our computational pipeline to determine host specificity and spatial structure of microbial communities, and to relate these to plant health. In phase 2 we will move to metagenomics and plant inoculation experiments following methods published by our team.