Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108
Performing Department
Plant Pathology
Non Technical Summary
Plant-associated microbial communities (plant microbiomes) have significant influences on plant fitness in agricultural and natural habitats. Because of their significance to crop production, research on plant-associated microbes has focused predominantly on pathogens in agricultural systems. However, we have much less understanding of the potential for non-pathogenic microbes, including antagonists, symbionts, and saprophytes, to provide significant benefits to plant fitness. Moreover, the strict focus on agricultural systems has limited our understanding of the breadth of ecological and evolutionary interactions between plants and microbes. This lack of understanding of the significance of non-pathogenic microbes to plant fitness and of the manner in which plants may actively influence the ecological and evolutionary dynamics of their associated microbial communities constrains our capacity to design novel strategies for controlling plant diseases. Furthermore, studies of plant-microbe interactions have tended to focus on pairwise interactions of the plant and a microbial partner. Plants and microbes are embedded in enormously complex communities that can have dramatic impacts on the interactions between the plant and the microbe. Research is needed on the cascade of species interactions occurring within plant and microbial communities that mediate microbial community dynamics and plant productivity. The proposed research focuses on soil and plant microbiomes, and especially on antibiotic-producing Streptomyces, and on identifying abiotic and biotic factors that influence the ecology, evolutionary biology, and dynamics of secondary metabolites in these populations in soil. We will characterize the diversity, composition, and functional characteristics of rhizosphere and endophytic microbiomes associated with diverse plant hosts in agricultural and natural habitats. Our work will focus on identifying significant correlates of key functional characteristics, including pathogen suppression and plant growth promotion, of rhizosphere and endophytic microbiomes. This work will provide insights into the ecology and evolutionary biology of plant-associated beneficial microbes, and will provide a basis for developing sustainable strategies for active management of soilborne microbial communities to minimize plant diseases in diverse cropping systems.
Animal Health Component
20%
Research Effort Categories
Basic
80%
Applied
20%
Developmental
(N/A)
Goals / Objectives
1. Explore the ecology and evolutionary biology of pathogen and disease suppression by soil microbial communities in relation to cropping history, soil nutrient characteristics, plant and microbial community characteristics (including composition, diversity, and network structure), and presence of natural enemies (foliar fungi, foliar insects, soilborne pathogens) using natural history, experimental coevolution, and quantitative modeling approaches in agricultural and experimental prairie settings.2. Advance biological methods for controlling soilborne plant diseases. 3. Characterize the effects of exclusion of foliar fungi, soil fungi, and insects on plants, plant and soil microbiomes, and soil nutrient dynamics in prairie plant communities.4. Characterize fitness tradeoffs among pathogenic, saprophytic, and antagonistic Streptomyces populations, considering in particular potential for tradeoffs among inhibitory phenotypes, antibiotic resistance, pathogen aggressiveness (thaxtomin production, disease severity), growth capacities (niche width, growth efficiency), and decomposition traits (enzymatic efficiencies) under diverse environmental conditions (e.g. nutrient quantity and diversity, temperature). 5. Use genomic and transcriptomic analyses to characterize variation in the diversity and dynamics of secondary metabolite biosynthetic pathways among Streptomyces populations from diverse cropping systems and natural habitats, to enhance coevolutionary models for predicting arms race and character displacement dynamics, and to create optimal isolate mixtures for plant productivity enhancement.6. Characterize the roles of plant host and cropping system, soil chemical characteristics, local source pools, nutrient management, and within-plant interactions in determining the composition, structure, and function of foliar and soil microbiomes. A.Natural systems B. Agricultural systems
Project Methods
Procedures/Methods/Approach: Objective 1: We have developed a rigorous collection of methods for sampling and characterizing genetic, phenotypic, and especially pathogen-suppressive characteristics of soil microbial communities, especially Streptomyces (Davelos et al., 2004 a, b; Schlatter et al., 2009) including: amplicon sequencing and shotgun metagenomic analyses, whole genome sequence analyses, targeted analysis of 16S and ITS sequences of cultured strains, metabolomics and transcriptomics of cultured isolates alone and in complex mixtures, nutrient utilization profile analyses (using Biolog SF-P2 plates), antibiotic inhibitory and resistance phenotype characterization using both a collection of Streptomyces standards and clinical antibiotic disks, and evaluation of interspecies and interstrain signaling phenotypes. We will continue to extend our collection of microbial isolates (including especially Streptomyces, Fusarium, Bacillus/Brevibacillus, and Pseudomonas) and environmental samples to include consideration of a broad range of natural habitats and experimental platforms from all continents.Objective 2: We have developed an extensive collection of Streptomyces and Bacillus/Brevibacillus isolates that have been characterized for their capacities to inhibit a broad collection of plant pathogens (up to 45 distinct pathogen isolates), their growth dynamics on 95 distinct nutrients and at different temperatures, their abilities to enhance plant biomass in the absence of plant pathogens, and to inhibit and/or signal one another. We will continue to investigate mixtures of these isolates on diverse crops under challenge by multiple pathogens and at a wide range of temperature and soil nutrient conditions. We will also study the potential for targeted nutrient inputs to enhance the effectiveness of disease suppression and plant growth promotion among our inoculants. We have attracted external investments to advance a subset of our inoculants to commercialization.Objective 3: Our field and greenhouse work currently explores the potential role that generalist fungi (not host-specific plant pathogens) play in mediating above- and belowground plant productivity/biomass allocation, and how these dynamics are influenced by plant diversity. In our most recent efforts, we are exploring variation in impacts (costs) of natural enemies over time and found that: i) surprisingly, the costs of foliar fungi to plant productivity in perennial prairie species are greatest in the first half vs. the second half of the growing season (prior to peak biomass); ii) the costs of foliar fungi to plant productivity increase over time, and the costs increase significantly more steeply over time in monoculture vs. polyculture (16-species) prairie communities. These data will be linked with (4), below, to get a more comprehensive understanding of foliar enemy effects on plant productivity as mediated by the soil microbiome.Objective 4: We have recently completed our first work investigating the potential fitness costs of antibiotic inhibitory and resistance phenotypes to the growth potential of Streptomyces populations (Schlatter and Kinkel, 2015). We have extended our studies of fitness tradeoffs to pathogenic Streptomyces, focusing specifically on tradeoffs between thaxtomin production and nutrient utilization (niche width and growth efficiency). Overall, these studies will provide quantitative information on the fitness costs of distinct trait combinations which will be used in developing models for predicting the environmental and biotic conditions when specific traits are most likely to be selectively enriched.Objective 5: We have recently obtained whole genome sequences of nearly 120 Streptomyces isolates. We are mining our collection to determine the numbers of biosynthetic pathways, the diversity of chemicals produced by individual isolates, and the potential synergy among compounds produced by the same or different isolates. We are especially interested in determining the potential impacts of selective environment/history to influence genome structure and content. Transcriptomic data are being used to characterize the signal responsiveness and aggregate secondary metabolite production among isolates when co-growing vs. when growing individually. This information will be critical to guiding the selection of strain mixtures for achieving successful pathogen suppression, and for understanding how sympatric vs. allopatric isolate combinations may yield fundamentally different suppressive outcomes as the result of co-adaptation among coexisting populations.Objective 6: We are studying the endophytic communities associated with native grass species across a global network of temperate grassland sites (Nutrient Network, or NutNet). Amplicon sequencing data and analyses of cultured isolates have shown a significant selective effect of NPK amendments on fungal (but not bacterial) phenotypes, and a significant effect of within-plant microbial species interactions in community assembly.