SPONSORED CORE RESEARCH PROJECTS


 FY 2017

Effects of hybridization on the maize metagenome

PIs: Dan Bowman, Ph.D., Professor, Crop and Soil Science, and Jim Holland, Ph.D., USDA Professor, Crop and Soil Science. Postdoc: Maggie Wagner, NSF Plant Genome Postdoctoral Fellow

Heterosis, the phenomenon in which hybridization between inbred genotypes results in phenotypically superior offspring, is a subject of immense economic value and research interest. In maize, many different traits have been shown to exhibit transgressive segregation in F1 offspring; however, the effect of hybridization on maize microbiome composition and diversity (which are known to be heritable) has never been tested. The proposed research will compare the rhizosphere and foliar microbiomes of inbred maize lines and their hybrid offspring, and explore the consequences for metagenome content and plant growth. Because crosses between inbred lines are a crucial mechanism in crop breeding, understanding the relationship between hybridization, metagenome content, and microbiome function is an important step toward incorporating microbiome science into breeding programs.

 

Extension and validation of maximum resolution amplicon bioinformatics methods to fungal marker-gene data

PIs: Benjamin Callahan, Ph.D., Assistant Professor, Population Health & Pathobiology and Ignazio Carbone, Ph.D., Professor, Center for Integrated Fungal Research, Department of Entomology and Plant Pathology

Fungal communities are crucial components of soil communities, and fungi are the most important microbial partners for plant health and function. High-throughput amplicon sequencing has become a powerful tool to characterize soil and plant-associated fungal communities, but the variable length of the ITS region presents different challenges that often interfere with methods developed primarily for the 16S rRNA gene. We propose to bring the state-of-the-art bioinformatics methods from the bacterial world into the fungal world by extending the DADA2 method for sequence variant inference to work on variable-length amplicons like those generated from the ITS gene region, and to validate those methods on fungal data. These new methods will allow marker-gene studies of fungal communities to resolve individual fungi more precisely, and to better discriminate between related fungi that may functionally differ.

 

Investigating the impact of bacterial endophytes on mycorrhizal fungi, rhizosphere microbiome and plant nutrient acquisition in switchgrass

PI: Shuijin Hu, Ph.D., Professor, Entomology & Plant Pathology Collaborator: Chuansheng Mei, Ph.D., The Center for Sustainable and Renewable Resources, The Institute for Advanced Learning and Research (IALR)

The rhizosphere microbiome, including saprophytic microbes and arbuscular mycorrhizal fungi (AMF), plays a major role in plant nutrient and water acquisition. Endophytes, bacterial or fungal symbionts living within the plant, are ubiquitous and can confer some beneficial effects on host plants through improving plant growth and tolerance to abiotic and biotic stresses. They can be particularly useful for forage and fuel crops such as switchgrass that will preferentially be planted on marginal lands where environmental stresses are routine. The primary objective of this study is to assess the impact of endophytic bacteria on AMF in roots, the rhizosphere microbiome (with a focus on N-cycling microbes), and plant nutrient acquisition, using switchgrass a model plant. Results from this study will help understand the drivers that control tripartite interactions among plants, endophytes in roots, and soil microbes in the context of plant C allocation for microbes in exchange for nutrient acquisition.

 

 FY 2016

Multiple Disease Resistance and the Maize Microbiome

PIs: Eric Davis, Ph.D.,William Neal Reynolds Distinguished Professor of Plant Pathology and Peter Balint-Kurti, Ph.D., Professor of Plant Pathology. Postdoc: Maggie Wagner, NSF Plant Genome Postdoctoral Fellow

Robust genetic resistance to multiple diseases is a key goal for crop breeding programs. However, non-pathogenic endophytic microbes also affect plant health and productivity. Do loci conferring broad-spectrum pathogen resistance have side-effects on the maize microbiome? Are there trade-offs between multiple disease resistance and accumulation of beneficial endophytes? The proposed research will improve our understanding of how host genotype influences the microbiome of maize roots and leaves; specifically, whether QTL associated with multiple disease resistance also alter microbiome diversity and composition. This study will reveal which microbial taxa within the endophyte community are sensitive to or robust to host genes conferring broad-spectrum resistance. In addition, this work will generate a collection of fungal strains isolated from maize leaves in the field, and will screen them for plant growth promotion in disease-resistant and disease-susceptible maize lines.

 

The Microbiome of Rice Seed and Seedlings

PI: Ralph Dean, Ph.D., William Neal Reynolds Distinguished Professor of Plant Pathology.

The manipulation of the plant microbiome has untapped potential for reducing chemical inputs, tolerating stressful environments, lowering disease and enhancing agricultural productivity. In this project, the microbiome of rice seeds and seedlings growing independently of natural soil will be characterized. Specifically, the role of genotype, source of seeds as well as seed age on the microbiome will be examined by pyrosequencing of 16S ribosomal (prokaryotes) and ITS region of the rRNA operon (fungi) as well as Sanger sequencing of isolated microbes. Sequence data will be examined for microbial diversity and determination of a core seed and seedling microbiome.