ABSTRACT

PI: Venkatesan Sundaresan (University of California-Davis)

CoPIs: Jonathan Eisen and David Mackill (University of California-Davis), and Merle Anders (University of Arkansas-Fayetteville)

Collaborator: James Garner (University of Arkansas-Pine Bluff)

Plants grow in close association with large communities of microbes called microbiomes, that influence nutrient composition and uptake of nutrients in the soil, as well as disease susceptibility. Major advances in understanding the health effects of human microbiomes have resulted from using gnotobiotic animal systems, in which germ-free animals are exposed to defined microbiomes to study their effects. Gnotobiotic systems to study microbiome function in plants are harder to implement because plant microbiomes are a combination of internal and external (e.g. soil) components. This project will use a gnotobiotic system developed for rice plants, in which root-associated microbiomes from different sources or conditions can be transplanted, and established in plants grown under controlled conditions. The project will enable the discovery of specific functions of plant microbiomes at the molecular level, and the evaluation of the impact of microbiomes on plant performance. Understanding the interactions of the host plant with its microbiome, and subsequent effects on crop performance and yields, provides possibilities for exploiting plant-microbe associations for future crop improvement. A second aim of the project addresses the concern that agriculture is a major source of global emissions of the potent greenhouse gas methane. Rice cultivation worldwide is estimated to contribute nearly half of these emissions by promoting the growth of methane producing microbes. The project will examine the effects of different rice varieties on methane producing microbes, as well as methane consuming microbes, found in rice root-associated microbiomes. The findings can lead to strategies for reducing methane emissions from paddy fields, and reduce the impacts of rice cultivation on climate change. In addition to the training of students and postdoctoral associates, the project will provide summer research internships for selected undergraduate students from University of Arkansas-Pine Bluff, a Historically Black University.

The project will use genomic approaches to understand the impact of microbial associations on the crop plant rice (Oryza sativa). Preliminary data show that root microbiomes of soil grown rice plants are modulated by several environmental factors, including soil type, cultivation practice and drought, suggesting that changes to microbiomes constitute part of the plant adaptation to the environment. The growth preference of rice for semi-aquatic substrates has been exploited to establish a gnotobiotic rice model, such that plants grown under controlled conditions can acquire a defined microbiome. In this project, microbiomes used for transplantation will be characterized by 16SrDNA sequencing to identify the constituent taxa, and the transcriptomes of the treated rice plants will be studied using RNAseq. The transcriptional responses of gnotobiotic rice plants with transplanted microbiomes from different sources and stress treatments, including drought stress, will be analyzed for global changes in gene expression, as well as specific functional classes of genes that might reflect adaptive responses by the plant induced by the microbiome. Lastly, the association of archaea with cultivated rice, a significant contribution to planetary methane emissions, and potentially to climate change, will be investigated. Specifically, the effects of genotype on methanogenic archaea and methanotrophic bacteria, as well as computationally identified associated microbial networks in field grown rice, will be characterized, towards the goal of breeding low emission rice. Plant transcriptomic and microbial sequence data generated by the project will be released through public databases that include the NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA), respectively.

Please report errors in award information by writing to: awardsearch@nsf.gov.