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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Research Project #429944

Research Project: Enabling Improved Environmental Stress Tolerance in Crops through Novel Computational Strategies and Tool Development

Location: Plant Gene Expression Center

Project Number: 2030-12210-001-00-D
Project Type: In-House Appropriated

Start Date: Oct 1, 2015
End Date: Mar 19, 2018

The ultimate goal of this research is to generate a better understanding of the interrelationship between crop plant abiotic stress tolerance and crop plant microbiomes. The specific objectives of this project are: Objective 1: Assess universal and host-specific responses of crop-associated microbial communities to environmental stress in diverse crop species, and the relationship between host genetic diversity and microbiome composition. Subobjective 1A: Investigate rhizosphere and root endosphere bacterial communities of diverse cereal crops and related grass species exposed to drought conditions. Subobjective 1B: Investigate temporal shifts in the rhizosphere and root endosphere bacterial community structure of two Sorghum bicolor cultivars as they acclimate to and recover from drought stress. Subobjective 1C: Evaluate the colonization efficiency of candidate endophytes in grasses grown under drought conditions, identify drought tolerance inducing microbes in Sorghum bicolor, and evaluate the effectiveness of identified strains in other grass species. Objective 2: Develop computational methods and statistical tools to enable the analysis of large-scale data-rich biological "omics" datasets generated from crop species and their associated microbial communities.

Objective 1: Subobjective 1A, Experimental Design: Grow fourteen diverse grass species under drought and control conditions, map the bacterial community structure of their associated rhizosphere and root endosphere communities using 16S rRNA iTags sequencing, identify core grass endophytes and epiphytes, and correlate differences in community structure with evolutionary distance in the plant host. Subobjective 1B, Experimental Design: Grow two cultivars of Sorghum bicolor under drought and control conditions, map the bacterial community structure of their associated rhizosphere and root endosphere communities during the course of drought progression and plant development using 16S rRNA iTags sequencing. Subobjective 1C, Experimental Design: Identify strains capable of colonizing sorghum using putative grass endophyte isolates, apply these strains to additional candidate grass species, characterize changes in rhizosphere and root endosphere microbiomes, and evaluate effect of isolate strains on drought tolerance. Objective 2: A state of the art 16S rRNA sequencing approach is being developed in conjunction with the Joint Genome Institute (JGI) in Walnut Creek, California. This new method will be based on the approach developed by Fadrosh et al. (2014), and incorporates a number of technical advantages over other standard pipelines, including increased phylogenetic resolution, improved sequence quality, reduced run time and lower sequencing costs. Pilot experiments in collaboration with the JGI are underway to test this new methodology.