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Susannah Tringe, Ph.D.

Evironmental Genomics and Systems Biology Director and head of the Joint Genome Institute microbial systems group at Lawrence Berkeley National Laboratory 

 

Join us on Wednesday June 9th at 10:00AM PDT as Susannah Tringe, Division Director of Environmental Genomics and Systems Biology at Lawrence Berkeley National Laboratory, presents the findings of her recent study. Please find more information below. 

Sorghum bicolor is a genetically diverse crop cultivated for a variety of agronomic uses, including grain, sugar, and energy productions. However, cultivation of energy sorghum for biofuel produtction will require the use of marginal lands with potentially low nutrient availability and/or periods of water stress. All plants growing in soil harbor diverse communities of microbes that inhabit the areas in, on, and around their roots. Selected members of these microbial communities can provide benefits to their plant hosts, including direct growth promotion and conferring tolerances to abiotic and biotic stress. To examine the effects of nutrient and water stress on soil and root microbial communities and explore possible microbial solution to increase the nutrient use efficiency and resilience to water stress in sorghum, we are utilizing 16S rRNA sequencing to survey the bacterial communities in replicate soil, rhizosphere, and root samples collected from ~30 different sorghum genotypes grown under different nitrogen (N;high/low) and water (watered/drought) treatments over multiple growing seasons at two sites in Nebraska. 

In a small-scale pilot experiment in 2015, we collected ~200 soil, rhizosphere, and root samples from 10 different sorghum genotypes grown under high or low N conditions. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity attributable to a dramatic increase in the bacterial genus Pseudomonas which occurred independent of hose genotype in both high and low N fields, and was not observed in the surrounding soil or associated root endosphere samples. Nearly all the Pseudomonas reads in this dataset were assined to a single OTU at 97% identity; however, ASV-level resolution demonstrated that this OTU comprises a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long read sequencing enabled high-resolution taxonomic profiling of the Pseudomonas lineages within the dataset. in additional field experiments in 2016 and 2017, we sampled three selected genotypes at four time points throughout the growing season to monitor changes in the bacterial communities over time and again observed decreases in Shannon diversity in rhizosphere samples early in the growth season concomitant with a marked increase in the relative abundance of Pseudomonas. Our ongoing work focuses on characterizing the genomic and metabolic features of the Pseudomonas populations and integrating our findings with the metabolomic and phenotypic data generated with project collaborators. 

This project was funded by the DOE BER Sustainable Bioenergy Research Program, Award DESC0014395, and was also supported by DOE JGI Community Science Program: The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231