Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Bacterial Degradation of Sorgoleone, a Step Towards Enforcing Rhizobacteria Containment

Authors:

Yasuhiro Oda1* (yasuhiro@uw.edu), Joshua Elmore2, William Nelson2, Andrew Wilson2, Yuliya Farris2, Ritu Shrestha2, Citlali Fonseca Garcia3, Dean Pettinga3, Aaron Ogden2, Henri Baldino2, Molly Stephenson1, William Alexander4, Adam Deutschbauer5, Catalina Vega Hurtado5, Jason McDermott2, Adam Guss4, Devin Coleman-Derr3, Ryan McClure2, Caroline Harwood1, Robert Egbert2

Institutions:

1University of Washington; 2Pacific Northwest National Laboratory; 3University of California–Berkeley; 4Oak Ridge National Laboratory; 5Lawrence Berkeley National Laboratory

Goals

The Persistence Control Science Focus Area (PerCon SFA) at Pacific Northwest National Laboratory seeks to understand plant-microbiome interactions in bioenergy crops to establish plant growth-promoting microbiomes that are contained to the rhizosphere of a target plant. This vision requires the discovery of exudate catabolism pathways from plant roots, the elimination of genes that support fitness in bulk soil environments without decreasing rhizosphere fitness, and the engineering of rhizosphere niche occupation traits in phylogenetically distant bacteria. Researchers anticipate the impacts of these efforts will be to increase understanding of plant-microbe interactions and to extend high-throughput systems and synthetic biology tools to non-model microbes.

Abstract

Metabolite exchange between plant roots and their associated rhizosphere microbiomes underpins plant growth promotion by microbes. Root tips of the bioenergy crop Sorghum bicolor exude large amounts of a lipophilic benzoquinone called sorgoleone. This allelochemical suppresses the growth of competing plant seedlings and is slowly mineralized by microbes in soil. As an avenue to understanding how sorghum and its root microbiome may be connected through root exudates, the group identified the molecular determinants of microbial sorgoleone degradation and the distribution of this trait among microbes. The team isolated and studied three bacterial strains from sorghum-cultivated soils that were classified as Acinetobacter, Burkholderia, and Pseudomonas species able to grow with sorgoleone as a sole carbon and energy source. The genomes of these strains were sequenced and subjected to transcriptomic and gene fitness analyses to identify candidate sorgoleone degradation genes. Follow up mutational analysis showed that sorgoleone catabolism is dependent on four contiguous genes that are conserved among the strains the teams sequenced. Researchers refer to these four genes as the srg (sorgoleone degradation) cluster. Phylogenetic analysis of the srg cluster using Snekmer showed that sorgoleone catabolism is enriched in sorghum-associated Streptomyces strains over isolates from the Populus rhizosphere. The discovery of bacteria that grow on a compound like sorgoleone that is plant specific and not widely distributed in the environment provides an opportunity for the PerCon SFA to study how sorghum exudates can enforce the development of a rhizosphere specific microbiome for the mutual benefit of plant and microbe.

References

Chang, C. H., et al. 2023. “Snekmer: a Scalable Pipeline for Protein Sequence Fingerprinting Based on Amino Acid Recoding,” Bioinformatics Advances 3(1). DOI:10.1093/bioadv/vbad005.

Oda, Y., et al. 2023. “Sorgoleone Degradation by Sorghum-Associated Bacteria; An Opportunity for Enforcing Plant Growth Promotion,” bioRxiv. DOI:10.1101/2023.05.26.542311.

Funding Information

This research was supported by the U.S. DOE BER program as part of BER’s GSP and is a contribution of the Pacific Northwest National Laboratory (PNNL) Secure Biosystems Design Science Focus Area “Persistence Control of Engineered Functions in Complex Soil Microbiomes” (FWP 76333). Additional funding was provided by a KBase plus-up award (FWP 78925). PNNL is a multi-program national laboratory operated by Battelle Memorial Institute for the DOE under Contract DE-AC05-76RL01830.