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

Plant-Microbe Interfaces: Defining Quorum Sensing Signal Potential in the Populus Microbiome and Examining its Role in Community Selection and Structure

Authors:

Dale A. Pelletier1* (pelletierda@ornl.gov), Ethan G. Murdock2, April Armes1, Amy L. Schaefer3, Leah H. Burdick1, Dawn M. Klingeman1, Katherine B. Louie4, Benjamin P. Bowen4, Trent R. Northen4, Ian K. Blaby4, Yasuo Yoshikuni4, Christopher W. Schadt1, Paul E. Abraham1, Caroline S. Harwood3, E. Peter Greenberg3, Aaron W. Puri2, Mitchel J. Doktycz1

Institutions:

1Biosciences Division, Oak Ridge National Laboratory; 2Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah; 3Department of Microbiology, University of Washington; 4DOE Joint Genome Institute

URLs:

Goals

The overriding goal of the Oak Ridge National Laboratory (ORNL) Plant-Microbe Interfaces (PMI) Science Focus Area is to predictively understand the productive relationship between a plant host and its microbiome based on molecular and environmentally defined information. Populus and its associated microbial community serve as the experimental system for understanding this dynamic, complex multi-organism system. To achieve this goal, research focuses on (1) defining the bidirectional progression of molecular and cellular events involved in selecting and maintaining specific, mutualistic Populus-microbe interfaces; (2) defining the chemical environment and molecular signals that influence community structure and function; and (3) understanding the dynamic relationship and extrinsic stressors that shape microbiome composition and affect host performance.

Abstract

Microbial communities play an integral role in the health and survival of their plant hosts. Environmental and host factors drive microbial community structure in the rhizosphere, but microbe-microbe chemical signaling undoubtably has a role in structuring the microbial community. The impact of microbe-microbe interactions on multispecies community structure and dynamics is not well understood. Researchers previously established that acyl-homoserine lactone (AHL), quorum sensing (QS), and natural product biosynthesis genes are prevalent in the Populus microbiome. QS often regulates extracellular enzyme production, biofilm formation, competence, and secondary metabolite production contributing to microbe-microbe interactions. Here the group utilized a synthetic biology approach to explore the diversity of AHL signals and an approach based on synthetic communities (SynCom) to investigate the influence of QS on microbial community structure and dynamics.

Bioinformatic analyses identified a large amount of unexplored AHL signal synthase gene (LuxI) diversity in the Populus metagenome and bacterial isolate genomes. As part of a DOE Joint Genome Institute (JGI) DNA Synthesis Community Sequencing Project, researchers selected 140 representative undefined LuxI homologs from the Populus microbiome for DNA synthesis and expression in the heterologous host Escherichia. coli. The group identified AHL signals synthesized by these LuxI homologs in E. coli using the JGI non-polar metabolomics pipeline and mass query language analyses. Researchers detected AHL production in about half of the synthesized LuxI homologs, including the first well-described AHL signal structures for several genera (Bosea, Duganella, Janthinobacterium, Massilia, Novosphingobium, Rhodanobacter, Rhodoferax, Sphingobium, Sphingomonas, Sphingopyxis, and Variovorax). Interestingly, the predicted AHL signal inventory of the endosphere is distinct compared to that of the rhizosphere/soil and is dominated by LuxI homologs that synthesize atypical AHL signals.

Next, the team utilized a AiiA-lactonase QS-off method with a previously established SynCom to assess the effects of AHL inactivation on microbial community structure, pairwise interactions, biofilm formation, and secondary metabolite production. Preliminary results demonstrate disruption of AHL signaling leads to changes in the community structure. Current efforts are focused on elucidating the molecular mechanisms through which AHL signaling mediates microbial community assembly. Collectively, these diverse applications of metagenomics and cultured representatives of Populus’ microbial community are facilitating researchers’ understanding of how Populus selects microbial partners and how its microbiome is structured.

Funding Information

Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. DOE under contract no. DE-AC05-00OR22725. The Plant-Microbe Interfaces Science Focus Area is supported by the U.S. DOE, Office of Science, through the GSP, BER program under FWP ERKP730. DNA synthesis and metabolomic analyses were conducted under Community Science Program award 507288 (proposal: https://doi.org/10.46936/10.25585/60001376) by the U.S. DOE Joint Genome Institute, a DOE Office of Science User Facility supported by the Office of Science of the U.S. DOE operated under Contract No. DE-AC02-05CH11231.