Carper, D.L., et al., 2021. MSystems

Cultivating the Bacterial Microbiota of Populus Roots

Dana L. Carper, David J. Weston, Aditya Barde, Collin M. Timm, Tse-Yuan Lu, Leah H. Burdick, Sara S. Jawdy, Dawn M. Klingeman, Michael S. Robeson II, Allison M. Veach, Melissa A. Cregger, Udaya C. Kalluri, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz and Dale A. Pelletier.  

22 June 2021, mSystems 6(3); https://doi.org/10.1128/mSystems.01306-20

Abstract

The integral role of microbial communities in plant growth and health is now widely recognized, and, increasingly, the constituents of the microbiome are being defined. While phylogenetic surveys have revealed the taxa present in a microbiome and show that this composition can depend on, and respond to, environmental perturbations, the challenge shifts to determining why particular microbes are selected and how they collectively function in concert with their host. In this study, we targeted the isolation of representative bacterial strains from environmental samples of Populus roots using a direct plating approach and compared them to amplicon-based sequencing analysis of root samples. The resulting culture collection contains 3,211 unique isolates representing 10 classes, 18 orders, 45 families, and 120 genera from 6 phyla, based on 16S rRNA gene sequence analysis. The collection accounts for ∼50% of the natural community of plant-associated bacteria as determined by phylogenetic analysis. Additionally, a representative set of 553 had their genomes sequenced to facilitate functional analyses. The top sequence variants in the amplicon data, identified as Pseudomonas, had multiple representatives within the culture collection. We then explore a simplified microbiome, comprised of 10 strains representing abundant taxa from environmental samples, and tested for their ability to reproducibly colonize Populus root tissue. The 10-member simplified community was able to reproducibly colonize on Populus roots after 21 days, with some taxa found in surface-sterilized aboveground tissue. This study presents a comprehensive collection of bacteria isolated from Populus for use in exploring microbial function and community inoculation experiments to understand basic concepts of plant and environmental selection.

Citation