| Autor: |
Carper DL; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Weston DJ; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Barde A; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA.; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA., Timm CM; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Lu TY; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Burdick LH; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Jawdy SS; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Klingeman DM; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Robeson MS 2nd; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA.; Department of Biomedical Informatics, grid.241054.6University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA., Veach AM; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA.; Department of Environmental Science and Ecology, University of Texas at San Antonio, San Antonio, Texas, USA., Cregger MA; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Kalluri UC; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Schadt CW; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Podar M; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Doktycz MJ; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA., Pelletier DA; Biosciences Division, Oak Ridge National Laboratorygrid.135519.a, Oak Ridge, Tennessee, USA. |
| Abstrakt: |
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. IMPORTANCE Microbial communities play an integral role in the health and survival of their plant hosts. Many studies have identified key members in these communities and led to the use of synthetic communities for elucidating their function; however, these studies are limited by the available cultured bacterial representatives. Here, we present a bacterial culture collection comprising 3,211 isolates that is representative of the root community of Populus. We then demonstrate the ability to examine underlying microbe-microbe interactions using a synthetic community approach. This culture collection will allow for the greater exploration of the microbial community function through targeted experimentation and manipulation. |
