Cultivating the Bacterial Microbiota of Populus Roots

Journal Article · Tue Jun 29 00:00:00 EDT 2021 · mSystems

DOI:https://doi.org/10.1128/mSystems.01306-20· OSTI ID:1798005

Carper, Dana L.  ^[1]; Weston, David J.  ^[1]; Barde, Aditya ^[2]; Timm, Collin M.  ^[1]; Lu, Tse-Yuan ^[1]; Burdick, Leah H. ^[1]; Jawdy, Sara S.  ^[1]; Klingeman, Dawn M.  ^[1]; Robeson, II, Michael S.  ^[3]; Veach, Allison M.  ^[4]; Cregger, Melissa A.  ^[1]; Kalluri, Udaya C.  ^[1]; Schadt, Christopher W.  ^[1]; Podar, Mircea  ^[1]; Doktycz, Mitchel J.  ^[1]; Pelletier, Dale A.  ^[1]; Lindemann, ed., Stephen R.

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1. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
2. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA, Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
3. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
4. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA, Department of Environmental Science and Ecology, University of Texas at San Antonio, San Antonio, Texas, USA

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 21days, 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.

• Research Organization: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES)
• Grant/Contract Number: AC05-00OR22725; AC02-05CH11231
• OSTI ID: 1798005
• Alternate ID(s): OSTI ID: 1807291
• Journal Information: mSystems, Journal Name: mSystems Vol. 6 Journal Issue: 3; ISSN 2379-5077
• Publisher: American Society for Microbiology
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
poplar
plant microbiome
isolation
culture collection
16S rRNA gene sequencing
bacterial isolation