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.
Original language | English |
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Article number | e01306-20 |
Journal | mSystems |
Volume | 6 |
Issue number | 3 |
DOIs | |
State | Published - Jun 2021 |
Funding
We thank Zamin Yang (Oak Ridge National Laboratory) for help with sequencing library preparation. DNA sequencing and library preparation for some isolates were performed as part of JGI Community Science Program user projects (CSP503495 and CSP1429). We thank Kerrie Barry and Nicole Shapiro (JGI) for project management. The work conducted by the U.S. DOE JGI, a DOE Office of Science User Facility, is supported under contract DE-AC02-05CH11231. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. We declare that we have no competing interests. Citation Carper DL, Weston DJ, Barde A, Timm CM, Lu T-Y, Burdick LH, Jawdy SS, Klingeman DM, Robeson MS, II, Veach AM, Cregger MA, Kalluri UC, Schadt CW, Podar M, Doktycz MJ, Pelletier DA. 2021. Cultivating the bacterial microbiota of Populus roots. mSystems 6: e01306-20. https://doi.org/10.1128/mSystems .01306-20. Editor Stephen R. Lindemann, Purdue University Copyright © 2021 Carper et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Dale A. Pelletier, [email protected]. * Present address: Collin M. Timm, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA. The manuscript has been authored by UT- Battelle, LLC, under contract no. DE-AC05-00OR22725 with the U.S. Department of Energy. Received 11 December 2020 Accepted 2 June 2021 Published 22 June 2021 We thank Zamin Yang (Oak Ridge National Laboratory) for help with sequencing library preparation. DNA sequencing and library preparation for some isolates were performed as part of JGI Community Science Program user projects (CSP503495 and CSP1429). We thank Kerrie Barry and Nicole Shapiro (JGI) for project management. The work conducted by the U.S. DOE JGI, a DOE Office of Science User Facility, is supported under contract DE-AC02-05CH11231. Oak Ridge National Laboratory is managed by UTBattelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. We declare that we have no competing interests. This research was sponsored by the Genomic Science Program, U.S. Department of Energy, Office of Science, Biological, and Environmental Research as part of the Plant Microbe Interfaces Scientific Focus Area. This research used resources of the Compute and Data Environment for Science (CADES) at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC05-00OR22725. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. D.L.C., D.J.W., and D.A.P. authored the manuscript. D.L.C., D.J.W., C.M.T., M.S.R., C.W.S., M.P., M.J.D., and D.A.P. edited and prepared the manuscript for publication. U.C.K., M.S.R., A.M.V., M.A.C., C.W.S., M.J.D., and D.A.P. contributed to the poplar study designs and sampling. T.L., L.H.B., D.M.K., M.P., and D.A.P. cultivated the members of the culture collection. A.B., C.M.T., T.L., L.H.B., S.S.J., D.M.K., and D.A.P. designed and performed the 10-member community experiments. D.L.C., A.B., C.M.T., and D.A.P. analyzed all the data and created figures for themanuscript. This research was sponsored by the Genomic Science Program, U.S. Department of Energy, Office of Science, Biological, and Environmental Research as part of the Plant Microbe Interfaces Scientific Focus Area. This research used resources of the Compute and Data Environment for Science (CADES) at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC05-00OR22725. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.
Keywords
- 16S rRNA gene sequencing
- Bacterial isolation
- Culture collection
- Isolation
- Plant microbiome
- Poplar