Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Jr., Michael S.; Yang, Zamin K.; Klingeman, Dawn M.; Land, Miriam L.; Allman, Steve L.; Lu, Tse-Yuan S.; Brown, Steven D.; Schadt, Christopher W.; Podar, Mircea; Doktycz, Mitchel J.; Pelletier, Dale A.; Drake, ed., H. L.

doi:10.1128/AEM.01285-16

Title: Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

Journal Article · Thu Sep 15 00:00:00 EDT 2016 · Applied and Environmental Microbiology

DOI:https://doi.org/10.1128/AEM.01285-16· OSTI ID:1786375

Utturkar, Sagar M. ^[1]; Cude, W. Nathan ^[2]; Robeson, Jr., Michael S. ^[2]; Yang, Zamin K. ^[2]; Klingeman, Dawn M. ^[2]; Land, Miriam L. ^[2]; Allman, Steve L. ^[2]; Lu, Tse-Yuan S. ^[2]; Brown, Steven D. ^[2]; Schadt, Christopher W. ^[2]; Podar, Mircea ^[2]; Doktycz, Mitchel J. ^[2]; Pelletier, Dale A. ^[2]; Drake, ed., H. L.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA, Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. In this paper, we present a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from the plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Finally, comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1786375

Alternate ID(s):: OSTI ID: 1324106

Journal Information:: Applied and Environmental Microbiology, Journal Name: Applied and Environmental Microbiology Vol. 82 Journal Issue: 18; ISSN 0099-2240

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 33 works

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