title: Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis.
abstract: 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. Here, we describe 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. Comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria.
  
  
  
  Plant roots harbor a diverse collection of microbes that live within host tissues. To gain a comprehensive understanding of microbial adaptations to this endophytic lifestyle from strains that cannot be cultivated, it is necessary to separate bacterial cells from the predominance of plant tissue. This study provides a valuable approach for the separation and isolation of endophytic bacteria from plant root tissue. Isolated live bacteria provide material for microbiome sequencing, single-cell genomics, and analyses of genomes of uncultured bacteria to provide genomics information that will facilitate future cultivation attempts.
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA.
authors.forename: Sagar M
authors.initials: SM
authors.lastname: Utturkar
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: W Nathan
authors.initials: WN
authors.lastname: Cude
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Robeson
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Zamin K
authors.initials: ZK
authors.lastname: Yang
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Klingeman
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Miriam L
authors.initials: ML
authors.lastname: Land
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Steve L
authors.initials: SL
authors.lastname: Allman
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Tse-Yuan S
authors.initials: TY
authors.lastname: Lu
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Schadt
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Mircea
authors.initials: M
authors.lastname: Podar
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Mitchel J
authors.initials: MJ
authors.lastname: Doktycz
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA pelletierda@ornl.gov.
authors.forename: Dale A
authors.initials: DA
authors.lastname: Pelletier
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D002499:Centrifugation, Density Gradient / Q000379:methods; D019295:Computational Biology; D060026:Endophytes / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D056186:Metagenomics; D018517:Plant Roots / Q000382:microbiology*; D032107:Populus / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis / Q000379:methods