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Title: Chryseobacterium populi sp. nov., isolated from Populus deltoides endosphere

Abstract

Here, as part of a study investigating the rhizosphere and endosphere of the Eastern cottonwood tree, Populus deltoides, a number of isolates were subjected to genome sequencing. The genome-derived 16S rRNA gene sequence of strain CF314T was 97.0 % similar to those of the Chryseobacterium daecheongense and Chryseobacterium polytrichastri type strains, but was essentially equidistant from many other Chryseobacterium type strains. Overall genome similarity metrics (average nucleotide identity, digital DNA–DNA hybridization, average amino acid identity) revealed greatest similarity to the Chryseobacterium daecheongense , Chryseobacterium piperi and Chryseobacterium soldanellicola type strains, but were well below the species thresholds. Strain CF314T had a typical fatty acid composition for Chryseobacterium species and produced flexirubin pigments, but not carotenoids. The genome encodes a number of proteins such as a C-type lectin and terpene synthases that are also found in other plant-associated Bacteroidetes. Based on phenotypic and genomic characteristics of the strain, we propose the new species Chryseobacterium populi. Finally, the type strain is CF314T=KCTC 62722T=LMG 30786T.

Authors:
 [1]; ORCiD logo [2];  [3]
  1. Lycoming College, Williamsport, PA (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Lycoming College, Williamsport, PA (United States); University of the Free State, Bloemfontein (South Africa)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1490595
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
International Journal of Systematic and Evolutionary Microbiology
Additional Journal Information:
Journal Volume: 69; Journal Issue: 2; Journal ID: ISSN 1466-5026
Publisher:
International Union of Microbiological Societies
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; Chryseobacterium; populus deltoides; endosphere

Citation Formats

Bortniak, Victoria L., Pelletier, Dale A., and Newman, Jeffrey D. Chryseobacterium populi sp. nov., isolated from Populus deltoides endosphere. United States: N. p., 2018. Web. doi:10.1099/ijsem.0.003140.
Bortniak, Victoria L., Pelletier, Dale A., & Newman, Jeffrey D. Chryseobacterium populi sp. nov., isolated from Populus deltoides endosphere. United States. doi:10.1099/ijsem.0.003140.
Bortniak, Victoria L., Pelletier, Dale A., and Newman, Jeffrey D. Thu . "Chryseobacterium populi sp. nov., isolated from Populus deltoides endosphere". United States. doi:10.1099/ijsem.0.003140. https://www.osti.gov/servlets/purl/1490595.
@article{osti_1490595,
title = {Chryseobacterium populi sp. nov., isolated from Populus deltoides endosphere},
author = {Bortniak, Victoria L. and Pelletier, Dale A. and Newman, Jeffrey D.},
abstractNote = {Here, as part of a study investigating the rhizosphere and endosphere of the Eastern cottonwood tree, Populus deltoides, a number of isolates were subjected to genome sequencing. The genome-derived 16S rRNA gene sequence of strain CF314T was 97.0 % similar to those of the Chryseobacterium daecheongense and Chryseobacterium polytrichastri type strains, but was essentially equidistant from many other Chryseobacterium type strains. Overall genome similarity metrics (average nucleotide identity, digital DNA–DNA hybridization, average amino acid identity) revealed greatest similarity to the Chryseobacterium daecheongense , Chryseobacterium piperi and Chryseobacterium soldanellicola type strains, but were well below the species thresholds. Strain CF314T had a typical fatty acid composition for Chryseobacterium species and produced flexirubin pigments, but not carotenoids. The genome encodes a number of proteins such as a C-type lectin and terpene synthases that are also found in other plant-associated Bacteroidetes. Based on phenotypic and genomic characteristics of the strain, we propose the new species Chryseobacterium populi. Finally, the type strain is CF314T=KCTC 62722T=LMG 30786T.},
doi = {10.1099/ijsem.0.003140},
journal = {International Journal of Systematic and Evolutionary Microbiology},
number = 2,
volume = 69,
place = {United States},
year = {2018},
month = {12}
}

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Works referenced in this record:

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains
journal, May 2015

  • Whitman, William B.; Woyke, Tanja; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0017-x

Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead
journal, October 2007

  • Konstantinidis, Konstantinos T.; Tiedje, James M.
  • Current Opinion in Microbiology, Vol. 10, Issue 5
  • DOI: 10.1016/j.mib.2007.08.006

Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium
journal, December 2014


Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types
journal, July 2011

  • Gottel, Neil R.; Castro, Hector F.; Kerley, Marilyn
  • Applied and Environmental Microbiology, Vol. 77, Issue 17
  • DOI: 10.1128/AEM.05255-11

Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides
journal, October 2012

  • Brown, S. D.; Utturkar, S. M.; Klingeman, D. M.
  • Journal of Bacteriology, Vol. 194, Issue 21
  • DOI: 10.1128/JB.01243-12

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, February 2014

  • Kim, M.; Oh, H. -S.; Park, S. -C.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
  • DOI: 10.1099/ijs.0.059774-0

Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants
journal, February 2006

  • Park, M. S.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 2
  • DOI: 10.1099/ijs.0.63825-0

NOTES: New Perspectives in the Classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev.
journal, October 1994

  • Vandamme, P.; Bernardet, J. -F.; Segers, P.
  • International Journal of Systematic Bacteriology, Vol. 44, Issue 4
  • DOI: 10.1099/00207713-44-4-827

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
journal, June 2017

  • Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J.
  • Nature Biotechnology, Vol. 35, Issue 7
  • DOI: 10.1038/nbt.3886

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea
journal, February 2014

  • Chun, J.; Rainey, F. A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
  • DOI: 10.1099/ijs.0.054171-0

Towards a Genome-Based Taxonomy for Prokaryotes
journal, September 2005


Chryseobacterium limigenitum sp. nov., isolated from dehydrated sludge
journal, March 2015


LPSN—list of prokaryotic names with standing in nomenclature
journal, November 2013


Closed Genome Sequence of Chryseobacterium piperi Strain CTM T /ATCC BAA-1782, a Gram-Negative Bacterium with Clostridial Neurotoxin-Like Coding Sequences
journal, November 2017


Genome-based reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus
journal, August 2014

  • Stropko, S. J.; Pipes, S. E.; Newman, J. D.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 11
  • DOI: 10.1099/ijs.0.068205-0

Chryseobacterium daecheongense sp. nov., isolated from freshwater lake sediment
journal, January 2005

  • Kim, K. K.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 1
  • DOI: 10.1099/ijs.0.02931-0

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016

  • Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
  • Molecular Biology and Evolution, Vol. 33, Issue 7
  • DOI: 10.1093/molbev/msw054

GCAT-SEEKquence: Genome Consortium for Active Teaching of Undergraduates through Increased Faculty Access to Next-Generation Sequencing Data
journal, December 2011

  • Buonaccorsi, Vincent P.; Boyle, Michael D.; Grove, Deborah
  • CBE—Life Sciences Education, Vol. 10, Issue 4
  • DOI: 10.1187/cbe.11-08-0065

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


Vision and Change through the Genome Consortium for Active Teaching Using Next-Generation Sequencing (GCAT-SEEK)
journal, March 2014

  • Buonaccorsi, Vincent; Peterson, Mark; Lamendella, Gina
  • CBE—Life Sciences Education, Vol. 13, Issue 1
  • DOI: 10.1187/cbe.13-10-0195

A large-scale evaluation of algorithms to calculate average nucleotide identity
journal, February 2017


Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013

  • Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-60

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

  • Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1226

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
journal, August 2014


A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
journal, August 2018

  • Parks, Donovan H.; Chuvochina, Maria; Waite, David W.
  • Nature Biotechnology, Vol. 36, Issue 10
  • DOI: 10.1038/nbt.4229

Microbial species delineation using whole genome sequences
journal, July 2015

  • Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
  • Nucleic Acids Research, Vol. 43, Issue 14
  • DOI: 10.1093/nar/gkv657

Chryseobacterium piperi sp. nov., isolated from a freshwater creek
journal, October 2010

  • Strahan, B. L.; Failor, K. C.; Batties, A. M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 9
  • DOI: 10.1099/ijs.0.027805-0

OrthoANI: An improved algorithm and software for calculating average nucleotide identity
journal, February 2016

  • Lee, Imchang; Ouk Kim, Yeong; Park, Sang-Cheol
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 2
  • DOI: 10.1099/ijsem.0.000760

LPSN – List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on
journal, June 2018

  • Parte, Aidan C.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 6
  • DOI: 10.1099/ijsem.0.002786

A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees
journal, October 2013


Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family.
journal, May 2002

  • Bernardet, Jean-Francois; Holmes, Barry; Nakagawa, Yasuyoshi
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 3
  • DOI: 10.1099/00207713-52-3-1049

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009

  • Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
  • Nature, Vol. 462, Issue 7276
  • DOI: 10.1038/nature08656

The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

  • Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
  • BMC Genomics, Vol. 9, Issue 1, Article No. 75
  • DOI: 10.1186/1471-2164-9-75