skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions

Abstract

Many studies have shown that microbes, which share nearly identical 16S rRNA genes, can have highly divergent genomes. Microbes from distinct parts of the ocean also exhibit biogeographic patterning. Here we seek to better understand how certain microbes from the same species have adapted for growth under local conditions. The phenotypic and genomic heterogeneity of three strains of Colwellia psychrerythraea was investigated in order to understand adaptions to local environments. Colwellia are psychrophilic heterotrophic marine bacteria ubiquitous in cold marine ecosystems. We have recently isolated two Colwellia strains: ND2E from the Eastern Mediterranean and GAB14E from the Great Australian Bight. The 16S rRNA sequence of these two strains were greater than 98.2% identical to the well-characterized C. psychrerythraea 34H, which was isolated from arctic sediments. Salt tolerance, and carbon source utilization profiles for these strains were determined using Biolog Phenotype MicoArrays. These strains exhibited distinct salt tolerance, which was not associated with the salinity of sites of isolation. The carbon source utilization profiles were distinct with less than half of the tested carbon sources being metabolized by all three strains. Whole genome sequencing revealed that the genomes of these three strains were quite diverse with some genomes having up tomore » 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. There appears to be a link between carbon source utilization and location of isolation with distinctions observed between the Colwellia isolate recovered from sediment compared to water column isolates.« less

Authors:
 [1];  [2];  [2];  [2];  [3];  [2];  [2];  [3];  [2]
  1. Michigan Technological Univ., Houghton, MI (United States)
  2. Univ. of Tennessee, Knoxville, TN (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1311281
Alternate Identifier(s):
OSTI ID: 1580808
Grant/Contract Number:  
AC05-00OR22725; A13-0119-001; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Environmental Science
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 2296-665X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; genomicdiversity; comparative genomics; psychrophile; phenotype; evolution; marine ecology

Citation Formats

Techtmann, Stephen M., Fitzgerald, Kathleen S., Stelling, Savannah C., Joyner, Dominique C., Utturkar, Sagar M., Harris, Austin P., Alshibli, Noor K., Brown, Steven D., and Hazen, Terry C. Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions. United States: N. p., 2016. Web. https://doi.org/10.3389/fenvs.2016.00033.
Techtmann, Stephen M., Fitzgerald, Kathleen S., Stelling, Savannah C., Joyner, Dominique C., Utturkar, Sagar M., Harris, Austin P., Alshibli, Noor K., Brown, Steven D., & Hazen, Terry C. Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions. United States. https://doi.org/10.3389/fenvs.2016.00033
Techtmann, Stephen M., Fitzgerald, Kathleen S., Stelling, Savannah C., Joyner, Dominique C., Utturkar, Sagar M., Harris, Austin P., Alshibli, Noor K., Brown, Steven D., and Hazen, Terry C. Mon . "Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions". United States. https://doi.org/10.3389/fenvs.2016.00033. https://www.osti.gov/servlets/purl/1311281.
@article{osti_1311281,
title = {Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions},
author = {Techtmann, Stephen M. and Fitzgerald, Kathleen S. and Stelling, Savannah C. and Joyner, Dominique C. and Utturkar, Sagar M. and Harris, Austin P. and Alshibli, Noor K. and Brown, Steven D. and Hazen, Terry C.},
abstractNote = {Many studies have shown that microbes, which share nearly identical 16S rRNA genes, can have highly divergent genomes. Microbes from distinct parts of the ocean also exhibit biogeographic patterning. Here we seek to better understand how certain microbes from the same species have adapted for growth under local conditions. The phenotypic and genomic heterogeneity of three strains of Colwellia psychrerythraea was investigated in order to understand adaptions to local environments. Colwellia are psychrophilic heterotrophic marine bacteria ubiquitous in cold marine ecosystems. We have recently isolated two Colwellia strains: ND2E from the Eastern Mediterranean and GAB14E from the Great Australian Bight. The 16S rRNA sequence of these two strains were greater than 98.2% identical to the well-characterized C. psychrerythraea 34H, which was isolated from arctic sediments. Salt tolerance, and carbon source utilization profiles for these strains were determined using Biolog Phenotype MicoArrays. These strains exhibited distinct salt tolerance, which was not associated with the salinity of sites of isolation. The carbon source utilization profiles were distinct with less than half of the tested carbon sources being metabolized by all three strains. Whole genome sequencing revealed that the genomes of these three strains were quite diverse with some genomes having up to 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. There appears to be a link between carbon source utilization and location of isolation with distinctions observed between the Colwellia isolate recovered from sediment compared to water column isolates.},
doi = {10.3389/fenvs.2016.00033},
journal = {Frontiers in Environmental Science},
number = ,
volume = 4,
place = {United States},
year = {2016},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Beyond biogeographic patterns: processes shaping the microbial landscape
journal, May 2012

  • Hanson, China A.; Fuhrman, Jed A.; Horner-Devine, M. Claire
  • Nature Reviews Microbiology, Vol. 10, Issue 7
  • DOI: 10.1038/nrmicro2795

Evidence for a persistent microbial seed bank throughout the global ocean
journal, March 2013

  • Gibbons, S. M.; Caporaso, J. G.; Pirrung, M.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 12
  • DOI: 10.1073/pnas.1217767110

Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill
journal, October 2011

  • Redmond, M. C.; Valentine, D. L.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 50
  • DOI: 10.1073/Pnas.1108756108

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species
journal, April 2011

  • Luo, C.; Walk, S. T.; Gordon, D. M.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 17
  • DOI: 10.1073/Pnas.1015622108

Microbial biogeography: putting microorganisms on the map
journal, February 2006

  • Martiny, Jennifer B. Hughes; Bohannan, Brendan J. M.; Brown, James H.
  • Nature Reviews Microbiology, Vol. 4, Issue 2
  • DOI: 10.1038/nrmicro1341

Colwellia asteriadis sp. nov., a marine bacterium isolated from the starfish Asterias amurensis
journal, October 2009

  • Choi, E. J.; Kwon, H. C.; Koh, H. Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 8
  • DOI: 10.1099/Ijs.0.016055-0

Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench
journal, September 2004

  • Nogi, Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 5
  • DOI: 10.1099/Ijs.0.03049-0

RNAmmer: consistent and rapid annotation of ribosomal RNA genes
journal, April 2007

  • Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas
  • Nucleic Acids Research, Vol. 35, Issue 9
  • DOI: 10.1093/nar/gkm160

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton
journal, May 2008


The Unique Chemistry of Eastern Mediterranean Water Masses Selects for Distinct Microbial Communities by Depth
journal, March 2015


Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP
journal, June 2013

  • Gutierrez, Tony; Singleton, David R.; Berry, David
  • The ISME Journal, Vol. 7, Issue 11
  • DOI: 10.1038/Ismej.2013.98

Explaining microbial genomic diversity in light of evolutionary ecology
journal, March 2014

  • Cordero, Otto X.; Polz, Martin F.
  • Nature Reviews Microbiology, Vol. 12, Issue 4
  • DOI: 10.1038/nrmicro3218

The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses
journal, July 2005

  • Methe, B. A.; Nelson, K. E.; Deming, J. W.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 31
  • DOI: 10.1073/Pnas.0504766102

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007

  • Wang, Q.; Garrity, G. M.; Tiedje, J. M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 16
  • DOI: 10.1128/AEM.00062-07

CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics
journal, April 2013


Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill: Enrichment of oil degraders from Gulf of Mexico
journal, May 2012


BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
journal, February 2016

  • Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae
  • Journal of Molecular Biology, Vol. 428, Issue 4
  • DOI: 10.1016/j.jmb.2015.11.006

Remarkably low temperature optima for extracellular enzyme activity from Arctic bacteria and sea ice
journal, August 2000


Global biogeography of SAR11 marine bacteria
journal, January 2012

  • Brown, Mark V.; Lauro, Federico M.; DeMaere, Matthew Z.
  • Molecular Systems Biology, Vol. 8, Issue 1
  • DOI: 10.1038/msb.2012.28

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments
journal, January 2008

  • Kennedy, Jonathan; Marchesi, Julian R.; Dobson, Alan DW
  • Microbial Cell Factories, Vol. 7, Issue 1
  • DOI: 10.1186/1475-2859-7-27

Colwellia chukchiensis sp. nov., a psychrotolerant bacterium isolated from the Arctic Ocean
journal, May 2010

  • Yu, Y.; Li, H. -R.; Zeng, Y. -X.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 4
  • DOI: 10.1099/Ijs.0.022111-0

Horizontal gene transfer: building the web of life
journal, July 2015

  • Soucy, Shannon M.; Huang, Jinling; Gogarten, Johann Peter
  • Nature Reviews Genetics, Vol. 16, Issue 8
  • DOI: 10.1038/nrg3962

Cycloclasticus pugetii gen. nov., sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium from Marine Sediments
journal, January 1995

  • Dyksterhouse, S. E.; Gray, J. P.; Herwig, R. P.
  • International Journal of Systematic Bacteriology, Vol. 45, Issue 1
  • DOI: 10.1099/00207713-45-1-116

Active mud volcanoes on the upper slope of the western Nile deep-sea fan—first results from the P362/2 cruise of R/V Poseidon
journal, February 2010


Motility of Colwellia psychrerythraea Strain 34H at Subzero Temperatures
journal, July 2003


Mud volcanoes, gas chimneys, pockmarks and mounds in the Nile deep-sea fan (Eastern Mediterranean): geophysical evidences
journal, June 2004


Horizontal gene transfer, genome innovation and evolution
journal, August 2005

  • Gogarten, J. Peter; Townsend, Jeffrey P.
  • Nature Reviews Microbiology, Vol. 3, Issue 9
  • DOI: 10.1038/nrmicro1204

Genomic insights that advance the species definition for prokaryotes
journal, February 2005

  • Konstantinidis, K. T.; Tiedje, J. M.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 7
  • DOI: 10.1073/Pnas.0409727102

Ecology of marine Bacteroidetes: a comparative genomics approach
journal, January 2013

  • Fernández-Gómez, Beatriz; Richter, Michael; Schüler, Margarete
  • The ISME Journal, Vol. 7, Issue 5
  • DOI: 10.1038/Ismej.2012.169

Molecular adaptations to psychrophily: the impact of ‘omic’ technologies
journal, August 2010


Bacterial species may exist, metagenomics reveal: Bacterial species may exist
journal, December 2011


Biogeographic patterns in ocean microbes emerge in a neutral agent-based model
journal, September 2014


Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill
journal, July 2014


Differential aerobic and anaerobic oxidation of hydrocarbon gases discharged at mud volcanoes in the Nile deep-sea fan
journal, July 2009

  • Mastalerz, Vincent; de Lange, Gert J.; Dählmann, Anke
  • Geochimica et Cosmochimica Acta, Vol. 73, Issue 13
  • DOI: 10.1016/J.Gca.2008.12.030

Circos: An information aesthetic for comparative genomics
journal, June 2009


Shifting the genomic gold standard for the prokaryotic species definition
journal, October 2009

  • Richter, Michael; Rosselló-Móra, Ramon
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 45
  • DOI: 10.1073/Pnas.0906412106

Succession of Hydrocarbon-Degrading Bacteria in the Aftermath of the Deepwater Horizon Oil Spill in the Gulf of Mexico
journal, September 2013

  • Dubinsky, Eric A.; Conrad, Mark E.; Chakraborty, Romy
  • Environmental Science & Technology, Vol. 47, Issue 19
  • DOI: 10.1021/es401676y

Some like it cold: understanding the survival strategies of psychrophiles
journal, March 2014


Population Genomics of Early Events in the Ecological Differentiation of Bacteria
journal, April 2012

  • Shapiro, B. Jesse; Friedman, Jonathan; Cordero, Otto X.
  • Science, Vol. 336, Issue 6077
  • DOI: 10.1126/Science.1218198

Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences
journal, June 2014


Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis
journal, August 2012

  • Malmstrom, Rex R.; Rodrigue, Sébastien; Huang, Katherine H.
  • The ISME Journal, Vol. 7, Issue 1
  • DOI: 10.1038/ismej.2012.89

Colwellia meonggei sp. nov., a novel gammaproteobacterium isolated from sea squirt Halocynthia roretzi
journal, September 2013


Distinct features of protein folding by the GroEL system from a psychrophilic bacterium, Colwellia psychrerythraea 34H
journal, September 2012


ABySS: A parallel assembler for short read sequence data
journal, February 2009


Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean
journal, July 2010

  • Jiao, Nianzhi; Herndl, Gerhard J.; Hansell, Dennis A.
  • Nature Reviews Microbiology, Vol. 8, Issue 8
  • DOI: 10.1038/nrmicro2386

Colwellia aestuarii sp. nov., isolated from a tidal flat sediment in Korea
journal, January 2006

  • Jung, S. -Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 1
  • DOI: 10.1099/Ijs.0.63920-0

Trehalose transporter 1, a facilitated and high-capacity trehalose transporter, allows exogenous trehalose uptake into cells
journal, July 2007

  • Kikawada, T.; Saito, A.; Kanamori, Y.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 28
  • DOI: 10.1073/pnas.0702538104

Colwellia polaris sp. nov., a psychrotolerant bacterium isolated from Arctic sea ice
journal, August 2008

  • Zhang, D. -C.; Yu, Y.; Xin, Y. -H.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 8
  • DOI: 10.1099/Ijs.0.65596-0

Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard
journal, January 2011

  • Teske, A.; Durbin, A.; Ziervogel, K.
  • Applied and Environmental Microbiology, Vol. 77, Issue 6
  • DOI: 10.1128/Aem.01507-10

Degradation of Putrescine and Cadaverine in Seawater Cultures by Marine Bacteria
journal, January 1984


    Works referencing / citing this record:

    Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H
    journal, November 2018

    • Czajka, Jeffrey J.; Abernathy, Mary H.; Benites, Veronica T.
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 49
    • DOI: 10.1073/pnas.1807804115

    A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens
    journal, August 2018


    Biodegradation of Crude Oil and Corexit 9500 in Arctic Seawater
    journal, August 2018

    • McFarlin, Kelly M.; Perkins, Matt J.; Field, Jennifer A.
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.01788