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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 in this study 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 genomesmore » having up to 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. Finally, 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. doi: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. doi: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. doi: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 in this study 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. Finally, 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}
}

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Works referenced in this record:

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


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

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

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

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


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

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


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

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

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

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


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


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

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

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

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


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

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


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


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

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

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


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

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


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


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


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

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

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