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

Title: Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome: Natural resource landscapes of a marine bacterium

Abstract

Not provided.

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [3];  [1]
  1. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA 02139 USA
  2. Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA 02139 USA
  3. Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070 F-29280 Plouzané France; Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 F-29688 Roscoff cedex France
Publication Date:
Research Org.:
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1536714
DOE Contract Number:  
SC0008743
Resource Type:
Journal Article
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 19; Journal Issue: 6; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
Microbiology

Citation Formats

Takemura, Alison F., Corzett, Christopher H., Hussain, Fatima, Arevalo, Philip, Datta, Manoshi, Yu, Xiaoqian, Le Roux, Frederique, and Polz, Martin F. Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome: Natural resource landscapes of a marine bacterium. United States: N. p., 2017. Web. doi:10.1111/1462-2920.13765.
Takemura, Alison F., Corzett, Christopher H., Hussain, Fatima, Arevalo, Philip, Datta, Manoshi, Yu, Xiaoqian, Le Roux, Frederique, & Polz, Martin F. Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome: Natural resource landscapes of a marine bacterium. United States. doi:10.1111/1462-2920.13765.
Takemura, Alison F., Corzett, Christopher H., Hussain, Fatima, Arevalo, Philip, Datta, Manoshi, Yu, Xiaoqian, Le Roux, Frederique, and Polz, Martin F. Fri . "Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome: Natural resource landscapes of a marine bacterium". United States. doi:10.1111/1462-2920.13765.
@article{osti_1536714,
title = {Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome: Natural resource landscapes of a marine bacterium},
author = {Takemura, Alison F. and Corzett, Christopher H. and Hussain, Fatima and Arevalo, Philip and Datta, Manoshi and Yu, Xiaoqian and Le Roux, Frederique and Polz, Martin F.},
abstractNote = {Not provided.},
doi = {10.1111/1462-2920.13765},
journal = {Environmental Microbiology},
issn = {1462-2912},
number = 6,
volume = 19,
place = {United States},
year = {2017},
month = {5}
}

Works referenced in this record:

Microbial Extracellular Enzymes and the Marine Carbon Cycle
journal, January 2011


Microbial structuring of marine ecosystems
journal, October 2007

  • Azam, Farooq; Malfatti, Francesca
  • Nature Reviews Microbiology, Vol. 5, Issue 10
  • DOI: 10.1038/nrmicro1747

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

Approaches to querying bacterial genomes with transposon-insertion sequencing
journal, July 2013

  • Barquist, Lars; Boinett, Christine J.; Cain, Amy K.
  • RNA Biology, Vol. 10, Issue 7
  • DOI: 10.4161/rna.24765

Overflow metabolism in Escherichia coli results from efficient proteome allocation
journal, December 2015

  • Basan, Markus; Hui, Sheng; Okano, Hiroyuki
  • Nature, Vol. 528, Issue 7580
  • DOI: 10.1038/nature15765

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle
journal, December 2016

  • Cermak, Nathan; Becker, Jamie W.; Knudsen, Scott M.
  • The ISME Journal, Vol. 11, Issue 3
  • DOI: 10.1038/ismej.2016.161

The Mannose-Sensitive Hemagglutinin of Vibrio cholerae Promotes Adherence to Zooplankton
journal, July 2001


Positive Regulation of the Vibrio cholerae Porin OmpT by Iron and Fur
journal, September 2011

  • Craig, S. A.; Carpenter, C. D.; Mey, A. R.
  • Journal of Bacteriology, Vol. 193, Issue 23
  • DOI: 10.1128/JB.05681-11

Microbial interactions lead to rapid micro-scale successions on model marine particles
journal, June 2016

  • Datta, Manoshi S.; Sliwerska, Elzbieta; Gore, Jeff
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms11965

Organic solute accumulation in osmotically-stressed Enteromorpha intestinalis
journal, September 1987

  • Edwards, D. M.; Reed, R. H.; Chudek, J. A.
  • Marine Biology, Vol. 95, Issue 4
  • DOI: 10.1007/BF00393102

The Pfam protein families database: towards a more sustainable future
journal, December 2015

  • Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1344

Vibrio parahaemolyticus type IV pili mediate interactions with diatom-derived chitin and point to an unexplored mechanism of environmental persistence
journal, February 2013

  • Frischkorn, Kyle R.; Stojanovski, Asta; Paranjpye, Rohinee
  • Environmental Microbiology, Vol. 15, Issue 5
  • DOI: 10.1111/1462-2920.12093

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung
journal, September 2009

  • Gawronski, J. D.; Wong, S. M. S.; Giannoukos, G.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 38
  • DOI: 10.1073/pnas.0906627106

Microbial Metagenomics: Beyond the Genome
journal, January 2011


Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat
journal, September 2009


Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes
journal, September 2016

  • Hehemann, Jan-Hendrik; Arevalo, Philip; Datta, Manoshi S.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12860

Conservation of the Chitin Utilization Pathway in the Vibrionaceae
journal, October 2007

  • Hunt, D. E.; Gevers, D.; Vahora, N. M.
  • Applied and Environmental Microbiology, Vol. 74, Issue 1
  • DOI: 10.1128/AEM.01412-07

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


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

The Phyre2 web portal for protein modeling, prediction and analysis
journal, May 2015

  • Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M.
  • Nature Protocols, Vol. 10, Issue 6
  • DOI: 10.1038/nprot.2015.053

Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism
journal, March 2010

  • Kennedy, Jonathan; Flemer, Burkhardt; Jackson, Stephen A.
  • Marine Drugs, Vol. 8, Issue 3
  • DOI: 10.3390/md8030608

Hyperactive transposase mutants of the Himar1 mariner transposon
journal, September 1999

  • Lampe, D. J.; Akerley, B. J.; Rubin, E. J.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 20
  • DOI: 10.1073/pnas.96.20.11428

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
journal, October 2009

  • Langridge, G. C.; Phan, M. -D.; Turner, D. J.
  • Genome Research, Vol. 19, Issue 12
  • DOI: 10.1101/gr.097097.109

Construction of a Vibrio splendidus Mutant Lacking the Metalloprotease Gene vsm by Use of a Novel Counterselectable Suicide Vector
journal, November 2006

  • Le Roux, F.; Binesse, J.; Saulnier, D.
  • Applied and Environmental Microbiology, Vol. 73, Issue 3
  • DOI: 10.1128/AEM.02147-06

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014


The Entner-Doudoroff Pathway Is Obligatory for Gluconate Utilization and Contributes to the Pathogenicity of Vibrio cholerae
journal, April 2012

  • Patra, T.; Koley, H.; Ramamurthy, T.
  • Journal of Bacteriology, Vol. 194, Issue 13
  • DOI: 10.1128/JB.06379-11

Bacterial evolution: Genomics of metabolic trade-offs
journal, October 2016


Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes
journal, October 2006

  • Polz, Martin F.; Hunt, Dana E.; Preheim, Sarah P.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1475
  • DOI: 10.1098/rstb.2006.1928

Metapopulation structure of Vibrionaceae among coastal marine invertebrates
journal, September 2010


Characterization of polysaccharides extracted from brown seaweeds
journal, June 2007


Exploiting rRNA operon copy number to investigate bacterial reproductive strategies
journal, September 2016

  • Roller, Benjamin R. K.; Stoddard, Steven F.; Schmidt, Thomas M.
  • Nature Microbiology, Vol. 1, Issue 11
  • DOI: 10.1038/nmicrobiol.2016.160

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

Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column
journal, May 2009

  • Shi, Yanmei; Tyson, Gene W.; DeLong, Edward F.
  • Nature, Vol. 459, Issue 7244
  • DOI: 10.1038/nature08055

Marine Microbes See a Sea of Gradients
journal, November 2012


Reproducibility of Vibrionaceae population structure in coastal bacterioplankton
journal, November 2012

  • Szabo, Gitta; Preheim, Sarah P.; Kauffman, Kathryn M.
  • The ISME Journal, Vol. 7, Issue 3
  • DOI: 10.1038/ismej.2012.134

Associations and dynamics of Vibrionaceae in the environment, from the genus to the population level
journal, January 2014


Living in the matrix: assembly and control of Vibrio cholerae biofilms
journal, April 2015

  • Teschler, Jennifer K.; Zamorano-Sánchez, David; Utada, Andrew S.
  • Nature Reviews Microbiology, Vol. 13, Issue 5
  • DOI: 10.1038/nrmicro3433

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum
journal, March 2015

  • Turner, Keith H.; Wessel, Aimee K.; Palmer, Gregory C.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 13
  • DOI: 10.1073/pnas.1419677112

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms
journal, May 2013

  • van Opijnen, Tim; Camilli, Andrew
  • Nature Reviews Microbiology, Vol. 11, Issue 7
  • DOI: 10.1038/nrmicro3033

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
journal, September 2009

  • van Opijnen, Tim; Bodi, Kip L.; Camilli, Andrew
  • Nature Methods, Vol. 6, Issue 10
  • DOI: 10.1038/nmeth.1377

Marine metaproteomics: deciphering the microbial metabolic food web
journal, May 2014


Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations
journal, April 2014

  • Yawata, Y.; Cordero, O. X.; Menolascina, F.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 15
  • DOI: 10.1073/pnas.1318943111

Mannitol and the Mannitol-Specific Enzyme IIB Subunit Activate Vibrio cholerae Biofilm Formation
journal, May 2013

  • Ymele-Leki, Patrick; Houot, Laetitia; Watnick, Paula I.
  • Applied and Environmental Microbiology, Vol. 79, Issue 15
  • DOI: 10.1128/AEM.01184-13

Regulation of Levels of Proline as an Osmolyte in Plants under Water Stress
journal, January 1997


Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis
journal, September 2012