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

Title: Microbial Community Structure and Functional Potential Along a Hypersaline Gradient

; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1461649; OSTI ID: 1471857
Report Number(s):
Journal ID: ISSN 1664-302X; 1492
Grant/Contract Number:  
AC02-05CH11231; AC05-76RL01830; AC05-00OR22725
Resource Type:
Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Name: Frontiers in Microbiology Journal Volume: 9; Journal ID: ISSN 1664-302X
Frontiers Research Foundation
Country of Publication:
59 BASIC BIOLOGICAL SCIENCES; microbial communities; halophiles; biofuels; metagenomes; 16S rRNA

Citation Formats

Kimbrel, Jeffrey A., Ballor, Nicholas, Wu, Yu-Wei, David, Maude M., Hazen, Terry C., Simmons, Blake A., Singer, Steven W., and Jansson, Janet K. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Switzerland: N. p., 2018. Web. doi:10.3389/fmicb.2018.01492.
Kimbrel, Jeffrey A., Ballor, Nicholas, Wu, Yu-Wei, David, Maude M., Hazen, Terry C., Simmons, Blake A., Singer, Steven W., & Jansson, Janet K. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Switzerland. doi:10.3389/fmicb.2018.01492.
Kimbrel, Jeffrey A., Ballor, Nicholas, Wu, Yu-Wei, David, Maude M., Hazen, Terry C., Simmons, Blake A., Singer, Steven W., and Jansson, Janet K. Tue . "Microbial Community Structure and Functional Potential Along a Hypersaline Gradient". Switzerland. doi:10.3389/fmicb.2018.01492.
title = {Microbial Community Structure and Functional Potential Along a Hypersaline Gradient},
author = {Kimbrel, Jeffrey A. and Ballor, Nicholas and Wu, Yu-Wei and David, Maude M. and Hazen, Terry C. and Simmons, Blake A. and Singer, Steven W. and Jansson, Janet K.},
abstractNote = {},
doi = {10.3389/fmicb.2018.01492},
journal = {Frontiers in Microbiology},
number = ,
volume = 9,
place = {Switzerland},
year = {2018},
month = {7}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.3389/fmicb.2018.01492

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Figures / Tables:

Table 1 Table 1: Chemical analysis of pond water and sediments.

Save / Share:

Works referenced in this record:

Microbial interactions: from networks to models
journal, July 2012

  • Faust, Karoline; Raes, Jeroen
  • Nature Reviews Microbiology, Vol. 10, Issue 8
  • DOI: 10.1038/nrmicro2832

Global patterns in bacterial diversity
journal, June 2007

  • Lozupone, C. A.; Knight, R.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 27
  • DOI: 10.1073/pnas.0611525104

Identification of GH15 Family Thermophilic Archaeal Trehalases That Function within a Narrow Acidic-pH Range
journal, May 2015

  • Sakaguchi, Masayoshi; Shimodaira, Satoru; Ishida, Shin-nosuke
  • Applied and Environmental Microbiology, Vol. 81, Issue 15
  • DOI: 10.1128/AEM.00956-15

Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm
journal, May 2015

  • O’Dell, Kaela B.; Woo, Hannah L.; Utturkar, Sagar
  • Genome Announcements, Vol. 3, Issue 3
  • DOI: 10.1128/genomeA.00402-15

Characterization of a metagenome-derived halotolerant cellulase
journal, October 2006

New Abundant Microbial Groups in Aquatic Hypersaline Environments
journal, October 2011

  • Ghai, Rohit; Pašić, Lejla; Fernández, Ana Beatriz
  • Scientific Reports, Vol. 1, Issue 1
  • DOI: 10.1038/srep00135

Characterization and radiation resistance of new isolates of Rubrobacter radiotolerans and Rubrobacter xylanophilus
journal, November 1999

Bacterial chitin utilisation at extremely haloalkaline conditions
journal, September 2012

The ade4 Package: Implementing the Duality Diagram for Ecologists
journal, January 2007

  • Dray, Stéphane; Dufour, Anne-Béatrice
  • Journal of Statistical Software, Vol. 22, Issue 4
  • DOI: 10.18637/jss.v022.i04

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017

  • Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
  • Nature Biotechnology, Vol. 35, Issue 8
  • DOI: 10.1038/nbt.3893

ChloroplastDB: the Chloroplast Genome Database
journal, January 2006

Thiohalobacter thiocyanaticus gen. nov., sp. nov., a moderately halophilic, sulfur-oxidizing gammaproteobacterium from hypersaline lakes, that utilizes thiocyanate
journal, August 2009

  • Sorokin, D. Yu.; Kovaleva, O. L.; Tourova, T. P.
  • DOI: 10.1099/ijs.0.012880-0

Phylogenetic Distribution of Potential Cellulases in Bacteria
journal, December 2012

  • Berlemont, Renaud; Martiny, Adam C.
  • Applied and Environmental Microbiology, Vol. 79, Issue 5
  • DOI: 10.1128/AEM.03305-12

Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009

Applying metagenomics for the identification of bacterial cellulases that are stable in ionic liquids
journal, January 2009

  • Pottkämper, Julia; Barthen, Peter; Ilmberger, Nele
  • Green Chemistry, Vol. 11, Issue 7
  • DOI: 10.1039/b820157a

Diversity of halophilic microorganisms: Environments, phylogeny, physiology, and applications
journal, January 2002

Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea)
journal, December 2014

  • Pop Ristova, Petra; Wenzhöfer, Frank; Ramette, Alban
  • The ISME Journal, Vol. 9, Issue 6
  • DOI: 10.1038/ismej.2014.217

Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013

  • Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1076

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
journal, July 2014

Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification
journal, July 2010

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community
journal, December 2013

  • Podell, Sheila; Emerson, Joanne B.; Jones, Claudia M.
  • The ISME Journal, Vol. 8, Issue 5
  • DOI: 10.1038/ismej.2013.221

Biodegradation of Organic Pollutants by Halophilic Bacteria and Archaea
journal, January 2008

  • Le Borgne, Sylvie; Paniagua, Dayanira; Vazquez-Duhalt, Rafael
  • Journal of Molecular Microbiology and Biotechnology, Vol. 15, Issue 2-3
  • DOI: 10.1159/000121323

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

Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes
journal, January 2013

Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond
journal, September 2015

Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems
journal, March 2012

Gene cloning, expression and characterization of a new cold-active and salt-tolerant endo-β-1,4-xylanase from marine Glaciecola mesophila KMM 241
journal, June 2009

  • Guo, Bing; Chen, Xiu-Lan; Sun, Cai-Yun
  • Applied Microbiology and Biotechnology, Vol. 84, Issue 6
  • DOI: 10.1007/s00253-009-2056-y

Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern
journal, June 2002

Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance
journal, January 2011

  • Zhang, Tao; Datta, Supratim; Eichler, Jerry
  • Green Chemistry, Vol. 13, Issue 8
  • DOI: 10.1039/c1gc15193b

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

Relationship of sequence and structure to specificity in the α-amylase family of enzymes
journal, March 2001

  • MacGregor, E. Ann; Janeček, Štefan; Svensson, Birte
  • Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1546, Issue 1
  • DOI: 10.1016/S0167-4838(00)00302-2

Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics
journal, April 2014

  • Fernández, Ana B.; Ghai, Rohit; Martin-Cuadrado, Ana-Belen
  • FEMS Microbiology Ecology, Vol. 88, Issue 3
  • DOI: 10.1111/1574-6941.12329

dbCAN: a web resource for automated carbohydrate-active enzyme annotation
journal, May 2012

  • Yin, Yanbin; Mao, Xizeng; Yang, Jincai
  • Nucleic Acids Research, Vol. 40, Issue W1
  • DOI: 10.1093/nar/gks479

Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190
journal, March 2004

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015

Cyanobacterial reuse of extracellular organic carbon in microbial mats
journal, October 2015

  • Stuart, Rhona K.; Mayali, Xavier; Lee, Jackson Z.
  • The ISME Journal, Vol. 10, Issue 5
  • DOI: 10.1038/ismej.2015.180

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015

  • Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
  • Genome Research, Vol. 25, Issue 7
  • DOI: 10.1101/gr.186072.114

Potential halophilic cellulases for in situ enzymatic saccharification of ionic liquids pretreated lignocelluloses
journal, March 2014

Primer and platform effects on 16S rRNA tag sequencing
journal, August 2015

Molecular mechanisms underlying roseobacter–phytoplankton symbioses
journal, June 2010

Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments
journal, September 1998

Extremophiles as a source for novel enzymes
journal, June 2003

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
journal, April 2013

Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm
journal, June 2016

Salt-activated endoglucanase of a strain of alkaliphilic Bacillus agaradhaerens
journal, April 2006

  • Hirasawa, Kazumichi; Uchimura, Kohsuke; Kashiwa, Masami
  • Antonie van Leeuwenhoek, Vol. 89, Issue 2
  • DOI: 10.1007/s10482-005-9023-0

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012

Recent trends in ionic liquid (IL) tolerant enzymes and microorganisms for biomass conversion
journal, October 2013

How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens
journal, May 2005

Complete Genome Sequence of the Marine Cellulose- and Xylan-Degrading Bacterium Glaciecolasp. Strain 4H-3-7+YE-5
journal, June 2011

  • Klippel, B.; Lochner, A.; Bruce, D. C.
  • Journal of Bacteriology, Vol. 193, Issue 17
  • DOI: 10.1128/JB.05468-11

Microbial Diversity in Deep-sea Methane Seep Sediments Presented by SSU rRNA Gene Tag Sequencing
journal, January 2012

  • Nunoura, Takuro; Takaki, Yoshihiro; Kazama, Hiromi
  • Microbes and environments, Vol. 27, Issue 4
  • DOI: 10.1264/jsme2.ME12032

Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales
journal, September 2013

  • Youssef, Noha H.; Savage-Ashlock, Kristen N.; McCully, Alexandra L.
  • The ISME Journal, Vol. 8, Issue 3
  • DOI: 10.1038/ismej.2013.165

The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

  • Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1178

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
journal, May 2013

  • Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam
  • Nature Biotechnology, Vol. 31, Issue 6
  • DOI: 10.1038/nbt.2579

Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake
journal, November 2017

  • Jones, Adriane Clark; Hambright, K. David; Caron, David A.
  • Microbial Ecology, Vol. 75, Issue 4
  • DOI: 10.1007/s00248-017-1087-7

Using network analysis to explore co-occurrence patterns in soil microbial communities
journal, September 2011

  • Barberán, Albert; Bates, Scott T.; Casamayor, Emilio O.
  • The ISME Journal, Vol. 6, Issue 2
  • DOI: 10.1038/ismej.2011.119

Halophilic hydrolases as a new tool for the biotechnological industries
journal, August 2012

  • Delgado-García, Mariana; Valdivia-Urdiales, Blanca; Aguilar-González, Cristóbal Noe
  • Journal of the Science of Food and Agriculture, Vol. 92, Issue 13
  • DOI: 10.1002/jsfa.5860

Variability in habitat value of commercial salt production ponds: implications for waterbird management and tidal marsh restoration planning
journal, May 2012

  • Athearn, Nicole D.; Takekawa, John Y.; Bluso-Demers, Jill D.
  • Hydrobiologia, Vol. 697, Issue 1
  • DOI: 10.1007/s10750-012-1177-y

Genomic Potential for Polysaccharide Deconstruction in Bacteria
journal, December 2014

  • Berlemont, Renaud; Martiny, Adam C.
  • Applied and Environmental Microbiology, Vol. 81, Issue 4
  • DOI: 10.1128/AEM.03718-14

BLAST+: architecture and applications
journal, January 2009

  • Camacho, Christiam; Coulouris, George; Avagyan, Vahram
  • BMC Bioinformatics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2105-10-421

Deciphering microbial interactions and detecting keystone species with co-occurrence networks
journal, May 2014

Microbial diversity of hypersaline environments: a metagenomic approach
journal, June 2015

  • Ventosa, Antonio; de la Haba, Rafael R.; Sánchez-Porro, Cristina
  • Current Opinion in Microbiology, Vol. 25
  • DOI: 10.1016/j.mib.2015.05.002

Genome-wide analysis of lysine catabolism in bacteria reveals new connections with osmotic stress resistance
journal, July 2013

  • Neshich, Izabella AP; Kiyota, Eduardo; Arruda, Paulo
  • The ISME Journal, Vol. 7, Issue 12
  • DOI: 10.1038/ismej.2013.123

Microbial seed banks: the ecological and evolutionary implications of dormancy
journal, January 2011

  • Lennon, Jay T.; Jones, Stuart E.
  • Nature Reviews Microbiology, Vol. 9, Issue 2
  • DOI: 10.1038/nrmicro2504

Xyloglucan Is Recognized by Carbohydrate-binding Modules That Interact with β-Glucan Chains
journal, November 2005

  • Najmudin, Shabir; Guerreiro, Catarina I. P. D.; Carvalho, Ana L.
  • Journal of Biological Chemistry, Vol. 281, Issue 13
  • DOI: 10.1074/jbc.M510559200

Integrative analysis of environmental sequences using MEGAN4
journal, June 2011

  • Huson, D. H.; Mitra, S.; Ruscheweyh, H. -J.
  • Genome Research, Vol. 21, Issue 9
  • DOI: 10.1101/gr.120618.111

Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments
journal, April 2014

Sialic Acid Recognition by Vibrio cholerae Neuraminidase
journal, June 2004

  • Moustafa, Ibrahim; Connaris, Helen; Taylor, Margaret
  • Journal of Biological Chemistry, Vol. 279, Issue 39
  • DOI: 10.1074/jbc.M404965200

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus
journal, September 2014

  • Prestat, Emmanuel; David, Maude M.; Hultman, Jenni
  • Nucleic Acids Research, Vol. 42, Issue 19
  • DOI: 10.1093/nar/gku702

A novel salt-tolerant endo-β-1,4-glucanase Cel5A in Vibrio sp. G21 isolated from mangrove soil
journal, April 2010

  • Gao, Zhaoming; Ruan, Lingwei; Chen, Xiulan
  • Applied Microbiology and Biotechnology, Vol. 87, Issue 4, p. 1373-1382
  • DOI: 10.1007/s00253-010-2554-y

Genome-Based Taxonomic Classification of Bacteroidetes
journal, December 2016

  • Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina
  • Frontiers in Microbiology, Vol. 7
  • DOI: 10.3389/fmicb.2016.02003

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

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
journal, January 2014

  • Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio
  • The ISME Journal, Vol. 8, Issue 7
  • DOI: 10.1038/ismej.2013.254

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
journal, January 2013

  • Levasseur, Anthony; Drula, Elodie; Lombard, Vincent
  • Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 41
  • DOI: 10.1186/1754-6834-6-41

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.