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Title: Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

Abstract

Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absencemore » of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermace ae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [1]
  1. Univ. of Amsterdam (Netherlands). Inst. for Biodiversity and Ecosystem Dynamics
  2. Miguel Hernandez Univ., San Juan de Alicante (Spain); Biology Centre of the Czech Academy of Sciences, Ceske Budejovice (Czech Republic)
  3. Miguel Hernandez Univ., San Juan de Alicante (Spain)
  4. Russian Academy of Sciences (RAS), Moscow (Russian Federation). Research Centre of Biotechnology; Delft Univ. of Technology (Netherlands). Dept. of Biotechnology
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379108
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 7; Journal Issue: FEB; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip, and Muyzer, Gerard. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. United States: N. p., 2016. Web. doi:10.3389/fmicb.2016.00211.
Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip, & Muyzer, Gerard. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. United States. doi:10.3389/fmicb.2016.00211.
Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip, and Muyzer, Gerard. Thu . "Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines". United States. doi:10.3389/fmicb.2016.00211. https://www.osti.gov/servlets/purl/1379108.
@article{osti_1379108,
title = {Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines},
author = {Vavourakis, Charlotte D. and Ghai, Rohit and Rodriguez-Valera, Francisco and Sorokin, Dimitry Y. and Tringe, Susannah G. and Hugenholtz, Philip and Muyzer, Gerard},
abstractNote = {Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermace ae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.},
doi = {10.3389/fmicb.2016.00211},
journal = {Frontiers in Microbiology},
number = FEB,
volume = 7,
place = {United States},
year = {2016},
month = {2}
}

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Works referenced in this record:

Biodegradation Potential of Halo(alkali)philic Prokaryotes
journal, April 2012

  • Sorokin, Dimitry Y.; Janssen, Albert J. H.; Muyzer, Gerard
  • Critical Reviews in Environmental Science and Technology, Vol. 42, Issue 8
  • DOI: 10.1080/10643389.2010.534037

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
journal, September 2010

  • Cox, Murray P.; Peterson, Daniel A.; Biggs, Patrick J.
  • BMC Bioinformatics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2105-11-485

Ecology and exploration of the rare biosphere
journal, March 2015

  • Lynch, Michael D. J.; Neufeld, Josh D.
  • Nature Reviews Microbiology, Vol. 13, Issue 4
  • DOI: 10.1038/nrmicro3400

Salisaeta longa gen. nov., sp. nov., a red, halophilic member of the Bacteroidetes
journal, July 2009

  • Vaisman, N.; Oren, A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 10
  • DOI: 10.1099/ijs.0.010892-0

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

Molecular mechanism of energy conservation in polysulfide respiration
journal, June 2008

  • Jormakka, Mika; Yokoyama, Ken; Yano, Takahiro
  • Nature Structural & Molecular Biology, Vol. 15, Issue 7
  • DOI: 10.1038/nsmb.1434

KAAS: an automatic genome annotation and pathway reconstruction server
journal, May 2007

  • Moriya, Y.; Itoh, M.; Okuda, S.
  • Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185
  • DOI: 10.1093/nar/gkm321

Rhodobaca bogoriensis gen. nov. and sp. nov., an alkaliphilic purple nonsulfur bacterium from African Rift Valley soda lakes
journal, July 2000

  • Milford, Amy D.; Achenbach, Laurie A.; Jung, Deborah O.
  • Archives of Microbiology, Vol. 174, Issue 1-2
  • DOI: 10.1007/s002030000166

Bioinformatic Analysis Reveals High Diversity of Bacterial Genes for Laccase-Like Enzymes
journal, October 2011


TIGRFAMs: a protein family resource for the functional identification of proteins
journal, January 2001


Identification of ribosomal RNA genes in metagenomic fragments
journal, April 2009


MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015


The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink
journal, November 2012

  • Jones, Christopher M.; Graf, Daniel RH; Bru, David
  • The ISME Journal, Vol. 7, Issue 2
  • DOI: 10.1038/ismej.2012.125

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


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


Distribution, diversity and ecology of aerobic CO-oxidizing bacteria
journal, February 2007

  • King, Gary M.; Weber, Carolyn F.
  • Nature Reviews Microbiology, Vol. 5, Issue 2
  • DOI: 10.1038/nrmicro1595

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


Genomic Makeup of the Marine Flavobacterium Nonlabens (Donghaeana) dokdonensis and Identification of a Novel Class of Rhodopsins
journal, January 2013

  • Kwon, Soon-Kyeong; Kim, Byung Kwon; Song, Ju Yeon
  • Genome Biology and Evolution, Vol. 5, Issue 1
  • DOI: 10.1093/gbe/evs134

Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota
journal, December 2014

  • Petitjean, Céline; Deschamps, Philippe; López-García, Purificación
  • Genome Biology and Evolution, Vol. 7, Issue 1
  • DOI: 10.1093/gbe/evu274

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

Ribosomal Database Project: data and tools for high throughput rRNA analysis
journal, November 2013

  • Cole, James R.; Wang, Qiong; Fish, Jordan A.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1244

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


Genomes of “Spiribacter”, a streamlined, successful halophilic bacterium
journal, January 2013


Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem
journal, April 2015

  • Andrade, Karen; Logemann, Jörn; Heidelberg, Karla B.
  • The ISME Journal, Vol. 9, Issue 12
  • DOI: 10.1038/ismej.2015.66

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
journal, March 2015

  • Castelle, Cindy J.; Wrighton, Kelly C.; Thomas, Brian C.
  • Current Biology, Vol. 25, Issue 6
  • DOI: 10.1016/j.cub.2015.01.014

Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria
journal, January 2011

  • Ugalde, Juan A.; Podell, Sheila; Narasingarao, Priya
  • Biology Direct, Vol. 6, Issue 1
  • DOI: 10.1186/1745-6150-6-52

An integrative study of a meromictic lake ecosystem in Antarctica
journal, December 2010

  • Lauro, Federico M.; DeMaere, Matthew Z.; Yau, Sheree
  • The ISME Journal, Vol. 5, Issue 5
  • DOI: 10.1038/ismej.2010.185

A light-driven sodium ion pump in marine bacteria
journal, April 2013

  • Inoue, Keiichi; Ono, Hikaru; Abe-Yoshizumi, Rei
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms2689

Binning metagenomic contigs by coverage and composition
journal, September 2014

  • Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino
  • Nature Methods, Vol. 11, Issue 11
  • DOI: 10.1038/nmeth.3103

From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov.
journal, April 2014

  • León, María José; Fernández, Ana B.; Ghai, Rohit
  • Applied and Environmental Microbiology, Vol. 80, Issue 13
  • DOI: 10.1128/AEM.00430-14

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

Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north-western Mediterranean Sea
journal, August 2006

  • Urios, L.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 8
  • DOI: 10.1099/ijs.0.64285-0

Crystal Structure of a Carbon Monoxide Dehydrogenase Reveals a [Ni-4Fe-5S] Cluster
journal, August 2001


Novel and Unexpected Prokaryotic Diversity in Water and Sediments of the Alkaline, Hypersaline Lakes of the Wadi An Natrun, Egypt
journal, April 2007


Functional microbiology of soda lakes
journal, June 2015

  • Sorokin, Dimitry Y.; Banciu, Horia L.; Muyzer, Gerard
  • Current Opinion in Microbiology, Vol. 25
  • DOI: 10.1016/j.mib.2015.05.004

Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme
journal, March 2010


Bacterial Community Structure in a Semi-Arid Haloalkaline Soil Using Culture Independent Method
journal, July 2013


De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
journal, June 2011

  • Narasingarao, Priya; Podell, Sheila; Ugalde, Juan A.
  • The ISME Journal, Vol. 6, Issue 1
  • DOI: 10.1038/ismej.2011.78

Life at low water activity
journal, August 2004

  • Grant, W. D.
  • Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Vol. 359, Issue 1448
  • DOI: 10.1098/rstb.2004.1502

Archaeal Fructose-1,6-bisphosphate Aldolases Constitute a New Family of Archaeal Type Class I Aldolase
journal, May 2001

  • Siebers, Bettina; Brinkmann, Henner; Dörr, Christine
  • Journal of Biological Chemistry, Vol. 276, Issue 31
  • DOI: 10.1074/jbc.M103447200

Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

Nitrate reduction and the nitrogen cycle in archaea
journal, November 2004


Unveiling viral–host interactions within the ‘microbial dark matter’
journal, August 2014

  • Martínez-García, Manuel; Santos, Fernando; Moreno-Paz, Mercedes
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms5542

5S rRNA fingerprints of marine bacteria, halophilic archaea and natural prokaryotic assemblages along a salinity gradient
journal, December 2000


Diversity of Kenyan soda lake alkaliphiles assessed by molecular methods
journal, February 2004


Microbial Biogeography of Six Salt Lakes in Inner Mongolia, China, and a Salt Lake in Argentina
journal, July 2009

  • Pagaling, E.; Wang, H.; Venables, M.
  • Applied and Environmental Microbiology, Vol. 75, Issue 18
  • DOI: 10.1128/AEM.00040-09

Microbial diversity and biogeochemical cycling in soda lakes
journal, August 2014


Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies
journal, March 2002


Methanogenesis at extremely haloalkaline conditions in the soda lakes of Kulunda Steppe (Altai, Russia)
journal, February 2015

  • Sorokin, Dimitry Y.; Abbas, Ben; Geleijnse, Mitchell
  • FEMS Microbiology Ecology, Vol. 91, Issue 4
  • DOI: 10.1093/femsec/fiv016

Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach
journal, May 2014

  • Fernández, Ana B.; Vera-Gargallo, Blanca; Sánchez-Porro, Cristina
  • Frontiers in Microbiology, Vol. 5
  • DOI: 10.3389/fmicb.2014.00196

Gracilimonas mengyeensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-western China
journal, May 2013

  • Wang, Y. -X.; Li, Y. -P.; Liu, J. -H.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 11
  • DOI: 10.1099/ijs.0.052043-0

CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea
journal, October 2009

  • Martin-Cuadrado, A. -B.; Ghai, R.; Gonzaga, A.
  • Applied and Environmental Microbiology, Vol. 75, Issue 23
  • DOI: 10.1128/AEM.01283-09

The ecology of the extremely halophilic archaea
journal, April 1994


Roseinatronobacter thiooxidans gen. nov., sp. nov., a new alkaliphilic aerobic bacteriochlorophylla—containing bacterium isolated from a soda lake
journal, January 2000

  • Sorokin, D. Yu.; Tourova, T. P.; Kuznetsov, B. B.
  • Microbiology, Vol. 69, Issue 1
  • DOI: 10.1007/BF02757261

Psychroflexus salinarum sp. nov., isolated from a marine solar saltern
journal, July 2009

  • Yoon, J. -H.; Kang, S. -J.; Jung, Y. -T.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 10
  • DOI: 10.1099/ijs.0.008359-0

A procedure for the isolation of deoxyribonucleic acid from micro-organisms
journal, April 1961


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


Gracilimonas rosea sp. nov., isolated from tropical seawater, and emended description of the genus Gracilimonas
journal, May 2013

  • Cho, Y.; Chung, H.; Jang, G. I.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 11
  • DOI: 10.1099/ijs.0.052340-0

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


The structure of phototrophic communities of soda lakes of the southeastern Transbaikal Region
journal, April 2007


Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi
journal, August 2015

  • Martin-Cuadrado, Ana-Belen; Pašić, Lejla; Rodriguez-Valera, Francisco
  • BMC Genomics, Vol. 16, Issue 1
  • DOI: 10.1186/s12864-015-1794-8

The Pfam protein families database
journal, January 2004

  • Bateman, Alex; Coin, Lachlan; Durbin, Richard
  • Nucleic Acids Research, Vol. 32, Issue S1, p. D138-D141
  • DOI: 10.1093/nar/gkh121

Bacterial Diversity in the Haloalkaline Lake Elmenteita, Kenya
journal, June 2010


Patterns of microbial diversity along a salinity gradient in the Guerrero Negro solar saltern, Baja CA Sur, Mexico
journal, January 2013


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

Spatial and Temporal Patterns in the Microbial Diversity of a Meromictic Soda Lake in Washington State
journal, June 2008

  • Dimitriu, P. A.; Pinkart, H. C.; Peyton, B. M.
  • Applied and Environmental Microbiology, Vol. 74, Issue 15
  • DOI: 10.1128/AEM.00455-08

Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade
journal, November 2010


Different glycolytic pathways for glucose and fructose in the halophilic archaeon Halococcus saccharolyticus
journal, January 2001

  • Johnsen, Ulrike; Selig, Martina; Xavier, Karina B.
  • Archives of Microbiology, Vol. 175, Issue 1
  • DOI: 10.1007/s002030000237

The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea
journal, December 2005

  • Mongodin, E. F.; Nelson, K. E.; Daugherty, S.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 50
  • DOI: 10.1073/pnas.0509073102

Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds.
journal, March 2002

  • Rodríguez-Valera, Francisco; Benlloch, Susana; Amann, Rudolf
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 2
  • DOI: 10.1099/00207713-52-2-485

The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58
journal, December 2001


Variation of environmental features and microbial populations with salt concentrations in a multi-pond saltern
journal, June 1985

  • Rodriguez-Valera, F.; Ventosa, A.; Juez, G.
  • Microbial Ecology, Vol. 11, Issue 2
  • DOI: 10.1007/BF02010483

Haloarchaeal proteases and proteolytic systems
journal, January 2006


Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga-Flavobacterium-Bacteroides group bacterium from an Hawaiian hypersaline lake
journal, May 2004

  • Donachie, S. P.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 3
  • DOI: 10.1099/ijs.0.02733-0

Purification and characterization of the tungsten enzyme aldehyde:ferredoxin oxidoreductase from the hyperthermophilic denitrifier Pyrobaculum aerophilum
journal, March 2005

  • Hagedoorn, Peter L.; Chen, Tianhong; Schröder, Imke
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 10, Issue 3
  • DOI: 10.1007/s00775-005-0637-5

Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern
journal, June 2002


A Novel Binuclear [CuSMo] Cluster at the Active Site of Carbon Monoxide Dehydrogenase:  Characterization by X-ray Absorption Spectroscopy
journal, January 2003

  • Gnida, Manuel; Ferner, Reinhold; Gremer, Lothar
  • Biochemistry, Vol. 42, Issue 1
  • DOI: 10.1021/bi026514n

Novel archaeal phylotypes from an East African alkaline saltern
journal, May 1999

  • Grant, S.; Grant, William D.; Jones, Brian E.
  • Extremophiles, Vol. 3, Issue 2
  • DOI: 10.1007/s007920050109

Surprising Prokaryotic and Eukaryotic Diversity, Community Structure and Biogeography of Ethiopian Soda Lakes
journal, August 2013


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

Taxonomy of halophilic Archaea: current status and future challenges
journal, August 2014


Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter
journal, December 2006


7. Photosynthetic activity of phytoplankton in tropical African soda lakes
journal, June 1981


Communities of anoxygenic phototrophic bacteria in the saline soda lakes of the Kulunda steppe (Altai Krai)
journal, February 2010


Genomes from Metagenomics
journal, November 2013


Diversity of extremophilic purple phototrophic bacteria in Soap Lake, a Central Washington (USA) Soda Lake: Purple bacteria in Soap Lake
journal, March 2011


Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon
journal, May 2015

  • Sorokin, Dimitry Y.; Kublanov, Ilya V.; Gavrilov, Sergei N.
  • The ISME Journal, Vol. 10, Issue 1
  • DOI: 10.1038/ismej.2015.79

Extremely Halophilic Bacteria in Crystallizer Ponds from Solar Salterns
journal, July 2000


Halo(natrono)archaea isolated from hypersaline lakes utilize cellulose and chitin as growth substrates
journal, September 2015

  • Sorokin, Dimitry Y.; Toshchakov, Stepan V.; Kolganova, Tatyana V.
  • Frontiers in Microbiology, Vol. 6
  • DOI: 10.3389/fmicb.2015.00942

Community structure and metabolism through reconstruction of microbial genomes from the environment
journal, February 2004

  • Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip
  • Nature, Vol. 428, Issue 6978
  • DOI: 10.1038/nature02340

The nos gene cluster from gram-positive bacterium Geobacillus thermodenitrificans NG80-2 and functional characterization of the recombinant NosZ
journal, December 2008


Proteorhodopsin phototrophy in the ocean
journal, June 2001

  • Béjà, Oded; Spudich, Elena N.; Spudich, John L.
  • Nature, Vol. 411, Issue 6839
  • DOI: 10.1038/35081051

Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage
journal, January 2007


Carbon monoxide as a metabolic energy source for extremely halophilic microbes: Implications for microbial activity in Mars regolith
journal, March 2015


Hydrochemistry of the Lake Magadi basin, Kenya
journal, January 1977


The COG database: an updated version includes eukaryotes
journal, January 2003

  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
  • BMC Bioinformatics, Vol. 4, Article No. 41
  • DOI: 10.1186/1471-2105-4-41

Bacterial diversity and activity along a salinity gradient in soda lakes of the Kulunda Steppe (Altai, Russia)
journal, November 2007


Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics
journal, January 2015

  • Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes
  • The ISME Journal, Vol. 9, Issue 7
  • DOI: 10.1038/ismej.2014.254

EMBOSS: The European Molecular Biology Open Software Suite
journal, June 2000


CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database
journal, August 2010

  • Park, Byung H.; Karpinets, Tatiana V.; Syed, Mustafa H.
  • Glycobiology, Vol. 20, Issue 12
  • DOI: 10.1093/glycob/cwq106

Depth Distribution of Microbial Diversity in Mono Lake, a Meromictic Soda Lake in California
journal, February 2003


Gracilimonas tropica gen. nov., sp. nov., isolated from a Synechococcus culture
journal, April 2009

  • Choi, D. H.; Zhang, G. I.; Noh, J. H.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 5
  • DOI: 10.1099/ijs.0.005512-0

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
journal, October 2013

  • Tamura, Koichiro; Stecher, Glen; Peterson, Daniel
  • Molecular Biology and Evolution, Vol. 30, Issue 12
  • DOI: 10.1093/molbev/mst197

DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
journal, January 2007

  • Klappenbach, Joel A.; Goris, Johan; Vandamme, Peter
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 1
  • DOI: 10.1099/ijs.0.64483-0

Unusual pathways and enzymes of central carbohydrate metabolism in Archaea
journal, December 2005


Phylogenetic diversity of bacteria in soda lake stratified sediments
journal, November 2014


    Works referencing / citing this record:

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