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

Title: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

Abstract

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. Inmore » conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Authors:
 [1];  [2];  [3];  [4];  [2];  [5];  [6];  [4];  [7];  [5];  [8]
  1. Taiwan Univ., Taiwan (Republic of China)
  2. National Health Research Institutes, Taiwan (Republic of China)
  3. National Taiwan Univ., Taipei (Taiwan); Washington Univ. in St. Louis, St. Louis, MO (United States)
  4. National Taiwan Univ., Taipei (Taiwan)
  5. Academia Sinica, Taiwan (Republic of China)
  6. National Taiwan Univ., Taipei (Taiwan); Institute of Information Science, Taiwan (Republic of China)
  7. Joint BioEnergy Institute Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  8. National Taiwan Univ., Taipei (Taiwan); Academia Sinica, Taiwan (Republic of China)
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:
1256486
Grant/Contract Number:  
AC02-05CH11231; 95-2627-M-002-004; 97-2627-M-002-001
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Lin, Kuei -Han, Liao, Ben -Yang, Chang, Hao -Wei, Huang, Shiao -Wei, Chang, Ting -Yan, Yang, Cheng -Yu, Wang, Yu -Bin, Lin, Yu-Teh Kirk, Wu, Yu -Wei, Tang, Sen -Lin, and Yu, Hon -Tsen. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. United States: N. p., 2015. Web. doi:10.1186/s12864-015-2230-9.
Lin, Kuei -Han, Liao, Ben -Yang, Chang, Hao -Wei, Huang, Shiao -Wei, Chang, Ting -Yan, Yang, Cheng -Yu, Wang, Yu -Bin, Lin, Yu-Teh Kirk, Wu, Yu -Wei, Tang, Sen -Lin, & Yu, Hon -Tsen. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. United States. doi:10.1186/s12864-015-2230-9.
Lin, Kuei -Han, Liao, Ben -Yang, Chang, Hao -Wei, Huang, Shiao -Wei, Chang, Ting -Yan, Yang, Cheng -Yu, Wang, Yu -Bin, Lin, Yu-Teh Kirk, Wu, Yu -Wei, Tang, Sen -Lin, and Yu, Hon -Tsen. Thu . "Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics". United States. doi:10.1186/s12864-015-2230-9. https://www.osti.gov/servlets/purl/1256486.
@article{osti_1256486,
title = {Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics},
author = {Lin, Kuei -Han and Liao, Ben -Yang and Chang, Hao -Wei and Huang, Shiao -Wei and Chang, Ting -Yan and Yang, Cheng -Yu and Wang, Yu -Bin and Lin, Yu-Teh Kirk and Wu, Yu -Wei and Tang, Sen -Lin and Yu, Hon -Tsen},
abstractNote = {Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.},
doi = {10.1186/s12864-015-2230-9},
journal = {BMC Genomics},
number = 1,
volume = 16,
place = {United States},
year = {2015},
month = {12}
}

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

Citation Metrics:
Cited by: 2 works
Citation information provided by
Web of Science

Figures / Tables:

Table 1 Table 1: Geochemical and physical parameters of SHP hot spring water

Save / Share:

Works referenced in this record:

Malonyl-Coenzyme A Reductase in the Modified 3-Hydroxypropionate Cycle for Autotrophic Carbon Fixation in Archaeal Metallosphaera and Sulfolobus spp.
journal, October 2006

  • Alber, B.; Olinger, M.; Rieder, A.
  • Journal of Bacteriology, Vol. 188, Issue 24, p. 8551-8559
  • DOI: 10.1128/JB.00987-06

Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov
journal, March 2000

  • Kelly, D. P.; Wood, A. P.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 2
  • DOI: 10.1099/00207713-50-2-511

Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements
journal, February 2005

  • Mojica, Francisco J. M.; D�ez-Villase�or, Chc)sar; Garc�a-Mart�nez, Jes�s
  • Journal of Molecular Evolution, Vol. 60, Issue 2
  • DOI: 10.1007/s00239-004-0046-3

PILER-CR: Fast and accurate identification of CRISPR repeats
journal, January 2007


Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines
journal, May 2013

  • Huang, Qiuyuan; Jiang, Hongchen; Briggs, Brandon R.
  • FEMS Microbiology Ecology, Vol. 85, Issue 3
  • DOI: 10.1111/1574-6941.12134

Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation
journal, June 2011


Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow
journal, January 2014

  • Bachmann, Nathan L.; Petty, Nicola K.; Ben Zakour, Nouri L.
  • BMC Genomics, Vol. 15, Issue 1
  • DOI: 10.1186/1471-2164-15-389

Microbiology of acidic, geothermal springs of Montserrat: environmental rDNA analysis
journal, October 2000


Localization, purification and properties of a tetrathionate hydrolase from Acidithiobacillus caldus
journal, January 2004


Geochemistry and Dynamics of the Yellowstone National Park Hydrothermal System
journal, May 1989


Identification of a gene encoding a tetrathionate hydrolase in Acidithiobacillus ferrooxidans
journal, October 2007


Segregated Planktonic and Bottom-Dwelling Archaeal Communities in High-Temperature Acidic/Sulfuric Ponds of the Tatun Volcano Group, Northern Taiwan
journal, January 2011

  • Cheng, Ting-Wen; Wang, Pei-Ling; Song, Sheng-Rong
  • Terrestrial, Atmospheric and Oceanic Sciences, Vol. 24, Issue 3
  • DOI: 10.3319/TAO.2013.01.11.01(TT)

Impact of Molecular Hydrogen on Chalcopyrite Bioleaching by the Extremely Thermoacidophilic Archaeon Metallosphaera sedula
journal, February 2010

  • Auernik, K. S.; Kelly, R. M.
  • Applied and Environmental Microbiology, Vol. 76, Issue 8, p. 2668-2672
  • DOI: 10.1128/AEM.02016-09

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


Archaeal diversity in Icelandic hot springs: Archaeal diversity in Icelandic hot springs
journal, January 2007


Identification and cloning of Thiobacillus ferrooxidans structural nif genes in Escherichia coli
journal, January 1986


Sulfolobus tokodaii sp. nov. (f. Sulfolobus sp. strain 7), a new member of the genus Sulfolobus isolated from Beppu Hot Springs, Japan
journal, February 2002

  • Suzuki, Toshiharu; Iwasaki, Toshio; Uzawa, Taketoshi
  • Extremophiles, Vol. 6, Issue 1
  • DOI: 10.1007/s007920100221

Correlation between microbiological and chemical parameters of some hydrothermal springs in New Mexico, USA
journal, September 2003


Microbial Diversity of Acidic Hot Spring (Kawah Hujan B) in Geothermal Field of Kamojang Area, West Java-Indonesia
journal, April 2009

  • Aditiawati, Pingkan; Yohandini, Heni; Madayanti, Fida
  • The Open Microbiology Journal, Vol. 3, Issue 1
  • DOI: 10.2174/1874285800903010058

Characteristics of a phylogenetically ambiguous, arsenic-oxidizing Thiomonas sp., Thiomonas arsenitoxydans strain 3AsT sp. nov
journal, March 2011

  • Slyemi, Djamila; Moinier, Danielle; Brochier-Armanet, Céline
  • Archives of Microbiology, Vol. 193, Issue 6
  • DOI: 10.1007/s00203-011-0684-y

In-depth Characterization via Complementing Culture-Independent Approaches of the Microbial Community in an Acidic Hot Spring of the Colombian Andes
journal, September 2011

  • Bohorquez, Laura C.; Delgado-Serrano, Luisa; López, Gina
  • Microbial Ecology, Vol. 63, Issue 1
  • DOI: 10.1007/s00248-011-9943-3

The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
journal, October 2003

  • Waters, E.; Hohn, M. J.; Ahel, I.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 22
  • DOI: 10.1073/pnas.1735403100

Autotrophic carbon fixation in archaea
journal, May 2010

  • Berg, Ivan A.; Kockelkorn, Daniel; Ramos-Vera, W. Hugo
  • Nature Reviews Microbiology, Vol. 8, Issue 6, p. 447-460
  • DOI: 10.1038/nrmicro2365

Microbial diversity of boron-rich volcanic hot springs of  St. Lucia, Lesser Antilles
journal, December 2009


Complete Genome Sequence of the Thermoacidophilic Crenarchaeon Thermoproteus uzoniensis 768-20
journal, April 2011

  • Mardanov, A. V.; Gumerov, V. M.; Beletsky, A. V.
  • Journal of Bacteriology, Vol. 193, Issue 12
  • DOI: 10.1128/JB.00409-11

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
journal, July 2012

  • Namiki, Toshiaki; Hachiya, Tsuyoshi; Tanaka, Hideaki
  • Nucleic Acids Research, Vol. 40, Issue 20
  • DOI: 10.1093/nar/gks678

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
journal, February 2010

  • Marraffini, Luciano A.; Sontheimer, Erik J.
  • Nature Reviews Genetics, Vol. 11, Issue 3
  • DOI: 10.1038/nrg2749

Structural basis of [NiFe] hydrogenase maturation by Hyp proteins
journal, October 2012

  • Watanabe, Satoshi; Sasaki, Daisuke; Tominaga, Taiga
  • Biological Chemistry, Vol. 393, Issue 10
  • DOI: 10.1515/hsz-2012-0197

Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring
journal, August 2001


The Redox Potential of Hot Springs in Taiwan
journal, January 2009


A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont
journal, May 2002

  • Huber, Harald; Hohn, Michael J.; Rachel, Reinhard
  • Nature, Vol. 417, Issue 6884
  • DOI: 10.1038/417063a

Complete and Draft Genome Sequences of Six Members of the Aquificales
journal, January 2009

  • Reysenbach, A. -L.; Hamamura, N.; Podar, M.
  • Journal of Bacteriology, Vol. 191, Issue 6
  • DOI: 10.1128/JB.01645-08

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
journal, January 2007

  • Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine
  • BMC Bioinformatics, Vol. 8, Issue 1
  • DOI: 10.1186/1471-2105-8-172

The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota
journal, October 2011


3-Hydroxypropionyl-Coenzyme A Dehydratase and Acryloyl-Coenzyme A Reductase, Enzymes of the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in the Sulfolobales
journal, May 2009

  • Teufel, R.; Kung, J. W.; Kockelkorn, D.
  • Journal of Bacteriology, Vol. 191, Issue 14, p. 4572-4581
  • DOI: 10.1128/JB.00068-09

From The Cover: Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem
journal, January 2005

  • Spear, J. R.; Walker, J. J.; McCollom, T. M.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 7, p. 2555-2560
  • DOI: 10.1073/pnas.0409574102

Non-parametric multivariate analyses of changes in community structure
journal, March 1993


Diversity of 16S rRNA gene, ITS region and aclB gene of the Aquificales
journal, September 2006


Effects of Abiotic Factors on the Phylogenetic Diversity of Bacterial Communities in Acidic Thermal Springs
journal, January 2007

  • Mathur, J.; Bizzoco, R. W.; Ellis, D. G.
  • Applied and Environmental Microbiology, Vol. 73, Issue 8
  • DOI: 10.1128/AEM.02567-06

Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China
journal, May 2012


Thermoproteus uzoniensis sp. nov., a new extremely thermophilic archaebacterium from Kamchatka continental hot springs
journal, November 1990

  • Bonch-Osmolovskaya, E. A.; Miroshnichenko, M. L.; Kostrikina, N. A.
  • Archives of Microbiology, Vol. 154, Issue 6
  • DOI: 10.1007/BF00248836

Life in extreme environments
journal, February 2001

  • Rothschild, Lynn J.; Mancinelli, Rocco L.
  • Nature, Vol. 409, Issue 6823
  • DOI: 10.1038/35059215

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function
journal, March 2010


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


Novel Archaea and Bacteria Dominate Stable Microbial Communities in North America’s Largest Hot Spring
journal, December 2007

  • Wilson, Mark S.; Siering, Patricia L.; White, Christopher L.
  • Microbial Ecology, Vol. 56, Issue 2
  • DOI: 10.1007/s00248-007-9347-6

Microbial community structure and sulfur biogeochemistry in mildly-acidic sulfidic geothermal springs in Yellowstone National Park
journal, November 2012

  • Macur, R. E.; Jay, Z. J.; Taylor, W. P.
  • Geobiology, Vol. 11, Issue 1
  • DOI: 10.1111/gbi.12015

Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon
journal, April 2013

  • Jaubert, Carole; Danioux, Chloë; Oberto, Jacques
  • Open Biology, Vol. 3, Issue 4
  • DOI: 10.1098/rsob.130010

Seismicity characteristics of a potentially active Quaternary volcano: The Tatun Volcano Group, northern Taiwan
journal, February 2007

  • Konstantinou, Konstantinos I.; Lin, Cheng-Horng; Liang, Wen-Tzong
  • Journal of Volcanology and Geothermal Research, Vol. 160, Issue 3-4
  • DOI: 10.1016/j.jvolgeores.2006.09.009

The Genome of Sulfolobus acidocaldarius, a Model Organism of the Crenarchaeota
journal, July 2005


Metallosphaera sedula gen, and sp. nov. Represents a New Genus of Aerobic, Metal-Mobilizing, Thermoacidophilic Archaebacteria
journal, July 1989

  • Huber, Gertrud; Spinnler, Carola; Gambacorta, Agata
  • Systematic and Applied Microbiology, Vol. 12, Issue 1, p. 38-47
  • DOI: 10.1016/S0723-2020(89)80038-4

Characteristics and Origins of Hot Springs in the Tatun Volcano Group in Northern Taiwan
journal, January 2011

  • Liu, Chia-Mei; Song, Sheng-Rong; Chen, Yaw-Lin
  • Terrestrial, Atmospheric and Oceanic Sciences, Vol. 22, Issue 5
  • DOI: 10.3319/TAO.2011.05.25.01(TT)

Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China: Microbial diversities in hot springs
journal, November 2012

  • Song, Zhao-Qi; Wang, Feng-Ping; Zhi, Xiao-Yang
  • Environmental Microbiology, Vol. 15, Issue 4
  • DOI: 10.1111/1462-2920.12025

CO2 Uptake and Fixation by a Thermoacidophilic Microbial Community Attached to Precipitated Sulfur in a Geothermal Spring
journal, May 2009

  • Boyd, E. S.; Leavitt, W. D.; Geesey, G. G.
  • Applied and Environmental Microbiology, Vol. 75, Issue 13
  • DOI: 10.1128/AEM.02751-08

Bioleaching review part A:
journal, December 2003

  • Rohwerder, T.; Gehrke, T.; Kinzler, K.
  • Applied Microbiology and Biotechnology, Vol. 63, Issue 3
  • DOI: 10.1007/s00253-003-1448-7

Geochemical and Biological Diversity of Acidic, Hot Springs in Lassen Volcanic National Park
journal, March 2006

  • Siering, Patricia L.; Clarke, Jessica M.; Wilson, Mark S.
  • Geomicrobiology Journal, Vol. 23, Issue 2
  • DOI: 10.1080/01490450500533916

    Works referencing / citing this record:

    Characteristics of a phylogenetically ambiguous, arsenic-oxidizing Thiomonas sp., Thiomonas arsenitoxydans strain 3AsT sp. nov
    journal, March 2011

    • Slyemi, Djamila; Moinier, Danielle; Brochier-Armanet, Céline
    • Archives of Microbiology, Vol. 193, Issue 6
    • DOI: 10.1007/s00203-011-0684-y

    Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements
    journal, February 2005

    • Mojica, Francisco J. M.; D�ez-Villase�or, Chc)sar; Garc�a-Mart�nez, Jes�s
    • Journal of Molecular Evolution, Vol. 60, Issue 2
    • DOI: 10.1007/s00239-004-0046-3

    Novel Archaea and Bacteria Dominate Stable Microbial Communities in North America’s Largest Hot Spring
    journal, December 2007

    • Wilson, Mark S.; Siering, Patricia L.; White, Christopher L.
    • Microbial Ecology, Vol. 56, Issue 2
    • DOI: 10.1007/s00248-007-9347-6

    In-depth Characterization via Complementing Culture-Independent Approaches of the Microbial Community in an Acidic Hot Spring of the Colombian Andes
    journal, September 2011

    • Bohorquez, Laura C.; Delgado-Serrano, Luisa; López, Gina
    • Microbial Ecology, Vol. 63, Issue 1
    • DOI: 10.1007/s00248-011-9943-3

    Bioleaching review part A:
    journal, December 2003

    • Rohwerder, T.; Gehrke, T.; Kinzler, K.
    • Applied Microbiology and Biotechnology, Vol. 63, Issue 3
    • DOI: 10.1007/s00253-003-1448-7

    Diversity of 16S rRNA gene, ITS region and aclB gene of the Aquificales
    journal, September 2006


    Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China
    journal, May 2012


    Microbiology of acidic, geothermal springs of Montserrat: environmental rDNA analysis
    journal, October 2000


    Sulfolobus tokodaii sp. nov. (f. Sulfolobus sp. strain 7), a new member of the genus Sulfolobus isolated from Beppu Hot Springs, Japan
    journal, February 2002

    • Suzuki, Toshiharu; Iwasaki, Toshio; Uzawa, Taketoshi
    • Extremophiles, Vol. 6, Issue 1
    • DOI: 10.1007/s007920100221

    Identification and cloning of Thiobacillus ferrooxidans structural nif genes in Escherichia coli
    journal, January 1986


    Identification of a gene encoding a tetrathionate hydrolase in Acidithiobacillus ferrooxidans
    journal, October 2007


    Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation
    journal, June 2011


    Seismicity characteristics of a potentially active Quaternary volcano: The Tatun Volcano Group, northern Taiwan
    journal, February 2007

    • Konstantinou, Konstantinos I.; Lin, Cheng-Horng; Liang, Wen-Tzong
    • Journal of Volcanology and Geothermal Research, Vol. 160, Issue 3-4
    • DOI: 10.1016/j.jvolgeores.2006.09.009

    Life in extreme environments
    journal, February 2001

    • Rothschild, Lynn J.; Mancinelli, Rocco L.
    • Nature, Vol. 409, Issue 6823
    • DOI: 10.1038/35059215

    A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont
    journal, May 2002

    • Huber, Harald; Hohn, Michael J.; Rachel, Reinhard
    • Nature, Vol. 417, Issue 6884
    • DOI: 10.1038/417063a

    CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    journal, February 2010

    • Marraffini, Luciano A.; Sontheimer, Erik J.
    • Nature Reviews Genetics, Vol. 11, Issue 3
    • DOI: 10.1038/nrg2749

    Autotrophic carbon fixation in archaea
    journal, May 2010

    • Berg, Ivan A.; Kockelkorn, Daniel; Ramos-Vera, W. Hugo
    • Nature Reviews Microbiology, Vol. 8, Issue 6, p. 447-460
    • DOI: 10.1038/nrmicro2365

    Localization, purification and properties of a tetrathionate hydrolase from Acidithiobacillus caldus
    journal, January 2004


    Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring
    journal, August 2001


    From The Cover: Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem
    journal, January 2005

    • Spear, J. R.; Walker, J. J.; McCollom, T. M.
    • Proceedings of the National Academy of Sciences, Vol. 102, Issue 7, p. 2555-2560
    • DOI: 10.1073/pnas.0409574102

    The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
    journal, October 2003

    • Waters, E.; Hohn, M. J.; Ahel, I.
    • Proceedings of the National Academy of Sciences, Vol. 100, Issue 22
    • DOI: 10.1073/pnas.1735403100

    Geochemical and Biological Diversity of Acidic, Hot Springs in Lassen Volcanic National Park
    journal, March 2006

    • Siering, Patricia L.; Clarke, Jessica M.; Wilson, Mark S.
    • Geomicrobiology Journal, Vol. 23, Issue 2
    • DOI: 10.1080/01490450500533916

    MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
    journal, July 2012

    • Namiki, Toshiaki; Hachiya, Tsuyoshi; Tanaka, Hideaki
    • Nucleic Acids Research, Vol. 40, Issue 20
    • DOI: 10.1093/nar/gks678

    Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon
    journal, April 2013

    • Jaubert, Carole; Danioux, Chloë; Oberto, Jacques
    • Open Biology, Vol. 3, Issue 4
    • DOI: 10.1098/rsob.130010

    Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov
    journal, March 2000

    • Kelly, D. P.; Wood, A. P.
    • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 2
    • DOI: 10.1099/00207713-50-2-511

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


    Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China: Microbial diversities in hot springs
    journal, November 2012

    • Song, Zhao-Qi; Wang, Feng-Ping; Zhi, Xiao-Yang
    • Environmental Microbiology, Vol. 15, Issue 4
    • DOI: 10.1111/1462-2920.12025

    Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines
    journal, May 2013

    • Huang, Qiuyuan; Jiang, Hongchen; Briggs, Brandon R.
    • FEMS Microbiology Ecology, Vol. 85, Issue 3
    • DOI: 10.1111/1574-6941.12134

    Microbial community structure and sulfur biogeochemistry in mildly-acidic sulfidic geothermal springs in Yellowstone National Park
    journal, November 2012

    • Macur, R. E.; Jay, Z. J.; Taylor, W. P.
    • Geobiology, Vol. 11, Issue 1
    • DOI: 10.1111/gbi.12015

    Non-parametric multivariate analyses of changes in community structure
    journal, March 1993


    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


    Archaeal diversity in Icelandic hot springs: Archaeal diversity in Icelandic hot springs
    journal, January 2007


    Microbial diversity of boron-rich volcanic hot springs of  St. Lucia, Lesser Antilles
    journal, December 2009


    Geochemistry and Dynamics of the Yellowstone National Park Hydrothermal System
    journal, May 1989


    The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
    journal, January 2007

    • Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine
    • BMC Bioinformatics, Vol. 8, Issue 1
    • DOI: 10.1186/1471-2105-8-172

    PILER-CR: Fast and accurate identification of CRISPR repeats
    journal, January 2007


    Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow
    journal, January 2014

    • Bachmann, Nathan L.; Petty, Nicola K.; Ben Zakour, Nouri L.
    • BMC Genomics, Vol. 15, Issue 1
    • DOI: 10.1186/1471-2164-15-389

    Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function
    journal, March 2010


    The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota
    journal, October 2011


    Structural basis of [NiFe] hydrogenase maturation by Hyp proteins
    journal, October 2012

    • Watanabe, Satoshi; Sasaki, Daisuke; Tominaga, Taiga
    • Biological Chemistry, Vol. 393, Issue 10
    • DOI: 10.1515/hsz-2012-0197

    Microbial Diversity of Acidic Hot Spring (Kawah Hujan B) in Geothermal Field of Kamojang Area, West Java-Indonesia
    journal, April 2009

    • Aditiawati, Pingkan; Yohandini, Heni; Madayanti, Fida
    • The Open Microbiology Journal, Vol. 3, Issue 1
    • DOI: 10.2174/1874285800903010058