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 »
- Authors:
-
- Taiwan Univ., Taiwan (Republic of China)
- National Health Research Institutes, Taiwan (Republic of China)
- National Taiwan Univ., Taipei (Taiwan); Washington Univ. in St. Louis, St. Louis, MO (United States)
- National Taiwan Univ., Taipei (Taiwan)
- Academia Sinica, Taiwan (Republic of China)
- National Taiwan Univ., Taipei (Taiwan); Institute of Information Science, Taiwan (Republic of China)
- Joint BioEnergy Institute Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- National Taiwan Univ., Taipei (Taiwan); Academia Sinica, Taiwan (Republic of China)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- 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. https://doi.org/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. https://doi.org/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 = {Thu Dec 03 00:00:00 EST 2015},
month = {Thu Dec 03 00:00:00 EST 2015}
}
Web of Science
Figures / Tables:
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
High abundance of heterotrophic prokaryotes in hydrothermal springs of the Azores as revealed by a network of 16S rRNA gene-based methods
journal, May 2013
- Sahm, Kerstin; John, Patrick; Nacke, Heiko
- Extremophiles, Vol. 17, Issue 4
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
Geochemistry and Dynamics of the Yellowstone National Park Hydrothermal System
journal, May 1989
- Fournier, R. O.
- Annual Review of Earth and Planetary Sciences, Vol. 17, Issue 1
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
Identification and cloning of Thiobacillus ferrooxidans structural nif genes in Escherichia coli
journal, January 1986
- Pretorius, Inge-M.; Rawlings, Douglas E.; Woods, David R.
- Gene, Vol. 45, Issue 1
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
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
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
Microbial diversity of boron-rich volcanic hot springs of St. Lucia, Lesser Antilles
journal, December 2009
- Stout, Lisa M.; Blake, Ruth E.; Greenwood, James P.
- FEMS Microbiology Ecology, Vol. 70, Issue 3
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
Structural basis of [NiFe] hydrogenase maturation by Hyp proteins
journal, October 2012
- Watanabe, Satoshi; Sasaki, Daisuke; Tominaga, Taiga
- Biological Chemistry, Vol. 393, Issue 10
Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring
journal, August 2001
- Jackson, Colin R.; Langner, Heiko W.; Donahoe-Christiansen, Jessica
- Environmental Microbiology, Vol. 3, Issue 8
Acidithiobacillus caldus Sulfur Oxidation Model Based on Transcriptome Analysis between the Wild Type and Sulfur Oxygenase Reductase Defective Mutant
journal, September 2012
- Chen, Linxu; Ren, Yilin; Lin, Jianqun
- PLoS ONE, Vol. 7, Issue 9
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
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
The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota
journal, October 2011
- Siebers, Bettina; Zaparty, Melanie; Raddatz, Guenter
- PLoS ONE, Vol. 6, Issue 10
Non-parametric multivariate analyses of changes in community structure
journal, March 1993
- Clarke, K. R.
- Austral Ecology, Vol. 18, Issue 1
Life in extreme environments
journal, February 2001
- Rothschild, Lynn J.; Mancinelli, Rocco L.
- Nature, Vol. 409, Issue 6823
Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function
journal, March 2010
- Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.
- PLoS ONE, Vol. 5, Issue 3
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
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
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
Bioleaching review part A:
journal, December 2003
- Rohwerder, T.; Gehrke, T.; Kinzler, K.
- Applied Microbiology and Biotechnology, Vol. 63, Issue 3
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
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
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
PILER-CR: Fast and accurate identification of CRISPR repeats
journal, January 2007
- Edgar, Robert C.
- BMC Bioinformatics, Vol. 8, Issue 1
Versatile and open software for comparing large genomes
journal, January 2004
- Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.
- Genome Biology, Vol. 5, Issue 2, R12
Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation
journal, June 2011
- You, Xiao-Yan; Guo, Xu; Zheng, Hua-Jun
- Journal of Genetics and Genomics, Vol. 38, Issue 6
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
Microbiology of acidic, geothermal springs of Montserrat: environmental rDNA analysis
journal, October 2000
- Burton, Nicolas P.; Norris, P. R.
- Extremophiles, Vol. 4, Issue 5
Localization, purification and properties of a tetrathionate hydrolase from Acidithiobacillus caldus
journal, January 2004
- Bugaytsova, Zhanna; Lindstrom, E. Borje
- European Journal of Biochemistry, Vol. 271, Issue 2
Identification of a gene encoding a tetrathionate hydrolase in Acidithiobacillus ferrooxidans
journal, October 2007
- Kanao, Tadayoshi; Kamimura, Kazuo; Sugio, Tsuyoshi
- Journal of Biotechnology, Vol. 132, Issue 1
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
Circos: An information aesthetic for comparative genomics
journal, June 2009
- Krzywinski, M.; Schein, J.; Birol, I.
- Genome Research, Vol. 19, Issue 9
Archaeal diversity in Icelandic hot springs: Archaeal diversity in Icelandic hot springs
journal, January 2007
- Kvist, Thomas; Ahring, Birgitte K.; Westermann, Peter
- FEMS Microbiology Ecology, Vol. 59, Issue 1
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
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
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
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
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
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
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
Diversity of 16S rRNA gene, ITS region and aclB gene of the Aquificales
journal, September 2006
- Ferrera, I.; Longhorn, S.; Banta, A. B.
- Extremophiles, Vol. 11, Issue 1
Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China
journal, May 2012
- Pagaling, Eulyn; Grant, William D.; Cowan, Don A.
- Extremophiles, Vol. 16, Issue 4
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
- Hügler, Michael; Huber, Harald; Molyneaux, Stephen J.
- Environmental Microbiology, Vol. 9, Issue 1, p. 81-92
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
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
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
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
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
Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton.
journal, January 1990
- Giovannoni, S. J.; DeLong, E. F.; Schmidt, T. M.
- Applied and Environmental Microbiology, Vol. 56, Issue 8
Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
dataset, December 2015
- Lin, K.; Liao, B.; Chang, H.
- Dryad, vp
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
journal, January 2021
- Olm, Matthew R.; Crits-Christoph, Alexander; Bouma-Gregson, Keith
- Nature Biotechnology, Vol. 39, Issue 6
Draft Genome Sequence of Medusavirus Stheno, Isolated from the Tatakai River of Uji, Japan
journal, January 2021
- Yoshida, Koki; Zhang, Ruixuan; Garcia, Kimberly G.
- Microbiology Resource Announcements, Vol. 10, Issue 1
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.
text, January 2011
- Siebers, Bettina; Zaparty, Melanie; Raddatz, Guenter
- Universität Regensburg
Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
dataset, December 2015
- Lin, K.; Liao, B.; Chang, H.
- Dryad, vp
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
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
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
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
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
Diversity of 16S rRNA gene, ITS region and aclB gene of the Aquificales
journal, September 2006
- Ferrera, I.; Longhorn, S.; Banta, A. B.
- Extremophiles, Vol. 11, Issue 1
Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China
journal, May 2012
- Pagaling, Eulyn; Grant, William D.; Cowan, Don A.
- Extremophiles, Vol. 16, Issue 4
High abundance of heterotrophic prokaryotes in hydrothermal springs of the Azores as revealed by a network of 16S rRNA gene-based methods
journal, May 2013
- Sahm, Kerstin; John, Patrick; Nacke, Heiko
- Extremophiles, Vol. 17, Issue 4
Microbiology of acidic, geothermal springs of Montserrat: environmental rDNA analysis
journal, October 2000
- Burton, Nicolas P.; Norris, P. R.
- Extremophiles, Vol. 4, Issue 5
Identification and cloning of Thiobacillus ferrooxidans structural nif genes in Escherichia coli
journal, January 1986
- Pretorius, Inge-M.; Rawlings, Douglas E.; Woods, David R.
- Gene, Vol. 45, Issue 1
Identification of a gene encoding a tetrathionate hydrolase in Acidithiobacillus ferrooxidans
journal, October 2007
- Kanao, Tadayoshi; Kamimura, Kazuo; Sugio, Tsuyoshi
- Journal of Biotechnology, Vol. 132, Issue 1
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
Correlation between microbiological and chemical parameters of some hydrothermal springs in New Mexico, USA
journal, September 2003
- Rzonca, Bartłomiej; Schulze-Makuch, Dirk
- Journal of Hydrology, Vol. 280, Issue 1-4
Life in extreme environments
journal, February 2001
- Rothschild, Lynn J.; Mancinelli, Rocco L.
- Nature, Vol. 409, Issue 6823
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
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
Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons
journal, August 2019
- Wang, Baozhan; Qin, Wei; Ren, Yi
- The ISME Journal, Vol. 13, Issue 12
Site-specific molecular analysis of the bacteriota on worn spectacles
journal, March 2020
- Fritz, Birgit; März, Melanie; Weis, Severin
- Scientific Reports, Vol. 10, Issue 1
Localization, purification and properties of a tetrathionate hydrolase from Acidithiobacillus caldus
journal, January 2004
- Bugaytsova, Zhanna; Lindstrom, E. Borje
- European Journal of Biochemistry, Vol. 271, Issue 2
Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring
journal, August 2001
- Jackson, Colin R.; Langner, Heiko W.; Donahoe-Christiansen, Jessica
- Environmental Microbiology, Vol. 3, Issue 8
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
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
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
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
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
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
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
Aerobic and anaerobic oxidation of hydrogen by acidophilic bacteria
journal, October 2013
- Hedrich, Sabrina; Johnson, D. Barrie
- FEMS Microbiology Letters
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
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
- Hügler, Michael; Huber, Harald; Molyneaux, Stephen J.
- Environmental Microbiology, Vol. 9, Issue 1, p. 81-92
Arsenite oxidation by a chemoautotrophic moderately acidophilic Thiomonas sp.: from the strain isolation to the gene study
journal, September 2007
- Duquesne, Katia; Lieutaud, Aurélie; Ratouchniak, Jeanine
- Environmental Microbiology, Vol. 0, Issue 0
Archaeal diversity in Icelandic hot springs: Archaeal diversity in Icelandic hot springs
journal, January 2007
- Kvist, Thomas; Ahring, Birgitte K.; Westermann, Peter
- FEMS Microbiology Ecology, Vol. 59, Issue 1
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
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
The Genome of Sulfolobus acidocaldarius, a Model Organism of the Crenarchaeota
journal, July 2005
- Chen, L.; Brugger, K.; Skovgaard, M.
- Journal of Bacteriology, Vol. 187, Issue 14
Geochemistry and Dynamics of the Yellowstone National Park Hydrothermal System
journal, May 1989
- Fournier, R. O.
- Annual Review of Earth and Planetary Sciences, Vol. 17, Issue 1
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
PILER-CR: Fast and accurate identification of CRISPR repeats
journal, January 2007
- Edgar, Robert C.
- BMC Bioinformatics, Vol. 8, Issue 1
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
Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function
journal, March 2010
- Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.
- PLoS ONE, Vol. 5, Issue 3
The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota
journal, October 2011
- Siebers, Bettina; Zaparty, Melanie; Raddatz, Guenter
- PLoS ONE, Vol. 6, Issue 10
Acidithiobacillus caldus Sulfur Oxidation Model Based on Transcriptome Analysis between the Wild Type and Sulfur Oxygenase Reductase Defective Mutant
journal, September 2012
- Chen, Linxu; Ren, Yilin; Lin, Jianqun
- PLoS ONE, Vol. 7, Issue 9
Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes
journal, December 2012
- Jiménez, Diego Javier; Andreote, Fernando Dini; Chaves, Diego
- PLoS ONE, Vol. 7, Issue 12
A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing
journal, January 2013
- Hou, Weiguo; Wang, Shang; Dong, Hailiang
- PLoS ONE, Vol. 8, Issue 1
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
The Redox Potential of Hot Springs in Taiwan
journal, January 2009
- Chen, Wen-Fu; Sung, Menghau
- Terrestrial, Atmospheric and Oceanic Sciences, Vol. 20, Issue 3
Nucleic acid-based approaches to investigate microbial-related cheese quality defects
journal, January 2013
- O'Sullivan, Daniel J.; Giblin, Linda; McSweeney, Paul L. H.
- Frontiers in Microbiology, Vol. 4
Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages
journal, January 2013
- Takacs-Vesbach, Cristina; Inskeep, William P.; Jay, Zackary J.
- Frontiers in Microbiology, Vol. 4
Compact graphical representation of phylogenetic data and metadata with GraPhlAn
journal, January 2015
- Asnicar, Francesco; Weingart, George; Tickle, Timothy L.
- PeerJ, Vol. 3
Works referencing / citing this record:
Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes
journal, September 2016
- DeCastro, María-Eugenia; Rodríguez-Belmonte, Esther; González-Siso, María-Isabel
- Frontiers in Microbiology, Vol. 7
Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
dataset, December 2015
- Lin, K.; Liao, B.; Chang, H.
- Dryad, vp
Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
dataset, December 2015
- Lin, K.; Liao, B.; Chang, H.
- Dryad, vp
Metagenomic Insights Unveil the Dominance of Undescribed Actinobacteria in Pond Ecosystem of an Indian Shrine
journal, November 2018
- Manikkam, Radhakrishnan; Imchen, MAdangchanok; Kaari, Manigundan
- Meta Gene
Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture
journal, January 2017
- Driscoll, Connor B.; Otten, Timothy G.; Brown, Nathan M.
- Standards in Genomic Sciences, Vol. 12, Issue 1
Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes
journal, September 2016
- DeCastro, María-Eugenia; Rodríguez-Belmonte, Esther; González-Siso, María-Isabel
- Frontiers in Microbiology, Vol. 7
Diurnal Changes in Active Carbon and Nitrogen Pathways Along the Temperature Gradient in Porcelana Hot Spring Microbial Mat
journal, October 2018
- Alcamán-Arias, María E.; Pedrós-Alió, Carlos; Tamames, Javier
- Frontiers in Microbiology, Vol. 9