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

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:
Grant/Contract Number:
AC02-05CH11231; 95-2627-M-002-004; 97-2627-M-002-001
Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
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)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1256486

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., 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. 2015. "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}
}

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