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

Kuei Han Lin, Ben Yang Liao, Hao Wei Chang, Shiao Wei Huang, Ting Yan Chang, Cheng Yu Yang, Yu Bin Wang, Yu Teh Kirk Lin, Yu Wei Wu, Sen Lin Tang, Hon Tsen Yu

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Background: 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. Results: 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. Conclusions: 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.

Original languageEnglish
Article number1029
JournalBMC Genomics
Volume16
Issue number1
DOIs
Publication statusPublished - Dec 3 2015
Externally publishedYes

Fingerprint

Hot Springs
Metagenomics
Taiwan
Carbon
Microbial Interactions
Bacteria
rRNA Genes
Nanoarchaeota
Desulfurococcaceae
Hydrogen
Nitrogen
Acidithiobacillus
Clustered Regularly Interspaced Short Palindromic Repeats
Sulfur Compounds
Temperature
Archaea
Metabolic Networks and Pathways
Computational Biology
Ecosystem
Viruses

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Lin, K. H., Liao, B. Y., Chang, H. W., Huang, S. W., Chang, T. Y., Yang, C. Y., ... Yu, H. T. (2015). Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. BMC Genomics, 16(1), [1029]. https://doi.org/10.1186/s12864-015-2230-9

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

In: BMC Genomics, Vol. 16, No. 1, 1029, 03.12.2015.

Research output: Contribution to journalArticle

Lin, KH, Liao, BY, Chang, HW, Huang, SW, Chang, TY, Yang, CY, Wang, YB, Lin, YTK, Wu, YW, Tang, SL & Yu, HT 2015, 'Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics', BMC Genomics, vol. 16, no. 1, 1029. 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 ; Yu, Hon Tsen. / Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. In: BMC Genomics. 2015 ; Vol. 16, No. 1.
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