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

doi:10.1186/s12864-015-2230-9

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

Journal Article · Thu Dec 03 00:00:00 EST 2015 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-015-2230-9· OSTI ID:1256486

Lin, Kuei -Han ^[1]; Liao, Ben -Yang ^[2]; Chang, Hao -Wei ^[3]; Huang, Shiao -Wei ^[4]; Chang, Ting -Yan ^[2]; Yang, Cheng -Yu ^[5]; Wang, Yu -Bin ^[6]; Lin, Yu-Teh Kirk ^[4]; Wu, Yu -Wei ^[7]; Tang, Sen -Lin ^[5]; Yu, Hon -Tsen ^[8]

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)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; 95-2627-M-002-004; 97-2627-M-002-001

OSTI ID:: 1256486

Journal Information:: BMC Genomics, Vol. 16, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 21 works

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