title: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics.
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.
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. devespertine@hotmail.com.
authors.forename: Kuei-Han
authors.initials: KH
authors.lastname: Lin
authors.affiliation: Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China. liaoby@nhri.org.tw.
authors.forename: Ben-Yang
authors.initials: BY
authors.lastname: Liao
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. chang.hao-wei@go.wustl.edu.|Molecular Microbiology and Microbial Pathogenesis Program, Division of Biology and Biomedical Science, Washington University in St. Louis, St. Louis, MO, 63130, USA. chang.hao-wei@go.wustl.edu.
authors.forename: Hao-Wei
authors.initials: HW
authors.lastname: Chang
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. d2205002kimo@yahoo.com.tw.
authors.forename: Shiao-Wei
authors.initials: SW
authors.lastname: Huang
authors.affiliation: Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China. tingyan@nhri.org.tw.
authors.forename: Ting-Yan
authors.initials: TY
authors.lastname: Chang
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China. u9313025@gmail.com.
authors.forename: Cheng-Yu
authors.initials: CY
authors.lastname: Yang
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. yubin0611@gmail.com.|Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan, Republic of China. yubin0611@gmail.com.
authors.forename: Yu-Bin
authors.initials: YB
authors.lastname: Wang
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. kirklin@ntu.edu.tw.|Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. kirklin@ntu.edu.tw.
authors.forename: Yu-Teh Kirk
authors.initials: YT
authors.lastname: Lin
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA, 94608, USA. ywwei@lbl.gov.|Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. ywwei@lbl.gov.
authors.forename: Yu-Wei
authors.initials: YW
authors.lastname: Wu
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China. sltang@gate.sinica.edu.tw.
authors.forename: Sen-Lin
authors.initials: SL
authors.lastname: Tang
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. ayu@ntu.edu.tw.|Degree Program of Genome and Systems Biology, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan, Republic of China. ayu@ntu.edu.tw.
authors.forename: Hon-Tsen
authors.initials: HT
authors.lastname: Yu
mesh_terms: D044822:Biodiversity; D002244:Carbon / Q000378:metabolism; D057486:Carbon Cycle; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D045482:Hot Springs / Q000382:microbiology*; D055432:Metabolomics; D056186:Metagenomics; D056265:Microbial Interactions; D064307:Microbiota; D009584:Nitrogen / Q000378:metabolism; D058458:Nitrogen Cycle; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013624:Taiwan; D014871:Water Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S; D002244:Carbon; D009584:Nitrogen