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Extremophiles

, Volume 22, Issue 6, pp 983–991 | Cite as

Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California

  • En-Min Zhou
  • Wen-Dong Xian
  • Chrisabelle C. Mefferd
  • Scott C. Thomas
  • Arinola L. Adegboruwa
  • Nathan Williams
  • Senthil K. Murugapiran
  • Jeremy A. Dodsworth
  • Rakesh Ganji
  • Meng-Meng Li
  • Yi-Ping Ding
  • Lan Liu
  • Tanja Woyke
  • Wen-Jun Li
  • Brian P. Hedlund
Original Paper
  • 142 Downloads

Abstract

Thermus species are widespread in natural and artificial thermal environments. Two new yellow-pigmented strains, L198T and L423, isolated from Little Hot Creek, a geothermal spring in eastern California, were identified as novel organisms belonging to the genus Thermus. Cells are Gram-negative, rod-shaped, and non-motile. Growth was observed at temperatures from 45 to 75 °C and at salinities of 0–2.0% added NaCl. Both strains grow heterotrophically or chemolithotrophically by oxidation of thiosulfate to sulfate. L198T and L423 grow by aerobic respiration or anaerobic respiration with arsenate as the terminal electron acceptor. Values for 16S rRNA gene identity (≤ 97.01%), digital DNA–DNA hybridization (≤ 32.7%), OrthoANI (≤ 87.5%), and genome-to-genome distance (0.13) values to all Thermus genomes were less than established criteria for microbial species. The predominant respiratory quinone was menaquinone-8 and the major cellular fatty acids were iso-C15:0, iso-C17:0 and anteiso-C15:0. One unidentified phospholipid (PL1) and one unidentified glycolipid (GL1) dominated the polar lipid pattern. The new strains could be differentiated from related taxa by β-galactosidase and β-glucosidase activity and the presence of hydroxy fatty acids. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic evidence, the novel species Thermus sediminis sp. nov. is proposed, with the type strain L198T (= CGMCC 1.13590T = KCTC XXX).

Keywords

Thermus sediminis sp. nov. Thermophile Polyphasic taxonomy Genome sequencing Geothermal springs Little Hot Creek 

Abbreviations

ANI

Average nucleotide identity

dDDH

Digital DNA–DNA hybridization

GGDC

Genome-to-genome distance calculator

DOE

Department of Energy

JGI

Joint Genome Institute

IMG

Integrated microbial genomes

CTAB

Cetyl trimethyl ammonium bromide

CRISPRs

Clustered regularly interspaced short palindromic repeats

COGs

Clusters of orthologous groups

Notes

Acknowledgements

We thank the National Forest Service (Inyo National Forest, Mammoth Lakes Office) for permission to sample Little Hot Creek. This work was supported by the National Natural Science Foundation of China (nos. 31600103 and 31470139), China Postdoctoral Science Foundation (2016M602569), and National Science Foundation grants (OISE-0968421 and DBI-1005223). Whole genome sequencing conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract no. DE-AC02-05CH11231. Wen-Jun Li was also supported by Guangdong Province Higher Vocational Colleges and Schools Pearl River Scholar Funded Scheme (2014). B.P. Hedlund was also funded by a gift from Greg Fullmer through the UNLV Foundation.

Compliance with ethical standards

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary material

792_2018_1055_MOESM1_ESM.docx (2.2 mb)
Supplementary material 1 (DOCX 2296 kb)

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Copyright information

© Springer Japan KK, part of Springer Nature 2018

Authors and Affiliations

  • En-Min Zhou
    • 1
    • 2
  • Wen-Dong Xian
    • 1
  • Chrisabelle C. Mefferd
    • 2
  • Scott C. Thomas
    • 2
  • Arinola L. Adegboruwa
    • 2
  • Nathan Williams
    • 2
    • 3
  • Senthil K. Murugapiran
    • 2
  • Jeremy A. Dodsworth
    • 4
  • Rakesh Ganji
    • 2
  • Meng-Meng Li
    • 1
  • Yi-Ping Ding
    • 1
  • Lan Liu
    • 1
  • Tanja Woyke
    • 5
    • 6
  • Wen-Jun Li
    • 1
  • Brian P. Hedlund
    • 2
    • 7
  1. 1.State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life SciencesSun Yat-sen UniversityGuangzhouPeople’s Republic of China
  2. 2.School of Life SciencesUniversity of Nevada, Las VegasLas VegasUSA
  3. 3.Las Vegas High School PAL ProgramClark County School DistrictLas VegasUSA
  4. 4.Department of BiologyCalifornia State University, San BernardinoSan BernardinoUSA
  5. 5.Department of EnergyJoint Genome InstituteWalnut CreekUSA
  6. 6.Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyUSA
  7. 7.Nevada Institute of Personalized MedicineUniversity of Nevada, Las VegasLas VegasUSA

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