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

doi:10.1007/s00792-018-1055-2

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

Plant and Microbial Biology

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Abstract

Thermus species are widespread in natural and artificial thermal environments. Two new yellow-pigmented strains, L198^T 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. L198^T 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-C_15:0, iso-C_17:0 and anteiso-C_15:0. 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 L198^T (= CGMCC 1.13590^T = KCTC XXX).

Original language	English (US)
Pages (from-to)	983-991
Number of pages	9
Journal	Extremophiles
Volume	22
Issue number	6
DOIs	https://doi.org/10.1007/s00792-018-1055-2
State	Published - Nov 1 2018

Bibliographical note

Funding Information:
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.

Funding Information:
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. 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.

Publisher Copyright:
© 2018, Springer Japan KK, part of Springer Nature.

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1007/s00792-018-1055-2

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Zhou, E. M., Xian, W. D., Mefferd, C. C., Thomas, S. C., Adegboruwa, A. L., Williams, N., Murugapiran, S. K., Dodsworth, J. A., Ganji, R., Li, M. M., Ding, Y. P., Liu, L., Woyke, T., Li, W. J., & Hedlund, B. P. (2018). Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California. Extremophiles, 22(6), 983-991. https://doi.org/10.1007/s00792-018-1055-2

Zhou, EM, Xian, WD, Mefferd, CC, Thomas, SC, Adegboruwa, AL, Williams, N, Murugapiran, SK, Dodsworth, JA, Ganji, R, Li, MM, Ding, YP, Liu, L, Woyke, T, Li, WJ & Hedlund, BP 2018, 'Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California', Extremophiles, vol. 22, no. 6, pp. 983-991. https://doi.org/10.1007/s00792-018-1055-2

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

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

author = "Zhou, {En Min} and Xian, {Wen Dong} and Mefferd, {Chrisabelle C.} and Thomas, {Scott C.} and Adegboruwa, {Arinola L.} and Nathan Williams and Murugapiran, {Senthil K.} and Dodsworth, {Jeremy A.} and Rakesh Ganji and Li, {Meng Meng} and Ding, {Yi Ping} and Lan Liu and Tanja Woyke and Li, {Wen Jun} and Hedlund, {Brian P.}",

note = "Funding Information: 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. Funding Information: 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. 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. Publisher Copyright: {\textcopyright} 2018, Springer Japan KK, part of Springer Nature.",

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AU - Zhou, En Min

AU - Xian, Wen Dong

AU - Mefferd, Chrisabelle C.

AU - Thomas, Scott C.

AU - Adegboruwa, Arinola L.

AU - Williams, Nathan

AU - Murugapiran, Senthil K.

AU - Dodsworth, Jeremy A.

AU - Ganji, Rakesh

AU - Li, Meng Meng

AU - Ding, Yi Ping

AU - Liu, Lan

AU - Woyke, Tanja

AU - Li, Wen Jun

AU - Hedlund, Brian P.

N1 - Funding Information: 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. Funding Information: 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. 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. Publisher Copyright: © 2018, Springer Japan KK, part of Springer Nature.

PY - 2018/11/1

Y1 - 2018/11/1

N2 - 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).

AB - 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).

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KW - Geothermal springs

KW - Little Hot Creek

KW - Polyphasic taxonomy

KW - Thermophile

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

Abstract

Bibliographical note

Keywords

UN SDGs

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