Skip to main content
SpringerLink
Log in

Rhodoflexus caldus gen. nov., sp. nov., a new member of the phylum Bacteroidota isolated from a hot spring sediment

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A thermophilic bacterium, designated strain SYSU G04325T, was isolated from a hot spring sediment in Yunnan, China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G04325T shows high sequence similarity to Thermoflexibacter ruber NBRC 16677T (86.2%). The strain can be differentiated from other species of the family Thermoflexibacteraceae by its distinct phenotypic and genotypic characteristics. Cells of the strain SYSU G04325T were observed to be aerobic, Gram-stain negative and filamentous. Growth was found to occur optimally at 45 ºC and pH 7.0. In addition, the respiratory quinone was identified as menaquinone-7, while the major fatty acids (> 10%) were identified as iso-C15:0, iso-C17:0 and Summed Feature 9 (iso-C17:1ω9c). The polar lipids detected included phosphatidylethanolamine, three unidentified phospholipids, one unidentified glycolipid, five unidentified aminolipids and four unidentified polar lipids. The G + C content of the genomic DNA was determined to be 47.6% based on the draft genome sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G04325T is concluded to represent a novel species of a novel genus in the family Thermoflexibacteraceae, for which the name Rhodoflexus caldus gen. nov., sp. nov. is proposed. The type strain of Rhodoflexus caldus is SYSU G04325T (= MCCC 1K06127T = KCTC 82848T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Availability of data and material

The GenBank accession numbers for 16 S rRNA gene sequence and draft genome sequence of the strain SYSU G04325T are OK513197 and JAJPRF000000000, respectively. The genome raw data of SYSU G04325T have been deposited in Sequence Read Archive (SRA) under the accession number PRJNA775000. One supplementary table and six supplementary figures are included on the supplementary files.

References

  • Amend JP, Shock EL (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiol Rev 25(2):175–243

    Article  CAS  Google Scholar 

  • Buck JD (1982) Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    Article  CAS  Google Scholar 

  • Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 48:459–470

    Article  CAS  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    Article  CAS  Google Scholar 

  • Delcher A, Bratke K, Powers E, Salzberg S (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679

    Article  CAS  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  • Fox DL, Lewin RA (1963) A preliminary study of the carotenoids of some flexibacteria. Can J Microbiol 9:753–769

    Article  CAS  Google Scholar 

  • García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M (2019) Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 23(10):2083–2157

    Article  Google Scholar 

  • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  Google Scholar 

  • Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Göker M (2016) Genome-based taxonomic classification of Bacteroidetes. Front Microbiol 20(7):2003–2040

    Article  Google Scholar 

  • Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ (2018) Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 9(1):2832

    Article  Google Scholar 

  • Jiao JY, Fu L, Hua ZS, Liu L, Salam N, Liu PF, Lv AP, Wu G, Xian WD, Zhu Q, Zhou EM, Fang BZ, Oren A, Hedlund BP, Jiang HC, Knight R, Cheng L, Li WJ (2021a) Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. ISME J 15(10):3005–3018

    Article  CAS  Google Scholar 

  • Jiao JY, Liu L, Hua ZS, Fang BZ, Zhou EM, Salam N, Hedlund BP, Li WJ (2021b) Microbial dark matter coming to light: challenges and opportunities. Natl Sci Rev 8(3):280

    Article  Google Scholar 

  • Joseph F (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evo 16:111–120

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 35(6):1547–1549

    Article  CAS  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  Google Scholar 

  • Leighton P, Rachel HG, Sonia H, John GE, Ian KT (2016) Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 8:12–24

    Article  Google Scholar 

  • Lewin RA (1969) A classification of flexibacteria. J Gen Microbiol 58(2):189–206

    Article  CAS  Google Scholar 

  • Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  Google Scholar 

  • Liu ZT, Jiao JY, Liu L, Li MM, Ming YZ, Song JL, Lv AP, Xian WD, Fang BZ, Li WJ (2019) Rhabdothermincola sediminis gen. nov., sp. nov., a new actinobacterium isolated from hot spring sediment, and emended description of the family Iamiaceae. Int J Syst Evol Microbiol 71(3):1–6

    Google Scholar 

  • Liu ZT, Xian WD, Li MM, Liu L, Ming YZ, Jiao JY, Fang BZ, Xiao M, Li WJ (2020) Microvirga arsenatis sp. nov., an arsenate reduction bacterium isolated from Tibet hot spring sediments. Antonie Van Leeuwenhoek 113:1147–1153

    Article  CAS  Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18

    Article  Google Scholar 

  • Luo C, Rodriguez-R LM, Konstantinidis KT (2014) MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 42:73–74

    Article  Google Scholar 

  • Ming H, Yin YR, Li S, Nie GX, Yu TT, Zhou EM, Liu L, Dong L, Li WJ (2014) Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area. Int J Syst Evol Microbiol 64:650–656

    Article  CAS  Google Scholar 

  • Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32(1):268–274

    Article  CAS  Google Scholar 

  • Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME, Holmes B, Steigerwalt AG, Villarma A, Sheth M, Batra D, Rowe LA, Burroughs M, Pryor JC, Bernardet JF, Hugo C, Kämpfer P, Newman JD, McQuiston JR (2020) Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 70(8):4432–4450

    Article  CAS  Google Scholar 

  • Noel RK, James TS, Daniel RB, Brian PH, Bruce JP, Naomi LW, Wolfgang L, William BW (2010) Bergey’s manual of systematic bacteriology, vol 4. Springer, New York

    Google Scholar 

  • Oren A, Garrity GM (2021) Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 71(10):1–7

    Google Scholar 

  • Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M (2020) List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607–5612

    Article  Google Scholar 

  • Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhou J, Oren A, Zhang YZ (2014) A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 196:2210–2215

    Article  Google Scholar 

  • Raj HD, Maloy SR (1990) Proposal of Cyclobacterium marinus gen. nov., comb. nov., for a marine bacterium previously assigned to the genus Flectobacillus. Int J Syst Bacteriol 40:337–347

    Article  Google Scholar 

  • Reasoner DJ, Geldreich EE (1985) A new Medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49:1–7

    Article  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Salam N, Jiao JY, Zhang XT, Li WJ (2020) Update on the classification of higher ranks in the phylum Actinobacteria. Int J Syst Evol Microbiol 70:1331–1355

    Article  CAS  Google Scholar 

  • Smibert RA, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society of Microbiology, Washington, D.C., pp 607–654

    Google Scholar 

  • Walter MF (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416

    Article  Google Scholar 

  • Wirth JS, Whitman WB (2018) Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 68(7):2393–2411

    Article  CAS  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  Google Scholar 

  • Leadbetter ER (1974) Order II. Cytophagales Nomen novum. In: Buchanan RE, Gibbons NE (eds) Bergey’s manual of determinative bacteriology. The Williams & Wilkins Co., Baltimore, p 99

Download references

Acknowledgements

The authors are grateful to Prof. Aharon Oren (The Hebrew University of Jerusalem, Israel) for helping with the etymology.

Funding

This research was supported by National Natural Science Foundation of China (No. 91951205), National Science and Technology Fundamental Resources Investigation Program of China (2021FY100900), Guangdong Basic and Applied Basic Research Foundation (2019A1515110227), China Postdoctoral Science Foundation (2021M703757).

Author information

Author notes

  1. Ze-Tao Liu and Lan Liu are contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Ze-Tao Liu, Lan Liu, Wen-Dong Xian, Zheng-Han Lian, Jun-Yi Dai, Meng-Meng Li, Ai-Ping Lv, Zhen-Hao Luo, Jian-Yu Jiao & Wen-Jun Li

  2. State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People’s Republic of China

    Bao-Zhu Fang & Wen-Jun Li

Authors
  1. Ze-Tao Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wen-Dong Xian
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zheng-Han Lian
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jun-Yi Dai
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bao-Zhu Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Meng-Meng Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ai-Ping Lv
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Zhen-Hao Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jian-Yu Jiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Wen-Jun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

WJL designed research and project outline. ZTL obtained the hot spring sample. ZTL, LL, MML, JYD, BZF, APL, ZHL (Zhen-Hao Luo) and WDX performed isolation, deposition and polyphasic taxonomy. ZTL and ZHL (Zheng-Han Lian) performed genome analysis. LZT, JYJ and WJL drafted the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Jian-Yu Jiao or Wen-Jun Li.

Ethics declarations

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.

Ethics approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file 1 (DOCX 2.6 MB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, ZT., Liu, L., Xian, WD. et al. Rhodoflexus caldus gen. nov., sp. nov., a new member of the phylum Bacteroidota isolated from a hot spring sediment. Antonie van Leeuwenhoek 115, 889–898 (2022). https://doi.org/10.1007/s10482-022-01742-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-022-01742-8

Keywords

Search

Navigation