1887

Abstract

Two novel species, designated strains SYSU G04041 and SYSU G04536, were isolated from hot spring sediments collected in Yunnan, PR China. Phenotypic and chemotaxonomic analyses, and whole-genome sequencing were used to determine the taxonomic positions of the candidate strains. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain SYSU G04041 showed the highest sequence similarity to A50-7-3 (97.5 %), and SYSU G04536 showed the highest sequence similarity to SGM-6 (98.2 %). The strains could be differentiated from other species of the genus by their distinct phenotypic and genotypic characteristics. Cells of strains SYSU G04041 and SYSU G04536 were aerobic, motile and Gram-stain-negative. Growth both occurred optimally at 45 °C and pH 7.0 for SYSU G04041 and SYSU G04536. In addition, the predominant respiratory quinone in both isolates was ubiquinone Q-8. The major fatty acids (>10 %) of strain SYSU G04041 were C, iso-C and iso-C, while the major fatty acids (>10 %) of strain SYSU G04536 were iso-C and iso-C. The main detected polar lipids in strains SYSU G04041 and SYSU G04536 included phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The G+C contents of the genomic DNA of strains SYSU G04041 and SYSU G04536 based on draft genomic sequences were 72.5 and 68.3 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU G04041 and SYSU G04536 represent two novel species of the genus , for which the names sp. nov. and sp. nov. are proposed, with the type strains SYSU G04041 (=CGMCC 1.19366=KCTC 92228) and SYSU G04536 (=CGMCC 1.19367=KCTC 82839), respectively.

Funding
This study was supported by the:
  • Guangdong Basic and Applied Basic Research Foundation (Award 2019A1515110227)
    • Principle Award Recipient: LanLiu
  • Sun Yat-Sen University 'college students' innovation and entrepreneurship training program (Award 202210478)
    • Principle Award Recipient: Jun-YiDai
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2019FY100701)
    • Principle Award Recipient: Bao-ZhuFang
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100900)
    • Principle Award Recipient: Jian-YuJiao
  • National Natural Science Foundation of China (Award 91951205)
    • Principle Award Recipient: Wen-JunLi
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2022-06-24
2024-03-28
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References

  1. Busse HJ, Kämpfer P, Moore ERB, Nuutinen J, Tsitko IV et al. Thermomonas haemolytica gen. nov., sp. nov., a gamma-proteobacterium from kaolin slurry. Int J Syst Evol Microbiol 2002; 52:473–483 [View Article]
    [Google Scholar]
  2. Ju J-H, Kim J-S, Lee D-H, Jeon JH, Heo S-Y et al. Thermomonas aquatica sp. nov., isolated from an industrial wastewater treatment plant. Int J Syst Evol Microbiol 2019; 69:3399–3404 [View Article] [PubMed]
    [Google Scholar]
  3. Mergaert J, Cnockaert MC, Swings J. Thermomonas fusca sp. nov. and Thermomonas brevis sp. nov., two mesophilic species isolated from a denitrification reactor with poly(epsilon-caprolactone) plastic granules as fixed bed, and emended description of the genus Thermomonas. Int J Syst Evol Microbiol 2003; 53:1961–1966 [View Article] [PubMed]
    [Google Scholar]
  4. Wang L, Zheng S, Wang D, Wang L, Wang G. Thermomonas carbonis sp. nov., isolated from the soil of a coal mine. Int J Syst Evol Microbiol 2014; 64:3631–3635 [View Article] [PubMed]
    [Google Scholar]
  5. Alves MP, Rainey FA, Nobre MF, da Costa MS. Thermomonas hydrothermalis sp. nov., a new slightly thermophilic gamma-proteobacterium isolated from a hot spring in central Portugal. Syst Appl Microbiol 2003; 26:70–75 [View Article] [PubMed]
    [Google Scholar]
  6. Kim MK, Im WT, In JG, Kim SH, Yang DC. Thermomonas koreensis sp. nov., a mesophilic bacterium isolated from a ginseng field. Int J Syst Evol Microbiol 2006; 56:1615–1619 [View Article] [PubMed]
    [Google Scholar]
  7. Amend JP, Shock EL. Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiol Rev 2001; 25:175–243 [View Article] [PubMed]
    [Google Scholar]
  8. Jiao J-Y, Liu L, Hua Z-S, Fang B-Z, Zhou E-M et al. Microbial dark matter coming to light: challenges and opportunities. Natl Sci Rev 2021; 8:nwaa280 [View Article] [PubMed]
    [Google Scholar]
  9. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article] [PubMed]
    [Google Scholar]
  10. Ming H, Yin Y-R, Li S, Nie G-X, Yu T-T et al. Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area. Int J Syst Evol Microbiol 2014; 64:650–656 [View Article] [PubMed]
    [Google Scholar]
  11. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
    [Google Scholar]
  12. Smibert RA, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society of Microbiology; 1994 pp 607–654
    [Google Scholar]
  13. Liu Z-T, Xian W-D, Li M-M, Liu L, Ming Y-Z et al. Microvirga arsenatis sp. nov., an arsenate reduction bacterium isolated from Tibet hot spring sediments. Antonie van Leeuwenhoek 2020; 113:1147–1153 [View Article] [PubMed]
    [Google Scholar]
  14. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  15. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  16. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. 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 2007; 57:1424–1428 [View Article] [PubMed]
    [Google Scholar]
  17. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  18. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  19. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  23. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  25. Liu Z-T, Jiao J-Y, Liu L, Li M-M, Ming Y-Z et al. 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 2019; 71:1–6 [View Article]
    [Google Scholar]
  26. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article] [PubMed]
    [Google Scholar]
  27. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article] [PubMed]
    [Google Scholar]
  28. Salam N, Jiao JY, Zhang XT, Li WJ. Update on the classification of higher ranks in the phylum Actinobacteria. Int J Syst Evol Microbiol 2020; 70:1331–1355 [View Article] [PubMed]
    [Google Scholar]
  29. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  30. Hua Z-S, Qu Y-N, Zhu Q, Zhou E-M, Qi Y-L et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018; 9:2832 [View Article] [PubMed]
    [Google Scholar]
  31. Jiao J-Y, Fu L, Hua Z-S, Liu L, Salam N et al. Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria. ISME J 2021; 15:3005–3018 [View Article] [PubMed]
    [Google Scholar]
  32. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
    [Google Scholar]
  33. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  34. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–74 [View Article] [PubMed]
    [Google Scholar]
  35. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  36. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  37. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:73–74 [View Article] [PubMed]
    [Google Scholar]
  38. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
    [Google Scholar]
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