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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 7

sp. nov., sp. nov. and sp. nov., isolated from soil of the Qinghai-Tibet Plateau No Access

Abstract

Six novel bacterial strains, designated N016, N017, N022, N028, N056, and N064, were isolated from soil sampled on the Qinghai-Tibet Plateau. Cells were aerobic, orange or yellow, globular or rod-shaped, non-motile, non-spore-forming, Gram-stain-positive, catalase-positive and oxidase-negative. All the isolates were salt-tolerant and could grow in the range of 4–42 °C. Results of phylogenomic analyses based on 16S rRNA gene sequences and core genomic genes showed that the three pairs of strains (N016/N017, N022/N028, and N056/N064) were closely related to the members of the genus , and clustered with , , and . The digital DNA–DNA hybridization and average nucleotide identity values of the six novel strains with other members of the genus were within the ranges of 18.7–53 % and 70.58–93.49 %, respectively, all below the respective recommended thresholds of 70.0 % and 95–96 %. The genomic DNA G+C content of the six strains ranged from 43.5 to 46.0 mol%. The major fatty acids of the six strains were -C, -C, and C 7 alcohol. The predominant polar lipids of strains N016, N022, and N056 were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Menaquinones 7 and 8 were the respiratory quinones. The results of the above analyses indicated that the six strains represent three novel species of the genus , for which the names sp. nov. (type strain N016=GDMCC 1.4062=JCM 36224), sp. nov. (type strain N022=GDMCC 1.4063=JCM 36225), and sp. nov. (type strain N056=GDMCC 1.4064=JCM 36226) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): novel species , Planococcus , Qinghai-Tibet Plateau and soil
Funding
This study was supported by the:
  • Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
    • Principle Award Recipient: JianguoXu
© 2024 The Authors
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2024-07-23
2025-07-12
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References

  1. Migula W. Über ein neues system der bakterien. Arb BakteriolnInst Karlsruhe 1894; 1:235–238
     [Google Scholar]
  2. Gupta RS, Patel S. Robust demarcation of the family Caryophanaceae (Planococcaceae) and its different genera including three novel genera based on phylogenomics and highly specific molecular signatures. Front Microbiol 2019; 10:2821 [View Article] [PubMed]
     [Google Scholar]
  3. Zhang B, Yang R, Zhang G, Liu Y, Zhang D et al. Characteristics of Planococcus antioxidans sp. nov., an antioxidant-producing strain isolated from the desert soil in the Qinghai-Tibetan Plateau. Microbiol Open 2020; 9:1183–1196 [View Article] [PubMed]
     [Google Scholar]
  4. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article]
     [Google Scholar]
  5. Dai X, Wang YN, Wang BJ, Liu SJ, Zhou YG. Planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of Planococcus psychrophilus and Planococcus alkanoclasticus to Planomicrobium as Planomicrobium psychrophilum comb. nov. and Planomicrobium alkanoclasticum comb. nov. Int J Syst Evol Microbiol 2005; 55:699–702 [View Article] [PubMed]
     [Google Scholar]
  6. Choi J-H, Im W-T, Liu Q-M, Yoo J-S, Shin J-H et al. Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea. Int J Syst Evol Microbiol 2007; 57:2645–2650 [View Article] [PubMed]
     [Google Scholar]
  7. Yoon JH, Kang SS, Lee KC, Lee ES, Kho YH et al. Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium. Int J Syst Evol Microbiol 2001; 51:1511–1520 [View Article]
     [Google Scholar]
  8. Kaur I, Das AP, Acharya M, Klenk H-P, Sree A et al. Planococcus plakortidis sp. nov., isolated from the marine sponge Plakortis simplex (Schulze). Int J Syst Evol Microbiol 2012; 62:883–889 [View Article] [PubMed]
     [Google Scholar]
  9. Engelhardt MA, Daly K, Swannell RP, Head IM. Isolation and characterization of a novel hydrocarbon-degrading, Gram-positive bacterium, isolated from intertidal beach sediment, and description of Planococcus alkanoclasticus sp. nov. J Appl Microbiol 2001; 90:237–247 [View Article] [PubMed]
     [Google Scholar]
  10. Yoon JH, Weiss N, Kang KH, Oh TK, Park YH. Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea. Int J Syst Evol Microbiol 2003; 53:2013–2017 [View Article] [PubMed]
     [Google Scholar]
  11. Yoon JH, Kang SJ, Lee SY, Oh KH, Oh TK. Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus. Int J Syst Evol Microbiol 2010; 60:754–758 [View Article]
     [Google Scholar]
  12. Mykytczuk NCS, Wilhelm RC, Whyte LG. Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost. Int J Syst Evol Microbiol 2012; 62:1937–1944 [View Article] [PubMed]
     [Google Scholar]
  13. Zhang S, Ping W, Xin Y, Xin D, Zhang J. Planococcus soli sp. nov., isolated from antarctic soil. Antonie van Leeuwenhoek 2021; 114:1107–1115 [View Article] [PubMed]
     [Google Scholar]
  14. See-Too W-S, Ee R, Madhaiyan M, Kwon S-W, Tan JY et al. Planococcus versutus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:944–950 [View Article] [PubMed]
     [Google Scholar]
  15. Reddy GSN, Prakash JSS, Vairamani M, Prabhakar S, Matsumoto GI et al. Planococcus antarcticus and Planococcus psychrophilus spp. nov. isolated from cyanobacterial mat samples collected from ponds in Antarctica. Extremophiles 2002; 6:253–261 [View Article] [PubMed]
     [Google Scholar]
  16. Kim JH, Kang HJ, Yu BJ, Kim SC, Lee PC. Planococcus faecalis sp. nov., a carotenoid-producing species isolated from stools of Antarctic penguins. Int J Syst Evol Microbiol 2015; 65:3373–3378 [View Article] [PubMed]
     [Google Scholar]
  17. Alam SI, Singh L, Dube S, Reddy GSN, Shivaji S. Psychrophilic Planococcus maitriensis sp.nov. from Antarctica. Syst Appl Microbiol 2003; 26:505–510 [View Article] [PubMed]
     [Google Scholar]
  18. Junge K, Gosink JJ, Hoppe HG, Staley JT. Arthrobacter, Brachybacterium and Planococcus isolates identified from antarctic sea ice brine. Description of Planococcus mcmeekinii, sp. nov. Syst Appl Microbiol 1998; 21:306–314 [View Article] [PubMed]
     [Google Scholar]
  19. Ma C, Zhang G, Cheng Y, Lei W, Yang C et al. Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov., and Dyadobacter fanqingshengii sp. nov., isolated from soil of the Qinghai-Tibetan Plateau. Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  20. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp 125–175
     [Google Scholar]
  21. 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]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  26. McCarthy A. Third generation DNA sequencing: pacific biosciences’ single molecule real time technology. Chem Biol 2010; 17:675–676 [View Article] [PubMed]
     [Google Scholar]
  27. Chklovski A, Parks DH, Woodcroft BJ, Tyson GW. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods 2023; 20:1203–1212 [View Article] [PubMed]
     [Google Scholar]
  28. Hamamoto T, Hashimoto M, Hino M, Kitada M, Seto Y et al. Characterization of a gene responsible for the Na+/H+ antiporter system of alkalophilic Bacillus species strain C-125. Mol Microbiol 1994; 14:939–946 [View Article]
     [Google Scholar]
  29. Chen C, Zhang W, Zheng H, Lan R, Wang H et al. Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology. J Clin Microbiol 2013; 51:2582–2591 [View Article]
     [Google Scholar]
  30. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  31. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  32. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [View Article] [PubMed]
     [Google Scholar]
  33. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  34. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  35. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [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. Huang Y, Yang J, Lu S, Lai X-H, Jin D et al. Morphological and genomic characteristics of two novel halotolerant actinomycetes, Tomitella gaofuii sp. nov. and Tomitella fengzijianii sp. nov. isolated from bat faeces. Syst Appl Microbiol 2022; 45:126294 [View Article] [PubMed]
     [Google Scholar]
  38. Athalye M, Noble WC, Minnikin DE. Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 1985; 58:507–512 [View Article] [PubMed]
     [Google Scholar]
  39. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
     [Google Scholar]
  40. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  41. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  42. Wang X, Wang Z, Zhao X, Huang X, Zhou Y et al. Planococcus ruber sp. nov., isolated from a polluted farmland soil sample. Int J Syst Evol Microbiol 2017; 67:2549–2554 [View Article]
     [Google Scholar]
  43. Zhang D-C, Liu H-C, Xin Y-H, Yu Y, Zhou P-J et al. Planomicrobium glaciei sp. nov., a psychrotolerant bacterium isolated from a glacier. Int J Syst Evol Microbiol 2009; 59:1387–1390 [View Article] [PubMed]
     [Google Scholar]
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Planococcus shenhongbingii sp. nov., Planococcus shixiaomingii sp. nov. and Planococcus liqunii sp. nov., isolated from soil of the Qinghai-Tibet Plateau
Int J Syst Evol Microbiol 74, 006465 (2024); https://doi.org/10.1099/ijsem.0.006465
/content/journal/ijsem/10.1099/ijsem.0.006465
/content/journal/ijsem/10.1099/ijsem.0.006465
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