1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 7

Description of sp. nov., isolated from deep sea sediment from the Mariana Trench, and emended description of the genus No Access

Abstract

In this study, we reported a Gram-stain-negative, orange-coloured, rod-shaped, motile and faculatively anaerobic bacterium named strain PB63, which was isolated from the deep-sea sediment from the Mariana Trench. Growth of PB63 occurred at 10–35 °C (optimum, 28 °C), pH 5.0–8.0 (optimum, 5.0–6.0) and with 0–7 % (w/v) NaCl (optimum, 2–3 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PB63 represented a member of the genus and was closely related to DSM 16222 (97.9 % sequence similarity). PB63 showed tolerance to a variety of heavy metals, including Co, Zn, Mn and Cu. The complete genome of PB63 was obtained, and many genes involved in heavy metal resistance were found. The genomic DNA G+C content of PB63 was 62.8 mol%. The predominant respiratory quinone of PB63 was ubiquinone-10 (Q-10). The polar lipids of PB63 contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, glycolipid, phosphatidylcholines and three unidentified lipids. The major fatty acids of PB63 included summed feature 8 (Cω7 or/and Cω6), C 2-OH, 11-methyl Cω7c, C, summed feature 3 (Cω7 and/or Cω6) and Cω6. The results of phylogenetic, physiological, biochemical and morphological analyses indicated that strain PB63 represents a novel species of the genus , and the name sp. nov. is proposed with the type species PB63 (=CCTCC AB 2019195=JCM 34178).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Mariana Trench , Novel species and Novosphingopyxis
Funding
This study was supported by the:
  • Taishan Scholar Program of Shandong Province
    • Principle Award Recipient: NotApplicable
  • The Senior User Project of RV KEXUE (Award KEXUE2018G20)
    • Principle Award Recipient: SunQing-lei
  • Qingdao National Laboratory for Marine Science and Technology (Award QNLM2016ORP0309)
    • Principle Award Recipient: NotApplicable
  • National Key R&D Program of China (Award 2018YFC0310603 and 2018YFC0310801)
    • Principle Award Recipient: Qing-leiSun
© 2021 Institute of Oceanology, Chinese Academy of Sciences
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004910
2021-07-21
2024-04-25
Loading full text...

Full text loading...

References

  1. Feng GD, Zhang XJ, Yang SZ, Li AZ, Yao Q et al. Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacificacorrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae. Int J Syst Evol Microbiol 2020; 70:2147–2154
     [Google Scholar]
  2. Yoon JH, Lee CH, Yeo SH, Oh TK. Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:1223–1227
     [Google Scholar]
  3. Sheu SY, Guo YP, Kwon SW, Chen WM. Sphingobium fluviale sp. nov., isolated from a river. Int J Syst Evol Microbiol 2020; 70:827–834 [View Article] [PubMed]
     [Google Scholar]
  4. Chen WM, Guo YP, Sheu C, Sheu SY. Sphingobium algorifonticola sp. nov., isolated from a cold spring. Int J Syst Evol Microbiol 2020; 70:309–316 [View Article] [PubMed]
     [Google Scholar]
  5. Park YJ, Kim KH, Han DM, Lee DH, Jeon CO. Sphingobium terrigena sp. nov., isolated from gasoline-contaminated soil. Int J Syst Evol Microbiol 2019; 69:2459–2464 [View Article] [PubMed]
     [Google Scholar]
  6. Qin D, Ma C, Lv M, Yu C-P. Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:1822–1829
     [Google Scholar]
  7. Feng GD, Wang YH, Zhang XJ, Chen WD, Zhang J et al. Sphingomonas lenta sp. nov., a slowly growing bacterium isolated from an abandoned lead–zinc mine. Int J Syst Evol Microbiol 2019; 69:2214–2219 [View Article] [PubMed]
     [Google Scholar]
  8. Xian WD, Li M-M, Salam N, Ding YP, Zhou EM et al. Novosphingobium meiothermophilum sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2019; 69:1737–1743
     [Google Scholar]
  9. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article] [PubMed]
     [Google Scholar]
  10. Sharma M, Khurana H, Singh DN, Negi RK. The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review. J Environ Manage 2020; 280:111744 [View Article] [PubMed]
     [Google Scholar]
  11. Verma H, Dhingra GG, Sharma M, Gupta V, Negi RK et al. Comparative genomics of Sphingopyxis spp. unravelled functional attributes. Genomics 2019; 112:1956–1969 [View Article] [PubMed]
     [Google Scholar]
  12. Yang F, Feng H, Massey IY, Huang FY, Guo J et al. Genome-wide analysis reveals genetic potential for aromatic compounds biodegradation of Sphingopyxis. BioMed Res Int 2020; 5849123:
     [Google Scholar]
  13. Sreerag RS, Jayaprakas CA, Ragesh L, Kumar SN. Endosymbiotic bacteria associated with the mealy bug, Rhizoecus amorphophalli (Hemiptera: Pseudococcidae. Int Sch Res Notices 2014; 2014:268491 [View Article] [PubMed]
     [Google Scholar]
  14. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 55:1149–1153
     [Google Scholar]
  15. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  16. 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]
  17. 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 Meth 1984; 2:233–241
     [Google Scholar]
  18. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  19. Kim OS, Cho YJ, Lee K, Yoon SH, Kimet M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721
     [Google Scholar]
  20. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  21. Zhou J, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol 1996; 62:316–322 [View Article] [PubMed]
     [Google Scholar]
  22. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  23. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 9:2607–2618
     [Google Scholar]
  24. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 5:955–964
     [Google Scholar]
  25. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  26. Lee I, Ouk Kim Y, Park SC, 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]
  27. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  28. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019; 36:1925–1927
     [Google Scholar]
  29. 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]
  30. Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 2011; 27:1164–1165 [View Article] [PubMed]
     [Google Scholar]
  31. Meier-Kolthoff JP, Goker M, Sproer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article] [PubMed]
     [Google Scholar]
  32. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351
     [Google Scholar]
  33. 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]
  34. Uchida H, Hamana K, Miyazaki M, Yoshida T, Nogi Y. Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm. Int J Syst Evol Microbiol 2012; 62:2224–2228 [View Article] [PubMed]
     [Google Scholar]
  35. Kim BS, Lim YW, Chun J. Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2008; 58:2415–2419 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004910
Loading
Description of Novosphingopyxis iocasae sp. nov., isolated from deep sea sediment from the Mariana Trench, and emended description of the genus Novosphingopyxis
Int J Syst Evol Microbiol 71, 004910 (2021); https://doi.org/10.1099/ijsem.0.004910
/content/journal/ijsem/10.1099/ijsem.0.004910
/content/journal/ijsem/10.1099/ijsem.0.004910
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error