1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 10

sp. nov., an obligately chemolithoautotrophic, sulphur-oxidizing bacterium isolated from a deep-sea sediment sample from the South China Sea No Access

Abstract

A novel marine bacterium, designated strain B2, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were observed to be Gram-stain negative, motile and rod shaped with a single polar flagellum. B2 could grow at 10–45 °C (optimum, 35 °C), pH 4.5–9.0 (optimum, pH 7.0) and in the presence of 1.0–8.0 % (w/v) NaCl (optimum, 3.0%). The isolate grew chemolithoautotrophically with sulphide, elemental sulphur and thiosulphate as electron donors, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The predominant fatty acids of B2 were Cω7, C and Cω7. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that B2 represented a member of the genus , with the highest similarity to the 16S rRNA gene sequences of NW8N (95.9 %), SN118 (95.7 %), 1-1N (95.6 %) and GO25 (95.4 %). Sequence similarities to other members of the genus were less than 95.0 %. In addition, the average nucleotide identity (ANI) value and digital DNA–DNA hybridization (dDDH) estimate between B2 and NW8N were 73.0 and 23.7 %, respectively. The size of the complete genome of B2 is 22 61 034 bp, with a DNA G+C content of 36.0 mol %. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain B2 represent a novel species of the genus , for which the name sp. nov. is proposed, with the type strain B2 (=MCCC 1A14515=KCTC 15852).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Campylobacteria , polyphasic taxonomy , Sulfurimonas marina and Sulphur-oxidation
Funding
This study was supported by the:
  • Scientific Research Foundation of Third Institute of Oceanography (Award No. 2019021)
    • Principle Award Recipient: ZongzeShao
  • Postdoctoral Research Foundation of China (Award No. 2021TQ0397)
    • Principle Award Recipient: ShashaWang
  • COMRA program (Award No. DY135-B2-01)
    • Principle Award Recipient: ZongzeShao
  • National Key Research and Development Program of China (Award No. 2018YFC0310705)
    • Principle Award Recipient: ZongzeShao
  • National Natural Science Foundation of China (Award No. 42176134)
    • Principle Award Recipient: LijingJiang
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005582
2022-10-21
2024-12-03
Loading full text...

Full text loading...

References

  1. Inagaki F, Takai K, Kobayashi H, Nealson KH, Horikoshi K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing ε-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 2003; 53:1801–1805 [View Article]
     [Google Scholar]
  2. Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y et al. Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 2017; 8:682 [View Article]
     [Google Scholar]
  3. Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y et al. Addendum: comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 2018; 9:772 [View Article]
     [Google Scholar]
  4. Han Y, Perner M. The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines. Front Microbiol 2015; 6:989 [View Article]
     [Google Scholar]
  5. Grote J, Jost G, Labrenz M, Herndl GJ, Jürgens K. Epsilonproteobacteria represent the major portion of chemoautotrophic bacteria in sulfidic waters of pelagic redoxclines of the Baltic and Black Seas. Appl Environ Microbiol 2008; 74:7546–7551 [View Article] [PubMed]
     [Google Scholar]
  6. Akerman NH, Butterfield DA, Huber JA. Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids. Front Microbiol 2013; 4:185 [View Article] [PubMed]
     [Google Scholar]
  7. Perner M, Gonnella G, Hourdez S, Böhnke S, Kurtz S et al. In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field. Environ Microbiol 2013; 15:1551–1560 [View Article]
     [Google Scholar]
  8. Takai K, Suzuki M, Nakagawa S, Miyazaki M, Suzuki Y et al. Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas. Int J Syst Evol Microbiol 2006; 56:1725–1733 [View Article] [PubMed]
     [Google Scholar]
  9. Hu QT, Wang SS, Lai QL, Shao ZZ, Jiang LJ. Sulfurimonas indica sp. nov., a hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal sulfide chimney in the Northwest Indian Ocean. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  10. Wang S, Jiang L, Hu Q, Liu X, Yang S et al. Elemental sulfur reduction by a deep-sea hydrothermal vent Campylobacterium Sulfurimonas sp. NW10. Environ Microbiol 2021; 23:965–979 [View Article]
     [Google Scholar]
  11. Wang S, Shao Z, Lai Q, Liu X, Xie S et al. Sulfurimonas sediminis sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal vent at the Longqi system, southwestern Indian ocean. Antonie Van Leeuwenhoek 2021; 114:813–822 [View Article]
     [Google Scholar]
  12. Hoor A-T. A new type of thiosulphate oxidizing, nitrate reducing microorganism: Thiomicrospira denitrificans sp. nov. Net J Sea Res 1975; 9:344–350 [View Article]
     [Google Scholar]
  13. Cai L, Shao MF, Zhang T. Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from marine sediment. Stand Genomic Sci 2014; 9:1302–1310 [View Article] [PubMed]
     [Google Scholar]
  14. Wang SS, Jiang LJ, Liu XW, Yang SP, Shao ZZ. Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov., hydrogen- and sulfur-oxidizing chemolithoautotrophs within the Epsilonproteobacteria isolated from coastal sediments, and an emended description of the genus Sulfurimonas. Int J Syst Evol Microbiol 2020; 70:2657–2663 [View Article] [PubMed]
     [Google Scholar]
  15. Labrenz M, Grote J, Mammitzsch K, Boschker HTS, Laue M et al. Sulfurimonas gotlandica sp. nov., a chemoautotrophic and psychrotolerant Epsilonproteobacterium isolated from a pelagic redoxcline, and an emended description of the genus Sulfurimonas. Int J Syst Evol Microbiol 2013; 63:4141–4148 [View Article] [PubMed]
     [Google Scholar]
  16. Ratnikova NM, Slobodkin AI, Merkel AY, Kopitsyn DS, Kevbrin VV et al. Sulfurimonas crateris sp. nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano. Int J Syst Evol Microbiol 2020; 70:487–492 [View Article]
     [Google Scholar]
  17. Henkel JV, Vogts A, Werner J, Neu TR, Spröer C et al. Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea. Syst Appl Microbiol 2021; 44:126155 [View Article]
     [Google Scholar]
  18. Jiang LJ, Lyu J, Shao ZZ. Sulfur metabolism of Hydrogenovibrio thermophilus strain S5 and its adaptations to deep-sea hydrothermal vent environment. Front Microbiol 2017; 8:2513 [View Article] [PubMed]
     [Google Scholar]
  19. Liu X, Jiang L, Hu Q, Lyu J, Shao Z. Thiomicrorhabdus indica sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a deep-sea hydrothermal vent environment. Int J Syst Evol Microbiol 2020; 70:234–239 [View Article]
     [Google Scholar]
  20. Sasser M. Bacterial identification by Ggas Cchromatographic Aanalysis of Ffatty Aacids Mmethyl Eesters (GC-FAME) Newark: MIDI Labs Inc; 1990
     [Google Scholar]
  21. Jiang L, Zheng Y, Peng X, Zhou H, Zhang C et al. Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China. FEMS Microbiol Ecol 2009; 70:93–106 [View Article] [PubMed]
     [Google Scholar]
  22. Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BF et al. GenBank. Nucleic Acids Res 1999; 27:12–17 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article]
     [Google Scholar]
  25. 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]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  27. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–7 [View Article]
     [Google Scholar]
  30. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, 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]
  31. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article]
     [Google Scholar]
  32. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article]
     [Google Scholar]
  33. Yoon SH, Ha SM, 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]
  34. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [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]
/content/journal/ijsem/10.1099/ijsem.0.005582
Loading
Sulfurimonas marina sp. nov., an obligately chemolithoautotrophic, sulphur-oxidizing bacterium isolated from a deep-sea sediment sample from the South China Sea
Int J Syst Evol Microbiol 72, 005582 (2022); https://doi.org/10.1099/ijsem.0.005582
/content/journal/ijsem/10.1099/ijsem.0.005582
/content/journal/ijsem/10.1099/ijsem.0.005582
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