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Abstract

A novel mesophilic, chemolithoautotrophic, hydrogen-oxidizing bacterium, designated strain ST1-3, was isolated from mud sediment samples collected from mangroves in Jiulong River estuary. The cells were Gram-stain-negative, non-motile and rod-shaped. The temperature, pH and salinity ranges for growth of strain ST1-3 were 4–45 °C (optimum, 35 °C), pH 5.0–8.5 (optimum, pH 7.0) and 0–8.0 % (w/v) NaCl (optimum, 4.0 %). The isolate was an obligate chemolithoautotroph capable of growth using hydrogen as the only energy source, and molecular oxygen, thiosulphate and elemental sulphur as electron acceptors. The major cellular fatty acids of strain ST1-3 were summed feature 3 (C 7 and/or C 6), C and summed feature 8 (C 7). The major polar lipids were phosphatidylethanolamine, phosphatidyldimethyl ethanolamine and phosphatidylglycerol. The respiratory quinone was menaquinone-6. The genomic DNA G+C content was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus and was most closely related to 42BKT (94.7 % sequence identity). The average nucleotide identity and digital DNA–DNA hybridization values between ST1-3 and 42BKT were 74.6 and 16.3 %, respectively. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain ST1-3 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain ST1-3 (=MCCC M25234=KCTC 25639).

Funding
This study was supported by the:
  • Scientific Research Foundation of Third Institute of Oceanography (Award No. 2019021)
    • Principle Award Recipient: ZongzeShao
  • China Postdoctoral Science Foundation (Award No. 2021TQ0397)
    • Principle Award Recipient: ZongzeShao
  • China Ocean Mineral Resources Research and Development Association (Award No. DY135-B2-01)
    • Principle Award Recipient: ZongzeShao
  • National Natural Science Foundation of China (Award No. 42176134)
    • Principle Award Recipient: ZongzeShao
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2023-11-02
2024-10-08
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References

  1. Inagaki F, Takai K, Nealson KH, Horikoshi K. Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the ε-Proteobacteria isolated from Okinawa trough hydrothermal sediments. Int J Syst Evol Microbiol 2004; 54:1477–1482 [View Article] [PubMed]
    [Google Scholar]
  2. Moulana A, Anderson RE, Fortunato CS, Huber JA, Bik H. Selection is a significant driver of gene gain and loss in the pangenome of the bacterial genus Sulfurovum in geographically distinct deep-sea hydrothermal vents. mSystems 2020; 5:00673–19 [View Article] [PubMed]
    [Google Scholar]
  3. Forget NL, Kim Juniper S. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge. MicrobiologyOpen 2013; 2:259–275 [View Article] [PubMed]
    [Google Scholar]
  4. Dahle H, Roalkvam I, Thorseth IH, Pedersen RB, Steen IH. The versatile in situ gene expression of an Epsilonproteobacteria-dominated biofilm from a hydrothermal chimney. Environ Microbiol Rep 2013; 5:282–290 [View Article] [PubMed]
    [Google Scholar]
  5. Giovannelli D, d’Errico G, Manini E, Yakimov M, Vetriani C. Diversity and phylogenetic analyses of bacteria from a shallow-water hydrothermal vent in Milos island (Greece). Front Microbiol 2013; 4:184 [View Article]
    [Google Scholar]
  6. McCollom TM, Shock EL. Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim Cosmochim Acta 1997; 61:4375–4391 [View Article] [PubMed]
    [Google Scholar]
  7. Mino S, Kudo H, Arai T, Sawabe T, Takai K et al. Sulfurovum aggregans sp. nov., a hydrogen-oxidizing, thiosulfate-reducing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent chimney, and an emended description of the genus Sulfurovum. Int J Syst Evol Microbiol 2014; 64:3195–3201 [View Article] [PubMed]
    [Google Scholar]
  8. Giovannelli D, Chung M, Staley J, Starovoytov V, Le Bris N et al. Sulfurovum riftiae sp. nov., a mesophilic, thiosulfate-oxidizing, nitrate-reducing chemolithoautotrophic epsilonproteobacterium isolated from the tube of the deep-sea hydrothermal vent polychaete Riftia pachyptila. Int J Syst Evol Microbiol 2016; 66:2697–2701 [View Article] [PubMed]
    [Google Scholar]
  9. Mori K, Yamaguchi K, Hanada S. Sulfurovum denitrificans sp. nov., an obligately chemolithoautotrophic sulfur-oxidizing epsilonproteobacterium isolated from a hydrothermal field. Int J Syst Evol Microbiol 2018; 68:2183–2187 [View Article] [PubMed]
    [Google Scholar]
  10. Xie S, Wang S, Li D, Shao Z, Lai Q et al. Sulfurovum indicum sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal plume in the Northwestern Indian Ocean. Int J Syst Evol Microbiol 2019; 71: [View Article] [PubMed]
    [Google Scholar]
  11. Nakagawa S, Takaki Y, Shimamura S, Reysenbach A-L, Takai K et al. Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens. Proc Natl Acad Sci USA 2007; 104:12146–12150 [View Article] [PubMed]
    [Google Scholar]
  12. Park S-J, Ghai R, Martín-Cuadrado A-B, Rodríguez-Valera F, Jung M-Y et al. Draft genome sequence of the sulfur-oxidizing bacterium “Candidatus Sulfurovum sediminum” AR, which belongs to the Epsilonproteobacteria. J Bacteriol 2012; 194:4128–4129 [View Article] [PubMed]
    [Google Scholar]
  13. Jiang L, Lyu J, Shao Z. 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]
  14. 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]
  15. Takai K, Horikoshi K. Thermosipho japonicus sp. nov., an extremely thermophilic bacterium isolated from a deep-sea hydrothermal vent in Japan. Extremophiles 2000; 4:9–17 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  18. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  19. Garrity GM, Bell JA, Lilburn T. Epsilonproteobacteria class. nov. In Bergey's Manual of Systematic Bacteriology Springer; 2005 pp 1145–1194 [View Article]
    [Google Scholar]
  20. 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; 70:249–262 [View Article]
    [Google Scholar]
  21. Lane D. 16S/23S rRNA sequencing. In Stackbrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991 pp 115–176
    [Google Scholar]
  22. 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]
  23. 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] [PubMed]
    [Google Scholar]
  24. 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]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. 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] [PubMed]
    [Google Scholar]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  33. Wu Y, Gu CT. Leuconostoc falkenbergense sp. nov., isolated from a lactic culture, fermentating string beans and traditional yogurt. Int J Syst Evol Microbiol 2021; 71:1466–5026 [View Article] [PubMed]
    [Google Scholar]
  34. Na S-I, Kim YO, Yoon S-H, Ha S, 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]
    [Google Scholar]
  35. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article]
    [Google Scholar]
  36. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
    [Google Scholar]
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