1887

Abstract

is a group of marine bacteria with important industrial application potential and ecological functions. In this study, a Gram-stain-negative, rod-shaped, non-motile, strictly aerobic and bright yellow pigmented bacterial strain within this genus, designated C2-37M9, was isolated from a surface seawater sample from the Philippine Basin in the Western Pacific Ocean. Strain C2-37M9 grew at 10–44 °C (optimum, 28–30 °C), pH 6–9 (pH 7) and in the presence of 0–12 % NaCl (w/v; 2–3 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that it belonged to the genus and had 95.7–98.7 % sequence similarity to all type strains of this genus, with the highest value corresponding to (98.7 %). Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between strain C2-37M9 and all valid type strains were 27.5–32.3, 83.8–86.7 and 86.9–89.0 %, respectively. The principal fatty acids (>5 %) were iso-C, iso-C 3-OH, anteiso-C, summed feature 9 (C 10-methyl and/or iso-C 9), iso-C G and summed feature 3 (C 6 and/or C 7). The predominant respiratory quinone was MK-6. The polar lipids were one phosphatidylethanolamine, two unknown glycolipids, three unidentified aminolipids and six unidentified lipids. The genomic DNA G+C content of strain C2-37M9 was 36.7 mol%. Based on phylogenetic results and genomic-based relatedness indices, as well as phenotypic and genotypic characteristics, strain C2-37M9 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is C2-37M9 (=MCCC M21534=KCTC 82852).

Funding
This study was supported by the:
  • National Microbial Resource Center (Award NMRC-2022-9)
    • Principle Award Recipient: ZongzeShao
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100900)
    • Principle Award Recipient: QiliangLai
  • National Natural Science Foundation of Fujian Province, China (Award 2021J01508)
    • Principle Award Recipient: ChunmingDong
  • National Natural Science Foundation of China (Award 91851203)
    • Principle Award Recipient: ZongzeShao
  • National Natural Science Foundation of China (Award 42030412)
    • Principle Award Recipient: ZongzeShao
  • National Natural Science Foundation of China (Award 41976107)
    • Principle Award Recipient: ChunmingDong
  • Scientific Research Foundation of Third Institute of Oceanography, MNR (Award 2019021)
    • Principle Award Recipient: ZongzeShao
  • Scientific Research Foundation of Third Institute of Oceanography, MNR (Award 2020009)
    • Principle Award Recipient: ChunmingDong
  • China Ocean Mineral Resource R&D Association program (Award DY-XZ-04)
    • Principle Award Recipient: ZongzeShao
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005606
2022-11-23
2024-05-04
Loading full text...

Full text loading...

References

  1. Qin Q-L, Zhao D-L, Wang J, Chen X-L, Dang H-Y et al. Wangia profunda gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from southern Okinawa Trough deep-sea sediment. FEMS Microbiol Lett 2007; 271:53–58 [View Article] [PubMed]
    [Google Scholar]
  2. Rameshkumar N, Krishnan R, Lang E, Matsumura Y, Sawabe T et al. Zunongwangia mangrovi sp. nov., isolated from mangrove (Avicennia marina) rhizosphere, and emended description of the genus Zunongwangia. Int J Syst Evol Microbiol 2014; 64:545–550 [View Article] [PubMed]
    [Google Scholar]
  3. Fidalgo C, Martins R, Proença DN, Morais PV, Alves A et al. Zunongwangia endophytica sp. nov., an endophyte isolated from the salt marsh plant, Halimione portulacoides, and emended description of the genus Zunongwangia. Int J Syst Evol Microbiol 2017; 67:3004–3009 [View Article] [PubMed]
    [Google Scholar]
  4. Shao R, Lai Q, Liu X, Sun F, Du Y et al. Zunongwangia atlantica sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2014; 64:16–20 [View Article] [PubMed]
    [Google Scholar]
  5. Cho E-S, Cha I-T, Choi H-J, Roh SW, Nam Y-D et al. Zunongwangia flava sp. nov., belonging to the family Flavobacteriaceae, isolated from Salicornia europaea. J Microbiol 2018; 56:868–873 [View Article] [PubMed]
    [Google Scholar]
  6. Liu S-B, Qiao L-P, He H-L, Zhang Q, Chen X-L et al. Optimization of fermentation conditions and rheological properties of exopolysaccharide produced by deep-sea bacterium Zunongwangia profunda SM-A87. PLoS ONE 2011; 6:e26825 [View Article]
    [Google Scholar]
  7. Qin Q-L, Zhang X-Y, Wang X-M, Liu G-M, Chen X-L et al. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. BMC Genomics 2010; 11:247 [View Article] [PubMed]
    [Google Scholar]
  8. Sun M-L, Liu S-B, Qiao L-P, Chen X-L, Pang X et al. A novel exopolysaccharide from deep-sea bacterium Zunongwangia profunda SM-A87: low-cost fermentation, moisture retention, and antioxidant activities. Appl Microbiol Biotechnol 2014; 98:7437–7445 [View Article]
    [Google Scholar]
  9. Rahman MA, Culsum U, Tang W, Zhang SW, Wu G et al. Characterization of a novel cold active and salt tolerant esterase from Zunongwangia profunda. Enzyme Microb Technol 2016; 85:1–11 [View Article]
    [Google Scholar]
  10. Cheng Q, Gao H, Hu N. A trehalase from Zunongwangia sp.: characterization and improving catalytic efficiency by directed evolution. BMC Biotechnol 2016; 16:9 [View Article]
    [Google Scholar]
  11. Liu X, Huang Z, Zhang X, Shao Z, Liu Z. Cloning, expression and characterization of a novel cold-active and halophilic xylanase from Zunongwangia profunda. Extremophiles 2014; 18:441–450 [View Article]
    [Google Scholar]
  12. Qin Y, Huang Z, Liu Z. A novel cold-active and salt-tolerant α-amylase from marine bacterium Zunongwangia profunda: molecular cloning, heterologous expression and biochemical characterization. Extremophiles 2014; 18:271–281 [View Article]
    [Google Scholar]
  13. Wu G, Qin Y, Cheng Q, Liu Z. Characterization of a novel alkali-stable and salt-tolerant α-amylase from marine bacterium Zunongwangia profunda. J Mol Catal, B Enzym 2014; 110:8–15 [View Article]
    [Google Scholar]
  14. Rahman MA, Culsum U, Kumar A, Gao H, Hu N. Immobilization of a novel cold active esterase onto Fe3O4∼cellulose nano-composite enhances catalytic properties. Int J Biol Macromol 2016; 87:488–497 [View Article] [PubMed]
    [Google Scholar]
  15. Brojanigo S, Gronchi N, Cazzorla T, Wong TS, Basaglia M et al. Engineering Cupriavidus necator DSM 545 for the one-step conversion of starchy waste into polyhydroxyalkanoates. Bioresour Technol 2022; 347:126383 [View Article]
    [Google Scholar]
  16. Wu J, Bai Y, Lu B, Li C, Menzies NW et al. Application of sewage sludge containing environmentally-relevant silver sulfide nanoparticles increases emissions of nitrous oxide in saline soils. Environ Pollut 2020; 265:114807 [View Article]
    [Google Scholar]
  17. Li H, Zhang Q, Wang X-L, Ma X-Y, Lin K-F et al. Biodegradation of benzene homologues in contaminated sediment of the East China Sea. Bioresour Technol 2012; 124:129–136 [View Article] [PubMed]
    [Google Scholar]
  18. De Deckker P. The Indo-Pacific Warm Pool: critical to world oceanography and world climate. Geosci Lett 2016; 3: [View Article]
    [Google Scholar]
  19. Radenac M-H, Messié M, Léger F, Bosc C. A very oligotrophic zone observed from space in the equatorial Pacific warm pool. Remote Sensing of Environment 2016; 134:224–233 [View Article]
    [Google Scholar]
  20. Bernardet J-F, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article]
    [Google Scholar]
  21. Lane DJ. 16S/23S rRNA Sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley & Sons; 1991 pp 115–175
    [Google Scholar]
  22. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [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. 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. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  27. 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]
    [Google Scholar]
  28. 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]
  29. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
    [Google Scholar]
  30. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 2020; 70:e102 [View Article]
    [Google Scholar]
  31. 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]
  32. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  33. 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 [View Article]
    [Google Scholar]
  34. 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]
  35. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article]
    [Google Scholar]
  36. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  37. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  38. Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Zentralblatt für Bakteriologie, Mikrobiologie und Hygiene Series A 1988; 268:433–434 [View Article]
    [Google Scholar]
  39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  40. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article]
    [Google Scholar]
  41. Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M et al. myo-Inositol catabolism in Bacillus subtilis. J Biol Chem 2008; 283:10415–10424 [View Article]
    [Google Scholar]
  42. Turner BL, Papházy MJ, Haygarth PM, Mckelvie ID. Inositol phosphates in the environment. Phil Trans R Soc Lond B 2008; 357:449–469 [View Article] [PubMed]
    [Google Scholar]
  43. Wang F, Yuan Q, Chen F, Pang J, Pan C et al. Fundamental mechanisms of the cell death caused by nitrosative stress. Front Cell Dev Biol 2008; 9:742483 [View Article] [PubMed]
    [Google Scholar]
  44. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids. MIDI; 1990
  45. 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]
    [Google Scholar]
  46. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
    [Google Scholar]
  47. Kates M. Techniques of Lipidology: Isolation, Analysis, and Identification of Lipids, 2nd rev. edn. Amsterdam: Elsevier; 1986
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005606
Loading
/content/journal/ijsem/10.1099/ijsem.0.005606
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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