1887

Abstract

A Gram-stain-positive, aerobic, chemo-organotrophic, rod-shaped, non-spore-forming strain, which produced convex, circular, pink-pigmented colonies, designated as DY32-46, was isolated from seawater collected from the Pacific Ocean. DY32-46 was found to grow at 20–40 °C (optimum, 30–35 °C), pH 6.0–8.0 (optimum, pH 6.5) and with 0–5 % (w/v) NaCl (optimum, 1–2 %). The results of chemotaxonomic analysis indicated that the respiratory quinone of DY32-46 was MK-9(H), and major fatty acids (>10 %) were C 8, summed feature 3 (C 7 and/or C 6), C and C 6. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid, three unidentified glycolipids, three unidentified phospholipids, one unidentified phosphoglycolipid and five unidentified lipids. The DNA G+C content of DY32-46 was 70.6 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences and genomic data indicated that DY32-46 should be assigned to the genus . ANI and DNA–DNA hybridization values between strain DY32-46 and type strains of species were 73.1–87.2 % and 20.2–32.4 %, respectively. Different phenotypic properties, together with genetic distinctiveness, demonstrated that strain DY32-46 was clearly distinct from recognized species of the genus . Therefore, DY32-46 represents a novel species within the genus , for which the name sp. nov is proposed. The type strain is DY32-46 (=MCCC 1K03476=KCTC 49091).

Funding
This study was supported by the:
  • Natural Science Foundation of Zhejiang Province (Award LQ19C010006)
    • Principle Award Recipient: LinXu
  • China Postdoctoral Science Foundation (Award 2019M652042)
    • Principle Award Recipient: LinXu
  • Natural Science Foundation of China (Award 91851114)
    • Principle Award Recipient: Xue-WeiXu
  • China Ocean Mineral Resources R & D Association (COMRA) Special Foundation (Award DY135-E2-5-04)
    • Principle Award Recipient: Fan-XuMeng
  • Scientific Research Fund of the Second Institute of Oceanography, MNR (Award JB2003)
    • Principle Award Recipient: LinXu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004864
2021-07-13
2021-07-29
Loading full text...

Full text loading...

References

  1. Ludwig W, Euzéby JP, Whitman WB et al. Class IV. Nitriliruptoria class nov. Goodfellow M, Kämpfer P, Busse H-J, Trujillo M, Suzuki K-I. eds In Bergey’s Manual of Systematic Bacteriology, second edition, vol. 5 (The Actinobacteria), part B New York: Springer; 2012 pp 2000–2001
    [Google Scholar]
  2. Salam N, Jiao JY, Zhang XT, Li W-J. Update on the classification of higher ranks in the phylum Actinobacteria. Int J Syst Evol Microbiol 2020; 70:1331–1355
    [Google Scholar]
  3. Sorokin DY, van Pelt S, Tourova TP, Evtushenko LI. Nitriliruptor alkaliphilus gen. nov., sp. nov., a deep-lineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov. Int J Syst Evol Microbiol 2009; 59:248–253 [View Article] [PubMed]
    [Google Scholar]
  4. Kurahashi M, Fukunaga Y, Sakiyama Y, Harayama S, Yokota A. Euzebya tangerina gen. nov., sp. nov., a deeply branching marine actinobacterium isolated from the sea cucumber Holothuria edulis, and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. Int J Syst Evol Microbiol 2010; 60:2314–2319 [View Article] [PubMed]
    [Google Scholar]
  5. Zhang YG, Chen JY, Wang HF, Xiao M, Yang LL et al. Egicoccus halophilus gen. nov., sp. nov., a halophilic, alkalitolerant actinobacterium and proposal of Egicoccaceae fam. Int J Syst Evol Microbiol 2016; 66:530–535 [View Article] [PubMed]
    [Google Scholar]
  6. Zhang YG, Wang HF, Yang LL, Zhou XK, Zhi XY et al. Egibacter rhizosphaerae gen. nov., sp. nov., an obligately halophilic, facultatively alkaliphilic actinobacterium and proposal of Egibaceraceae fam. nov. and Egibacterales ord. nov. Int J Syst Evol Microbiol 2016; 66:283–289 [View Article] [PubMed]
    [Google Scholar]
  7. Yin Q, Zhang L, Song ZM, Wu Y, Hu Z-L et al. Euzebya rosea sp. nov., a rare actinobacterium isolated from the East China Sea and analysis of two genome sequences in the genus Euzebya. Int J Syst Evol Microbiol 2018; 68:2900–2905
    [Google Scholar]
  8. Xu L, Sun C, Huang MM, Wu Y-H, Yuan CQ et al. Complete genome sequence of Euzebya sp. DY32-46, a marine Actinobacteria isolated from the Pacific Ocean. Mar Genomics 2019; 44:65–69
    [Google Scholar]
  9. Xu L, Wu Y-H, Jian SL, Wang CS, Wu M et al. Pseudohongiella nitratireducens sp. nov., isolated from seawater, and emended description of the genus Pseudohongiella. Int J Syst Evol Microbiol 2016; 66:5155–5160
    [Google Scholar]
  10. Kim OS, Cho YJ, Lee K, Yoon SH, Kim 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 [View Article] [PubMed]
    [Google Scholar]
  11. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:1673–1680 [View Article]
    [Google Scholar]
  12. 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]
  13. 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]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific Tree Topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. 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]
  18. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2017; 35:725–731 [View Article] [PubMed]
    [Google Scholar]
  19. 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]
  20. Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–W57
    [Google Scholar]
  21. 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–D214 [View Article]
    [Google Scholar]
  22. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article] [PubMed]
    [Google Scholar]
  23. Gene Ontology Consortium Gene Ontology Consortium: Going forward. Nucleic Acids Res 2015; 43:1049–1056
    [Google Scholar]
  24. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article] [PubMed]
    [Google Scholar]
  25. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
    [Google Scholar]
  26. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
    [Google Scholar]
  27. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:W52–57 [View Article] [PubMed]
    [Google Scholar]
  28. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785–786 [View Article] [PubMed]
    [Google Scholar]
  29. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580 [View Article] [PubMed]
    [Google Scholar]
  30. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124 [View Article] [PubMed]
    [Google Scholar]
  31. Xu L, Ye K-X, Dai WH, Sun C, Xu L-H et al. Comparative genomic insights into secondary metabolism biosynthetic gene cluster distributions of marine Streptomyces. Mar Drugs 2019; 17:498
    [Google Scholar]
  32. Xu L, Wu Y-H, Zhou P, Cheng H, Liu Q et al. Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis. BMC Genomics 2018; 19:385
    [Google Scholar]
  33. 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]
  34. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
    [Google Scholar]
  35. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  36. Zhang XQ, Wu Y-H, Zhou X, Zhang X, Xu X-W et al. Parvularcula flava sp. nov., an alphaproteobacterium isolated from surface seawater of the South China Sea. Int J Syst Evol Microbiol 2016; 66:3498–3502
    [Google Scholar]
  37. Ye M-Q, Han JR, Wang C, Du Z-J. Alteromonas sediminis sp. nov., isolated from sediment in a sea cucumber culture pond. Int J Syst Evol Microbiol 2019; 69:1579–1584
    [Google Scholar]
  38. Shi XL, Wu Y-H, Jin XB, Wang CS, Xu X-W. Alteromonas lipolytica sp. nov., a poly-beta-hydroxybutyrate-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:237–242
    [Google Scholar]
  39. Tindall BJ, Sikorski J, Smibert RA, Snyder R, Krieg NR. Phenotypic characterization and the principles of comparative systematics. Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T. eds In Methods for General and Molecular Microbiology, 3rd. edn Washington, DC: ASM Press; 2007 pp 330–393
    [Google Scholar]
  40. Kim M, Oh H-S, 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]
  41. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004864
Loading
/content/journal/ijsem/10.1099/ijsem.0.004864
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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