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Volume 74, Issue 3

sp. nov., isolated from the skin of a deep-sea snub-nosed spiny eel Open Access

Abstract

A novel bacterial strain, APC 4016, was previously isolated from the skin of a snub-nosed spiny eel, , from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4–40 °C (optimum, 25–28 °C), pH 5.5–12 (optimum, pH 7–7.5), and 0–12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016 belonged to the genus and was most closely related to IFO 12536 (98.98 % 16S similarity). However, digital DNA–DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016 were iso-C, anteiso-C and C-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016 is deemed to represent a novel species of the genus , and for which the name sp. nov. is proposed. The type strain of this species is APC 4016 (=DSM 115753=NCIMB 15463).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): biosynthetic gene clusters , Caryophanaceae , deep-sea , marine fish , novel species and Planococcus
Funding
This study was supported by the:
  • Science Foundation Ireland (Award SFI/ 12/RC/2273_P2)
    • Principle Award Recipient: PaulP. Ross
  • European Research Council (Award BACtheWINNER, 101054719)
    • Principle Award Recipient: PaulP. Ross
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-03-21
2024-04-27
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References

  1. Migula W. Ueber ein neues System der Bakterien. In Arb. Bakt. Inst. Karlsruhe vol 1 1894 p 235
     [Google Scholar]
  2. Nakagawa Y, Sakane T, Yokota A. Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. nov. Int J Syst Bacteriol 1996; 46:866–870 [View Article] [PubMed]
     [Google Scholar]
  3. Yoon J-H, Kang S-J, Lee S-Y, Oh K-H, Oh T-K. Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus. Int J Syst Evol Microbiol 2010; 60:754–758 [View Article] [PubMed]
     [Google Scholar]
  4. Yoon JH, Kang SS, Lee KC, Lee ES, Kho YH et al. Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium. Int J Syst Evol Microbiol 2001; 51:1511–1520 [View Article] [PubMed]
     [Google Scholar]
  5. Dai X, Wang Y-N, Wang B-J, Liu S-J, Zhou Y-G. Planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of Planococcus psychrophilus and Planococcus alkanoclasticus to Planomicrobium as Planomicrobium psychrophilum comb. nov. and Planomicrobium alkanoclasticum comb. nov. Int J Syst Evol Microbiol 2005; 55:699–702 [View Article] [PubMed]
     [Google Scholar]
  6. Jung Y-T, Kang S-J, Oh T-K, Yoon J-H, Kim B-H. Planomicrobium flavidum sp. nov., isolated from a marine solar saltern, and transfer of Planococcus stackebrandtii Mayilraj et al. 2005 to the genus Planomicrobium as Planomicrobium stackebrandtii comb. nov. Int J Syst Evol Microbiol 2009; 59:2929–2933 [View Article] [PubMed]
     [Google Scholar]
  7. Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. The prokaryotes: firmicutes and tenericutes. Prokaryotes 2014; 1:3 [View Article]
     [Google Scholar]
  8. Gupta RS, Patel S. Robust demarcation of the family Caryophanaceae (Planococcaceae) and its different genera including three novel genera based on phylogenomics and highly specific molecular signatures. Front Microbiol 2019; 10:2821 [View Article] [PubMed]
     [Google Scholar]
  9. Reddy GSN, Prakash JSS, Vairamani M, Prabhakar S, Matsumoto GI et al. Planococcus antarcticus and Planococcus psychrophilus spp. nov. isolated from cyanobacterial mat samples collected from ponds in Antarctica. Extremophiles 2002; 6:253–261 [View Article] [PubMed]
     [Google Scholar]
  10. Alam SI, Singh L, Dube S, Reddy GSN, Shivaji S. Psychrophilic Planococcus maitriensis sp.nov. from Antarctica. Syst Appl Microbiol 2003; 26:505–510 [View Article] [PubMed]
     [Google Scholar]
  11. Hao MV, Komagata K. A new species of Planococcus, P. kocurii isolated from fish, frozen foods, and fish curing brine. J Gen Appl Microbiol 1985; 31:441–455 [View Article]
     [Google Scholar]
  12. Mykytczuk NCS, Wilhelm RC, Whyte LG. Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost. Int J Syst Evol Microbiol 2012; 62:1937–1944 [View Article] [PubMed]
     [Google Scholar]
  13. Zhang D-C, Liu H-C, Xin Y-H, Yu Y, Zhou P-J et al. Planomicrobium glaciei sp. nov., a psychrotolerant bacterium isolated from a glacier. Int J Syst Evol Microbiol 2009; 59:1387–1390 [View Article] [PubMed]
     [Google Scholar]
  14. Mayilraj S, Prasad GS, Suresh K, Saini HS, Shivaji S et al. Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India. Int J Syst Evol Microbiol 2005; 55:91–94 [View Article] [PubMed]
     [Google Scholar]
  15. Choi J-H, Im W-T, Liu Q-M, Yoo J-S, Shin J-H et al. Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea. Int J Syst Evol Microbiol 2007; 57:2645–2650 [View Article] [PubMed]
     [Google Scholar]
  16. Wang X, Wang Z, Zhao X, Huang X, Zhou Y et al. Planococcus ruber sp. nov., isolated from a polluted farmland soil sample. Int J Syst Evol Microbiol 2017; 67:2549–2554 [View Article] [PubMed]
     [Google Scholar]
  17. Yang R, Zhang B, Wang J, Tai X, Sun H et al. Planococcus lenghuensis sp. nov., an oil-degrading bacterium isolated from petroleum-contaminated soil. Antonie van Leeuwenhoek 2020; 113:839–850 [View Article] [PubMed]
     [Google Scholar]
  18. Zhang H, Mu H, Mo Q, Sun T, Liu Y et al. Gene cloning, expression and characterization of a novel cold-adapted protease from Planococcus sp. J Mol Cat B: Enzymat 2016; 130:1–8 [View Article]
     [Google Scholar]
  19. Huang X, Lin J, Ye X, Wang G. Molecular characterization of a thermophilic and salt- and alkaline-tolerant xylanase from Planococcus sp. SL4, a strain isolated from the sediment of a Soda Lake. J Microbiol Biotechnol 2015; 25:662–671 [View Article] [PubMed]
     [Google Scholar]
  20. Hu JM, Li H, Cao LX, Wu PC, Zhang CT et al. Molecular cloning and characterization of the gene encoding cold-active beta-galactosidase from a psychrotrophic and halotolerant Planococcus sp. L4. J Agric Food Chem 2007; 55:2217–2224 [View Article] [PubMed]
     [Google Scholar]
  21. Rao S, Chan OW, Lacap-Bugler DC, Pointing SB. Radiation-tolerant bacteria isolated from high altitude soil in Tibet. Indian J Microbiol 2016; 56:508–512 [View Article] [PubMed]
     [Google Scholar]
  22. Rajput L, Imran A, Mubeen F, Hafeez FY. Salt-tolerant PGPR strain Planococcus Rifietoensis promotes the growth and yield of wheat (Triticum aestivum L.) cultivated in saline soil. Pak J Bot 2013; 45:1955–1962
     [Google Scholar]
  23. Zhang B, Yang R, Zhang G, Liu Y, Zhang D et al. Characteristics of Planococcus antioxidans sp. nov., an antioxidant-producing strain isolated from the desert soil in the Qinghai-Tibetan Plateau. Microbiologyopen 2020; 9:1183–1196 [View Article] [PubMed]
     [Google Scholar]
  24. Shindo K, Endo M, Miyake Y, Wakasugi K, Morritt D et al. Methyl 5-glucosyl-5,6-dihydro-apo-4,4’-lycopenoate, a novel antioxidative glyco-C(30)-carotenoic acid produced by a marine bacterium Planococcus maritimus. J Antibiot 2008; 61:729–735 [View Article] [PubMed]
     [Google Scholar]
  25. Al-Awadhi H, Dashti N, Kansour M, Sorkhoh N, Radwan S. Hydrocarbon-utilizing bacteria associated with biofouling materials from offshore waters of the Arabian Gulf. Int Bio 2012; 69:10–16 [View Article]
     [Google Scholar]
  26. Vishnupriya S, Jabir T, Adarsh BM, Kattatheyil H, Kabeer S et al. Diversity of complex polysaccharide degrading bacteria from the sediments of interlinked high Arctic fjords, Svalbard. Reg Studies Mar Sci 2023; 63:102989 [View Article]
     [Google Scholar]
  27. Gaur VK, Gupta P, Tripathi V, Thakur RS, Regar RK et al. Valorization of agro-industrial waste for rhamnolipid production, its role in crude oil solubilization and resensitizing bacterial pathogens. Environ Technol Inn 2022; 25:102108 [View Article]
     [Google Scholar]
  28. Li H, Liu YH, Luo N, Zhang XY, Luan TG et al. Biodegradation of benzene and its derivatives by a psychrotolerant and moderately haloalkaliphilic Planococcus sp. strain ZD22. Res Microbiol 2006; 157:629–636 [View Article] [PubMed]
     [Google Scholar]
  29. Uniacke-Lowe S, Collins FWJ, Hill C, Ross RP. Bioactivity screening and genomic analysis reveals deep-sea fish microbiome isolates as sources of novel antimicrobials. Mar Drugs 2023; 21:444 [View Article] [PubMed]
     [Google Scholar]
  30. Collins FWJ, Walsh CJ, Gomez-Sala B, Guijarro-García E, Stokes D et al. The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes. Gut Microbes 2021; 13:1–13 [View Article] [PubMed]
     [Google Scholar]
  31. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  32. 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] [PubMed]
     [Google Scholar]
  33. 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]
  34. 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]
  35. 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]
  36. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  37. 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]
  38. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of molecular evolution 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  39. Nei M, Kumar S. Molecular Evolution and Phylogenetics Oxford university press; 2000
     [Google Scholar]
  40. 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]
  41. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  42. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
     [Google Scholar]
  43. 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] [PubMed]
     [Google Scholar]
  44. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  45. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  46. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  47. Bernardet J-F, Nakagawa Y, Holmes B. 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] [PubMed]
     [Google Scholar]
  48. Kurilenko VV, Romanenko LA, Isaeva MP, Svetashev VI, Mikhailov VV. Winogradskyella algae sp. nov., a marine bacterium isolated from the brown alga. Antonie van Leeuwenhoek 2019; 112:731–739 [View Article] [PubMed]
     [Google Scholar]
  49. Hudzicki J. Kirby-Bauer disk diffusion susceptibility test protocol. ASM 2009; 15:55–63
     [Google Scholar]
  50. 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]
  51. Kaur I, Das AP, Acharya M, Klenk H-P, Sree A et al. Planococcus plakortidis sp. nov., isolated from the marine sponge Plakortis simplex (Schulze). Int J Syst Evol Microbiol 2012; 62:883–889 [View Article] [PubMed]
     [Google Scholar]
  52. See-Too W-S, Ee R, Madhaiyan M, Kwon S-W, Tan JY et al. Planococcus versutus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:944–950 [View Article] [PubMed]
     [Google Scholar]
  53. Gan L, Zhang Y, Zhang L, Li X, Wang Z et al. Planococcus halotolerans sp. nov., isolated from a saline soil sample in China. Int J Syst Evol Microbiol 2018; 68:3500–3505 [View Article] [PubMed]
     [Google Scholar]
  54. Luo X, Zhang J, Li D, Xin Y, Xin D et al. Planomicrobium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:2700–2705 [View Article] [PubMed]
     [Google Scholar]
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Planococcus notacanthi sp. nov., isolated from the skin of a deep-sea snub-nosed spiny eel
Int J Syst Evol Microbiol 74, 006298 (2024); https://doi.org/10.1099/ijsem.0.006298
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