1887

Abstract

A novel bacterial strain, APC 3343, was isolated from the intestine of a deep-sea loosejaw dragon fish, , caught at a depth of 1000 m in the Northwest Atlantic Ocean. Cells were aerobic, rod-shaped, yellow/orange-pigmented, non-motile and Gram-negative. Growth of strain APC 3343 was observed at 4–30 °C (optimum, 21–25 °C), pH 5.5–10 (optimum, pH 7–8) and 0.5–8 % (w/v) NaCl (optimum, 2–4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain APC 3343 was most closely related to members of the genus , with the most closely related type strains being Kr9-9 (98.46 % identity), F081-2 (98.07 %), CECT 7946 (97.93 %), KMM 6491 (97.79 %) and HL2-2 (97.79 %). Major fatty acids (>10 % of total) were iso-C 3-OH, iso-C, anteiso-C and iso-C 3-OH. The predominant respiratory quinone was menaquinone-6 (MK-6). Polar lipids were phosphatidylethanolamine, three unknown aminolipids and eight unknown lipids. The draft genome sequence was 3.8 Mb in length with a G+C content of 33.43 mol%. Based on the phenotypic characteristics and phylogenetic analysis, strain APC 3343 is deemed to be a novel species of the genus , and for which the name sp. nov. is proposed. The type strain of this species is APC 3343 (=DSM 115832=NCIMB 15464).

Funding
This study was supported by the:
  • European Research Council (Award 101054719)
    • Principle Award Recipient: PaulRoss
  • Science Foundation Ireland (Award SFI/12/RC/2273_P2)
    • Principle Award Recipient: PaulRoss
  • 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.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006135
2023-10-25
2024-12-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/73/10/ijsem006135.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006135&mimeType=html&fmt=ahah

References

  1. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS et al. Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2005; 55:2583–2588 [View Article] [PubMed]
    [Google Scholar]
  2. Ivanova EP, Christen R, Gorshkova NM, Zhukova NV, Kurilenko VV et al. Winogradskyella exilis sp. nov., isolated from the starfish Stellaster equestris, and emended description of the genus Winogradskyella. Int J Syst Evol Microbiol 2010; 60:1577–1580 [View Article] [PubMed]
    [Google Scholar]
  3. Yoon B-J, Byun H-D, Kim J-Y, Lee D-H, Kahng H-Y et al. Winogradskyella lutea sp. nov., isolated from seawater, and emended description of the genus Winogradskyella. Int J Syst Evol Microbiol 2011; 61:1539–1543 [View Article] [PubMed]
    [Google Scholar]
  4. Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV. Winogradskyella ulvae sp. nov., an epiphyte of a Pacific seaweed, and emended descriptions of the genus Winogradskyella and Winogradskyella thalassocola, Winogradskyella echinorum, Winogradskyella exilis and Winogradskyella eximia. Int J Syst Evol Microbiol 2012; 62:1450–1456 [View Article] [PubMed]
    [Google Scholar]
  5. Begum Z, Srinivas TNR, Manasa P, Sailaja B, Sunil B et al. Winogradskyella psychrotolerans sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from Arctic sediment. Int J Syst Evol Microbiol 2013; 63:1646–1652 [View Article] [PubMed]
    [Google Scholar]
  6. Alejandre-Colomo C. Taxonomic study of nine new Winogradskyella species occurring in the shallow waters of Helgoland Roads, North Sea. Proposal of Winogradskyella schleiferi sp. nov., Winogradskyella costae sp. nov., Winogradskyella helgolandensis sp. nov., Winogradskyella vidalii sp. nov., Winogradskyella forsetii sp. nov., Winogradskyella ludwigii sp. nov., Winogradskyella ursingii sp. nov., Winogradskyella wichelsiae sp. nov., and candidatus “Winogradskyella atlantica” sp. nov. Syst Appl Microbiol 2020; 43: [View Article] [PubMed]
    [Google Scholar]
  7. Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV, Kim S-J, Rhee S-K et al. Winogradskyella litoriviva sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2015; 65:3652–3657 [View Article] [PubMed]
    [Google Scholar]
  8. Wang C, Han J-R, Liu C-L, Du Z-J. Winogradskyella tangerina sp. nov., a member of the Flavobacteriaceae isolated from coastal sediment. Int J Syst Evol Microbiol 2018; 68:2832–2837 [View Article] [PubMed]
    [Google Scholar]
  9. 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]
  10. Xu Y, Li J, Hu Y, Li H, Peng T et al. Winogradskyella endarachnes sp. nov., a marine bacterium isolated from the brown alga Endarachne binghamiae. Int J Syst Evol Microbiol 2020; 71:1 [View Article] [PubMed]
    [Google Scholar]
  11. Park S, Park JM, Won SM, Yoon JH. Winogradskyella crassostreae sp. nov., isolated from an oyster (Crassostrea gigas). Int J Syst Evol Microbiol 2015; 65:2890–2895 [View Article] [PubMed]
    [Google Scholar]
  12. Franco A, Busse H-J, Schubert P, Wilke T, Kämpfer P et al. Winogradskyella pocilloporae sp. nov. isolated from healthy tissue of the coral Pocillopora damicornis. Int J Syst Evol Microbiol 2018; 68:1689–1696 [View Article] [PubMed]
    [Google Scholar]
  13. Valdenegro-Vega V, Naeem S, Carson J, Bowman JP, Tejedor del Real JL et al. Culturable microbiota of ranched southern bluefin tuna (Thunnus maccoyii Castelnau). J Appl Microbiol 2013; 115:923–932 [View Article] [PubMed]
    [Google Scholar]
  14. Magzal F, Shochat T, Haimov I, Tamir S, Asraf K et al. Increased physical activity improves gut microbiota composition and reduces short-chain fatty acid concentrations in older adults with insomnia. Sci Rep 2022; 12:2265 [View Article] [PubMed]
    [Google Scholar]
  15. Rizzo C, Zammuto V, Lo Giudice A, Rizzo MG, Spanò A et al. Antibiofilm activity of antarctic sponge-associated bacteria against Pseudomonas aeruginosa and Staphylococcus aureus. JMSE 2021; 9:243 [View Article]
    [Google Scholar]
  16. Dash S, Jin C, Lee OO, Xu Y, Qian P-Y. Antibacterial and antilarval-settlement potential and metabolite profiles of novel sponge-associated marine bacteria. J Ind Microbiol Biotechnol 2009; 36:1047–1056 [View Article] [PubMed]
    [Google Scholar]
  17. Caruso C, Rizzo C, Mangano S, Poli A, Di Donato P et al. Production and biotechnological potential of extracellular polymeric substances from sponge-associated antarctic bacteria. Appl Environ Microbiol 2018; 84:e01624-17 [View Article] [PubMed]
    [Google Scholar]
  18. Wang W, Zhang R, Shan D, Shao Z. Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow sea, China. Appl Microbiol Biotechnol 2014; 98:7253–7269 [View Article] [PubMed]
    [Google Scholar]
  19. Pira H, Risdian C, Müsken M, Schupp PJ, Wink J. Winogradskyella luteola sp.nov., Erythrobacter ani sp. nov., and Erythrobacter crassostrea sp.nov., isolated from the hemolymph of the Pacific oyster Crassostrea gigas. Arch Microbiol 2022; 204:488 [View Article] [PubMed]
    [Google Scholar]
  20. Lee D-H, Cho SJ, Kim SM, Lee SB. Winogradskyella damuponensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:321–326 [View Article] [PubMed]
    [Google Scholar]
  21. Rapp JZ, Fernández-Méndez M, Bienhold C, Boetius A. Effects of ice-algal aggregate export on the connectivity of bacterial communities in the central arctic ocean. Front Microbiol 2018; 9:1035 [View Article] [PubMed]
    [Google Scholar]
  22. He X, Liu R, Liang J, Li Y, Zhao X et al. Winogradskyella ouciana sp. nov., isolated from the hadal seawater of the Mariana Trench. Int J Syst Evol Microbiol 2021; 71:3 [View Article] [PubMed]
    [Google Scholar]
  23. Somero GN. Biochemical ecology of deep-sea animals. Experientia 1992; 48:537–543 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. Harold A. Malacosteus niger in The IUCN Red List of Threatened Species; 2015 www.iucnredlist.org/species/190149/21909439
  26. Somiya H, Marshall NB. Yellow lens eyes of a Stomiatoid deep-sea fish. Proc R Soc Lond B Biol Sci 1982; 215:481–489 [View Article]
    [Google Scholar]
  27. Sutton TT. Trophic ecology of the deep-sea fish Malacosteus niger (Pisces: Stomiidae): an enigmatic feeding ecology to facilitate a unique visual system?. In Deep Sea Research Part I: Oceanographic Research Papers vol 52 2005 pp 2065–2076 [View Article]
    [Google Scholar]
  28. Shoemaker KM, Moisander PH. Seasonal variation in the copepod gut microbiome in the subtropical North Atlantic Ocean. Environ Microbiol 2017; 19:3087–3097 [View Article] [PubMed]
    [Google Scholar]
  29. Datta MS, Almada AA, Baumgartner MF, Mincer TJ, Tarrant AM et al. Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology. ISME J 2018; 12:2103–2113 [View Article] [PubMed]
    [Google Scholar]
  30. Oh HN, Ri MN, Kim T, Min G-S, Kim S et al. Changes in fecal pellet microbiome of the cold-adapted antarctic copepod Tigriopus kingsejongensis at different temperatures and developmental stages. Microb Ecol 2021; 84:1029–1041 [View Article]
    [Google Scholar]
  31. 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]
  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. 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] [PubMed]
    [Google Scholar]
  35. 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]
  36. 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]
  37. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  38. 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]
  39. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  40. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  41. 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]
  42. 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]
  43. 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]
  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. 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]
  47. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article] [PubMed]
    [Google Scholar]
  48. 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]
  49. Schellenberg J, Busse H-J, Hardt M, Schubert P, Wilke T et al. Winogradskyella haliclonae sp. nov., isolated from a marine sponge of the genus Haliclona. Int J Syst Evol Microbiol 2017; 67:4902–4910 [View Article] [PubMed]
    [Google Scholar]
  50. Lee JH, Kang JW, Shin SB, Seong CN. Winogradskyella flava sp. nov., isolated from the brown alga, Sargassum fulvellum. Int J Syst Evol Microbiol 2017; 67:3540–3546 [View Article] [PubMed]
    [Google Scholar]
  51. Kang H, Kim H, Joung Y, Joh K. Winogradskyella maritima sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:3840–3845 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006135
Loading
/content/journal/ijsem/10.1099/ijsem.0.006135
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