Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 1

sp. nov. and sp. nov., two bacteria isolated from marine sediment in the East China Sea No Access

Abstract

Two Gram-stain-negative, curved-rod-shaped, non-motile and aerobic bacteria W6 and I13 were isolated from marine sediment samples collected from Meishan Island located in the East China Sea. Catalase and oxidase activities and hydrolysis of Tween 40, 60 and 80 were positive for both strains, while nitrate reduction, indole production, methyl red reaction and HS production were negative. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains W6 and I13 formed distinct phylogenetic lineages within the genera and , respectively. Strain W6 showed the closest relatedness to N5DA8-2C with 93.9% 16S rRNA gene sequence similarity, 70.7% average nucleotide identity (ANI), 71.0% average amino acid identity (AAI) and 16.4% digital DNA–DNA hybridization (dDDH) values, while strain I13 was most closely related to YM3-301 with 92.1% 16S rRNA gene sequence similarity, 70.5% ANI, 72.1% AAI and 17.2% dDDH values. The two novel strains shared 92.0% 16S rRNA gene sequence similarity to each other and were identified as two distinct species based on 70.7% ANI, 70.4% AAI and 17.1% dDDH values calculated using whole-genome sequences. The genomes of strains W6 and I13 were 4.59 Mbp with a G+C content of 34.5 mol% and 2.38 Mbp with a G+C content of 36.2 mol%, respectively. The only respiratory quinone was menaquinone-6, the major polar lipid was phosphatidylethanolamine and the major cellular fatty acids were iso-C, iso-C G and iso-C 3-OH. Based on phenotypic, chemotaxonomic and genotypic data, strains W6 and I13 are considered to represent two novel species in the genera and , respectively, in the family Flavobacteriaceae, for which the names sp. nov. and sp. nov. are proposed. The type strains are W6 (=KCTC 102201=MCCC 1K08928) and I13 (=KCTC 102202=MCCC 1K08929), respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Ascidiimonas , Flavobacteriaceae , Leptobacterium , marine sediment and taxonomy
Funding
This study was supported by the:
  • Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Development Fund
    • Principal Award Recipient: DingLijian
  • the National 111 Project of China (Award D16013)
    • Principal Award Recipient: zhangWeiyan
  • the Ningbo Key Science and Technology Development Program (Award 2021Z046)
    • Principal Award Recipient: Weiyanzhang
  • the Scientific Research Foundation of Graduate School of Ningbo University (Award IF2021087)
    • Principal Award Recipient: zhangWeiyan
  • Natural Science Foundation of Zhejiang Province (Award LGF22C010001)
    • Principal Award Recipient: zhangWeiyan
  • National Natural Science Foundation of China (Award 42176101)
    • Principal Award Recipient: zhangWeiyan
  • National Natural Science Foundation of China (Award 32100001)
    • Principal Award Recipient: zhangWeiyan
© 2025 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006653
2025-01-28
2025-12-17

Metrics

Loading full text...

Full text loading...

References

  1. Garrity GM, Holt JG. The road map to the Manual. In In Bergey’s Manuals of Systematic Bacteriology, 2nd edn. vol 1 pp 119–166
     [Google Scholar]
  2. Ludwig W, Klenk HP. Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Bergey’s Manuals of Systematic Bacteriology, 2nd edn. vol 1 pp 49–65
     [Google Scholar]
  3. Jooste PJ. The Taxonomy and Significance of Flavobacterium-Cytophaga Strains from Dairy Sources University of the Orange Free State; 1985
     [Google Scholar]
  4. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
     [Google Scholar]
  5. 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]
  6. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 2019; 10:2083 [View Article] [PubMed]
     [Google Scholar]
  7. McCammon SA, Innes BH, Bowman JP, Franzmann PD, Dobson SJ et al. Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic lake. Int J Syst Bacteriol 1998; 48 Pt 4:1405–1412 [View Article] [PubMed]
     [Google Scholar]
  8. Kirchman DL. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 2002; 39:91–100 [View Article] [PubMed]
     [Google Scholar]
  9. O’Sullivan LA. Culturable phylogenetic diversity of the phylum “Bacteroidetes” from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. Int J Syst Evol Microbiol 2006; 56:169–180 [View Article]
     [Google Scholar]
  10. Wang YW, Wang XH, Zhang J, Du ZJ, Mu DS. Cerina litoralis gen. nov., sp. nov., a novel potential polysaccharide degrading bacterium of the family Flavobacteriaceae, isolated from marine sediment. Anton Leeuw Int J G 2023; 116:1447–1455 [View Article]
     [Google Scholar]
  11. Yoon J, Adachi K, Kasai H. Citreitalea marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a marine red alga and emended description of the genus Gangjinia. Antonie van Leeuwenhoek 2014; 106:261–269 [View Article] [PubMed]
     [Google Scholar]
  12. Leyer C, Sassi M, Gourmelen F, Burel A, Beyrouthy R et al. Avrilella dinanensis gen. nov., sp. nov., a novel bacterium of the family Flavobacteriaceae isolated from human blood. Syst Appl Microbiol 2020; 43:126124 [View Article] [PubMed]
     [Google Scholar]
  13. Loch TP, Faisal M. Emerging Flavobacterial infections in fish: a review. J Adv Res 2015; 6:283–300 [View Article] [PubMed]
     [Google Scholar]
  14. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology, 1st ed Beijing: Scientific Press; 2001 pp 353–364
     [Google Scholar]
  15. Zhu XF. Modern Experimental Technique of Microbiology Zhejiang University Press, Hangzhou English translation; 2011
     [Google Scholar]
  16. Wang NN, Li CM, Li YX, Du ZJ. Aquimarina celericrescens sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2018; 68:1683–1688 [View Article] [PubMed]
     [Google Scholar]
  17. Sun C, Wu C, Su Y, Wang R-J, Fu G-Y et al. Hyphococcus flavus gen. nov., sp. nov., a novel alphaproteobacterium isolated from deep seawater. Int J Syst Evol Microbiol 2017; 67:4024–4031 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Fitch WM. Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  20. 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]
     [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. 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]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Zhang W, Zhu S, Cheng Y, Ding L, Li S et al. Rheinheimera mangrovi sp. nov., a bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 2020; 70:6188–6194 [View Article]
     [Google Scholar]
  26. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinf 2003; 4:1–14 [View Article] [PubMed]
     [Google Scholar]
  32. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S et al. NCBI BLAST: a better web interface. Nucleic Acids Res 2008; 36:W5–9 [View Article] [PubMed]
     [Google Scholar]
  33. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  34. Yoon S-H, Ha S, 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]
     [Google Scholar]
  35. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  36. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  37. Kim J, Na S-I, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article]
     [Google Scholar]
  38. Minh BQ, Trifinopoulos J, Schrempf D, Schmidt HA, Lanfear R. IQ-TREE version 2.0: tutorials and manual phylogenomic software by maximum likelihood. Nucleic Acids Res 2022; 44:W232–W235 [View Article]
     [Google Scholar]
  39. Er S, Soh M, Low A, Seedorf H. Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian seabass (Lates calcarifer). Antonie van Leeuwenhoek 2025; 118:25 [View Article]
     [Google Scholar]
  40. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  41. Yang S-H, Seo H-S, Oh H-M, Kim S-J, Lee J-H et al. Brumimicrobium mesophilum sp. nov., isolated from a tidal flat sediment, and emended descriptions of the genus Brumimicrobium and Brumimicrobium glaciale. Int J Syst Evol Microbiol 2013; 63:1105–1110 [View Article] [PubMed]
     [Google Scholar]
  42. 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 Meth 1984; 2:233–241 [View Article]
     [Google Scholar]
  43. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
     [Google Scholar]
  44. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006653
Loading
Ascidiimonas meishanensis sp. nov. and Leptobacterium meishanense sp. nov., two bacteria isolated from marine sediment in the East China Sea
Int J Syst Evol Microbiol 75, 006653 (2025); https://doi.org/10.1099/ijsem.0.006653
/content/journal/ijsem/10.1099/ijsem.0.006653
/content/journal/ijsem/10.1099/ijsem.0.006653
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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