1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 10

sp. nov., a novel bacterium isolated from Pearl River estuary Open Access

Abstract

A novel species of the genus , designated SYSU M41301, was isolated from water sample of the Pearl River estuary in Guangdong, China. Polyphasic, taxonomic and phylogenomic analyses were used to determine the taxonomy position of the strain. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain SYSU M41301 showed the highest sequence similarity to KCTC 22213 (97.9 %) and KCTC 23339 (96.4 %). The novel species could be differentiated from other species of the genus by its distinct phenotypic and genotypic characteristics. The isolate was Gram-staining-negative, aerobic, short rod-shape, oxidase-positive and non-motile. The predominant respiratory quinone was ubiquinone 8 (Q-8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and one unidentified polar lipid. The major fatty acids (>10 % of total) were 11-methyl C 7, summed feature 3 (C c / or C c) and summed feature 8 (C 7 and/or C 6). The G+C content of the novel isolate based on genomic DNA was 72.0 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU M41301 should be considered to represent a novel species in the genus for which the name sp. nov. is proposed with the type strain SYSU M41301 (=KCTC 72726=CGMCC 1.18613).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Pearl River estuary , Roseomonas and Roseomonas ponticola sp. nov
Funding
This study was supported by the:
  • guangdong basic and applied basic research foundation (Award 2020A1515011139)
    • Principle Award Recipient: Jia-LingLi
  • postdoctoral research foundation of china (Award 2020M683029)
    • Principle Award Recipient: PandengWang
  • postdoctoral research foundation of china (Award 2018M643294)
    • Principle Award Recipient: Jia-LingLi
  • national natural science foundation of china (Award 31850410475)
    • Principle Award Recipient: Wen-JunLi
  • national natural science foundation of china (Award 91751206)
    • Principle Award Recipient: Wen-JunLi
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004994
2021-10-08
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/10/ijsem004994.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004994&mimeType=html&fmt=ahah

References

  1. Rihs JD, Brenner DJ, Weaver RE, Steigerwalt AG, Hollis DG et al. Roseomonas, a new genus associated with bacteremia and other human infections. J Clin Microbiol 1993; 31:3275–3283 [View Article] [PubMed]
     [Google Scholar]
  2. Dé I, Rolston KVI, Han XY. Clinical significance of Roseomonas species isolated from catheter and blood samples: analysis of 36 cases in patients with cancer. Clin Infect Dis 2004; 38:1579–1584 [View Article] [PubMed]
     [Google Scholar]
  3. Gallego V, Sanchez-Porro C, Garcia MT, Ventosa A. Roseomonas aquatica sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2006; 56:2291–2295 [View Article] [PubMed]
     [Google Scholar]
  4. Jiang CY, Dai X, Wang BJ, Zhou YG, Liu SJ. Roseomonas lacus sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 2006; 56:25–28 [View Article] [PubMed]
     [Google Scholar]
  5. Kim MS, Baik KS, Park SC, Rhee MS, Oh H-M et al. Roseomonas frigidaquae sp. nov., isolated from a water-cooling system. Int J Syst Evol Microbiol 2009; 59:1630–1634 [View Article] [PubMed]
     [Google Scholar]
  6. Sfanos K, Harmody D, Dang P, Ledger A, Pomponi S et al. A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates. Syst Appl Microbiol 2005; 28:242–264 [View Article] [PubMed]
     [Google Scholar]
  7. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
     [Google Scholar]
  8. Leifson E. Atlas of Bacterial Flagellation London: Academic Press; 1960 [View Article]
     [Google Scholar]
  9. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article] [PubMed]
     [Google Scholar]
  10. Nie G-X, Ming H, Li S, Zhou E-M, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:2650–2656 [View Article] [PubMed]
     [Google Scholar]
  11. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov., an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
     [Google Scholar]
  12. Smibert RA, Krieg NR. Phenotypic characterization. Gerhardt P, Murray R, Wood W, Krieg N. eds In Methods for General and Molecular Bacteriology Washington, DC: American Society of Microbiology; 1994 pp 607–654
     [Google Scholar]
  13. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  14. Liu YH, Guo JW, Salam N, Li L, Zhang YG et al. Culturable endophytic bacteria associated with medicinal plant Ferula songorica: molecular phylogeny, distribution and screening for industrially important traits. 3 Biotech 2016; 6:209 [View Article] [PubMed]
     [Google Scholar]
  15. Yang ZW, Salam N, Hua ZS, Liu BB, Han MX et al. Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample. Int J Syst Evol Microbiol 2017; 67:4862–4867 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  23. Harrison PG, Strulo B. SPADES - a process algebra for discrete event simulation. Journal of Logic and Computation 2000; 10:3–42 [View Article]
     [Google Scholar]
  24. Jiménez G, Urdiain M, Cifuentes A, López-López A, Blanch AR. Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Syst Appl Microbiol 2013; 36:383–391 [View Article] [PubMed]
     [Google Scholar]
  25. Salam N, Jiao J-Y, Zhang X-T, Li W-J. Update on the classification of higher ranks in the phylum actinobacteria. Int J Syst Evol Microbiol 2020; 70:1331–1355 [View Article] [PubMed]
     [Google Scholar]
  26. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033 [View Article] [PubMed]
     [Google Scholar]
  27. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  28. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
     [Google Scholar]
  29. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article] [PubMed]
     [Google Scholar]
  30. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  31. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
     [Google Scholar]
  32. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  33. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004994
Loading
Roseomonas ponticola sp. nov., a novel bacterium isolated from Pearl River estuary
Int J Syst Evol Microbiol 71, 004994 (2021); https://doi.org/10.1099/ijsem.0.004994
/content/journal/ijsem/10.1099/ijsem.0.004994
/content/journal/ijsem/10.1099/ijsem.0.004994
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