1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 9

sp. nov., a novel member of the family isolated from seawater of the South China Sea and reclassification of as comb. nov. No Access

Abstract

A Gram-stain-negative, aerobic, motile, ovoid-shaped and yellow-coloured strain, designated SYSU M79828, was isolated from seawater collected from the South China Sea. Growth of this strain was observed at 4–37 °C (optimum, 28 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–6% NaCl (optimum, 3.0 %, w/v). The respiratory quinone was found to be Q-10. Major fatty acid constituents were C 7/C 6, C 711-methyl and C (>5 % of total). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, two unidentified phospholipid, one unidentified lipid and an unidentified glycolipid. The genomic DNA G+C content was 64.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M79828 belonged to the genus and had the highest sequences similarity to ‘’ TJ48 (98.41 %). Based on 16S rRNA gene phylogeny, physiological and chemotaxonomic characterizations, we consider that strain SYSU M79828 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU M79828 (=GDMCC 1.3803=KCTC 92893). In addition, according to the results of phylogenetic analysis and similar taxonomic characteristics, we propose that should be reclassified as comb. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Cereibacter flavus sp. nov. , polyphasic taxonomy and seawater
Funding
This study was supported by the:
  • Guangdong Basic and Applied Basic Research Foundation, China (Award 2023A1515012270)
    • Principle Award Recipient: Jia-LingLi
  • Guangdong Basic and Applied Basic Research Foundation, China (Award 2022A1515010756)
    • Principle Award Recipient: Pan-DengWang
  • Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) (Award 311021004)
    • Principle Award Recipient: Wen-JunLi
  • Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) (Award 311021006)
    • Principle Award Recipient: Jia-LingLi
  • National Natural Science Foundation of China (Award 32200090)
    • Principle Award Recipient: Jia-LingLi
© 2023 Sun Yat-Sen University
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006051
2023-09-29
2024-05-08
Loading full text...

Full text loading...

References

  1. Suresh G, Sasikala C, Ramana CV. Reclassification of Gemmobacter changlensis to a new genus as Cereibacter changlensis gen. nov., comb. nov. Int J Syst Evol Microbiol 2015; 65:794–798 [View Article] [PubMed]
     [Google Scholar]
  2. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article] [PubMed]
     [Google Scholar]
  3. Suresh G, Lodha TD, Indu B, Sasikala C, Ramana CV. Corrigendum: taxogenomics resolves conflict in the genus Rhodobacter: a two and hjalf decades pending thought to reclassify the genus Rhodobacter. Front Microbiol 2020; 11:1111 [View Article] [PubMed]
     [Google Scholar]
  4. Hameed A, Shahina M, Lin S-Y, Chen W-M, Hsu Y-H et al. Description of Gemmobacter aestuarii sp. nov., isolated from estuarine surface water and reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013. Arch Microbiol 2020; 202:1035–1042 [View Article] [PubMed]
     [Google Scholar]
  5. Ma T, Xue H, Piao C, Liu C, Yang M et al. Reclassification of 11 members of the family Rhodobacteraceae at genus and species levels and proposal of Pseudogemmobacter hezensis sp. nov. Front Microbiol 2022; 13:849695 [View Article] [PubMed]
     [Google Scholar]
  6. Oren A, Garrity G. Validation list no. 207. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  7. Anil Kumar P, Srinivas TNR, Sasikala C, Ramana CV. Rhodobacter changlensis sp. nov., a psychrotolerant, phototrophic alphaproteobacterium from the Himalayas of India. Int J Syst Evol Microbiol 2007; 57:2568–2571 [View Article] [PubMed]
     [Google Scholar]
  8. Srinivas TNR, Anil Kumar P, Sasikala C, Spröer C, Ramana CV. Rhodobacter ovatus sp. nov., a phototrophic alphaproteobacterium isolated from a polluted pond. Int J Syst Evol Microbiol 2008; 58:1379–1383 [View Article] [PubMed]
     [Google Scholar]
  9. Girija KR, Sasikala C, Ramana CV, Spröer C, Takaichi S et al. Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils. Int J Syst Evol Microbiol 2010; 60:2099–2107 [View Article] [PubMed]
     [Google Scholar]
  10. van Niel CB. The culture, general physiology, morphplogy, and classification of the non-sulfur purple and brown bacteria. Bacteriol Rev 1944; 8:1–118 [View Article] [PubMed]
     [Google Scholar]
  11. Hiraishi A, Muramatsu K, Ueda Y. Molecular genetic analyses of Rhodobacter azotoformans sp. nov. and related species of phototrophic bacteria. Syst Appl Microbiol 1996; 19:168–177 [View Article]
     [Google Scholar]
  12. Suresh G, Kumar D, A K, Ch S, Ch VR. Rhodobacter sediminicola sp. nov., isolated from a fresh water pond. Int J Syst Evol Microbiol 2020; 70:1294–1299 [View Article] [PubMed]
     [Google Scholar]
  13. Zheng L, Zhu X, Yang K, Zhu M, Farooqi AA et al. PBN11-8, a Cytotoxic Polypeptide Purified from Marine Bacillus, Suppresses Invasion and Migration of Human Hepatocellular Carcinoma Cells by Targeting Focal Adhesion Kinase Pathways. Polymers 2018; 10:1043 [View Article] [PubMed]
     [Google Scholar]
  14. El-Sersy NA, Abdelwahab AE, Abouelkhiir SS, Abou-Zeid DM, Sabry SA. Antibacterial and anticancer activity of ε-poly-L-lysine (ε-PL) produced by a marine Bacillus subtilis sp. J Basic Microbiol 2012; 52:513–522 [View Article] [PubMed]
     [Google Scholar]
  15. De Rop A-S, Rombaut J, Willems T, De Graeve M, Vanhaecke L et al. Novel alkaloids from marine actinobacteria: discovery and characterization. Mar Drugs 2021; 20:6 [View Article] [PubMed]
     [Google Scholar]
  16. Habbu P, Warad V, Shastri R, Madagundi S, Kulkarni VH. Antimicrobial metabolites from marine microorganisms. Chin J Nat Med 2016; 14:101–116 [View Article] [PubMed]
     [Google Scholar]
  17. Ameen F, AlNadhari S, Al-Homaidan AA. Marine microorganisms as an untapped source of bioactive compounds. Saudi J Biol Sci 2021; 28:224–231 [View Article] [PubMed]
     [Google Scholar]
  18. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp nov., a novel member of the family 'Oxalobacteraceae' isolated from China.. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
     [Google Scholar]
  19. Leifson E. Atlas of Bacterial Flagellation New York: Academic Press; 1960 [View Article]
     [Google Scholar]
  20. 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]
  21. 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]
  22. Smibert RM, Krieg NR. Phenotypic characterization. In methods for general and molecular bacteriology. In American Society For Microbiology 1994 pp 611–651
     [Google Scholar]
  23. 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]
  24. 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]
  25. Athalye M, Noble WC, Minnikin DE. Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 1985; 58:507–512 [View Article] [PubMed]
     [Google Scholar]
  26. Goodfellow M, Minnikin DE CM. 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]
  27. 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]
  28. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. 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]
  33. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. 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]
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  37. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  38. Jiao J-Y, Fu L, Hua Z-S, Liu L, Salam N et al. Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. ISME J 2021; 15:3005–3018 [View Article] [PubMed]
     [Google Scholar]
  39. Nguyen L-T, 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]
  40. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
     [Google Scholar]
  41. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [View Article] [PubMed]
     [Google Scholar]
  42. Salam N, Jiao JY, Zhang XT, Li WJ. 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]
  43. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article] [PubMed]
     [Google Scholar]
  44. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  45. 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]
  46. 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]
  47. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
     [Google Scholar]
  48. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  49. 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]
  50. Sun J, Lu F, Luo Y, Bie L, Xu L et al. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res 2023; 51:W397–W403 [View Article] [PubMed]
     [Google Scholar]
  51. Shi W, Sun Q, Fan G, Hideaki S, Moriya O et al. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 2021; 49:D694–D705 [View Article] [PubMed]
     [Google Scholar]
  52. 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]
  53. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  54. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  55. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  56. Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. J Appl Bacteriol 1988; 64:433–434 [View Article] [PubMed]
     [Google Scholar]
  57. Sedkova N, Tao L, Rouvière PE, Cheng Q. Diversity of carotenoid synthesis gene clusters from environmental Enterobacteriaceae strains. Appl Environ Microbiol 2005; 71:8141–8146 [View Article] [PubMed]
     [Google Scholar]
  58. Gandham S, Lodha T, Chintalapati S, Chintalapati VR. Rhodobacter alkalitolerans sp. nov., isolated from an alkaline brown pond. Arch Microbiol 2018; 200:1487–1492 [View Article] [PubMed]
     [Google Scholar]
  59. Han H, Wang T, Chen Z, Li Y, Yao L. Rhodobacter xinxiangensis sp. nov., isolated from pakchoi-cultivated soil contaminated with heavy metal and its potential to reduce Cd and Pb accumulation in pakchoi (Brassica campestris L.). Arch Microbiol 2020; 202:1741–1748 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006051
Loading
Cereibacter flavus sp. nov., a novel member of the family Rhodobacteraceae isolated from seawater of the South China Sea and reclassification of Rhodobacter alkalitolerans as Cereibacter alkalitolerans comb. nov.
Int J Syst Evol Microbiol 73, 006051 (2023); https://doi.org/10.1099/ijsem.0.006051
/content/journal/ijsem/10.1099/ijsem.0.006051
/content/journal/ijsem/10.1099/ijsem.0.006051
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