1887

Abstract

A Gram-stain-negative, yellow-pigmented, non-motile, rod-shaped, catalase-positive, strictly aerobic marine bacterium, designated XHP0103, was isolated from seawater collected from the southern Yellow Sea, PR China (34° 45′ 53″ N 119° 25′ 30″ E). Strain XHP0103 grew optimally at 28 °C, pH 7.5 and in 1.0–3.0 % (w/v) sea salt. MK-6 was the major respiratory quinone. The major cellular fatty acids (>10%) were iso-C, iso-C G and iso-C 3-OH. The polar lipid profile contained phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. Results of 16S rRNA gene sequence analysis indicated that strain XHP0103 displayed highest sequence similarity to IP7 (94.1 %). However, the phylogenetic trees based on 16S rRNA gene sequences suggested that strain XHP0103 clustered with HST1-43 (93.4 % sequence similarity) and AH-MY3 (93.5 %). Genome sequencing revealed that strain XHP0103 comprised 3 134 388 bp with 2770 protein-coding genes, and the DNA G+C content was 35.5 %. The average nucleotide identity and digital DNA–DNA hybridization values between strain XHP0103 and HST1-43 were 73.6 and 17.3 %, respectively. Based on phylogenetic, phenotypic, genomic and chemotaxonomic evidence, strain XHP0103 represents a novel genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain is XHP0103 (=MCCC 1K06060=JCM 34682).

Funding
This study was supported by the:
  • Jiangsu Innovation Center of Marine Bioresources (Award 822153216)
    • Principle Award Recipient: AiHua Zhang
  • Innovation Project for Marine Science and Technology of Jiangsu Province (Award No. JSZRHYKJ202209)
    • Principle Award Recipient: Dao-FengZhang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006107
2023-11-01
2024-05-08
Loading full text...

Full text loading...

References

  1. Bernardet J-F, Nakagawa Y, Holmes B, Flavobacterium SOTTO, Prokaryotes C-LBOTICOSO. 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]
  2. Bernardet J-F, 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 JSyst Bacteriol 1996; 46:128–148 [View Article]
    [Google Scholar]
  3. Garrity GM, Holt JG. The road map to the manual. In Bergey’s Manual of Systematic Bacteriology New York, NY: Springer; 2001 pp 119–166 [View Article]
    [Google Scholar]
  4. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:10 [View Article] [PubMed]
    [Google Scholar]
  5. Jooste PJ. The Taxonomy and Significance of Flavobacterium-Cytophaga Strains from Dairy Sources University of the Orange Free State; 1985
    [Google Scholar]
  6. Reichenbach H. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1992; 42:327–329 [View Article]
    [Google Scholar]
  7. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  8. Xu X, Zhang S, Sun X, Xu X, Zhang J. Description of Abyssalbus ytuae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the sediment of the Mariana Trench. Int J Syst Evol Microbiol 2022; 72:005459 [View Article] [PubMed]
    [Google Scholar]
  9. Ren W-T, Meng F-X, Guo L-L, Sun L, Xu X-W et al. Luteirhabdus pelagi gen. nov., sp. nov., a novel member of the family Flavobacteriaceae, isolated from the West Pacific Ocean. Arch Microbiol 2021; 203:6021–6031 [View Article] [PubMed]
    [Google Scholar]
  10. Huang Z, Guo Y, Xiao Q, Liu X, Lai Q. Aegicerativicinus sediminis gen. nov., sp. nov., a novel carotenoid-producing marine bacterium in the family Flavobacteriaceae. Antonie van Leeuwenhoek 2021; 114:1551–1563 [View Article] [PubMed]
    [Google Scholar]
  11. Bowman JP, Nichols DS. Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats. Int J Syst Evol Microbiol 2002; 52:1533–1541 [View Article] [PubMed]
    [Google Scholar]
  12. Nedashkovskaya O, Otstavnykh N, Zhukova N, Guzev K, Chausova V et al. Zobellia barbeyronii sp. nov., a new member of the family Flavobacteriaceae, isolated from seaweed, and emended description of the species Z. amurskyensis, Z. laminariae, Z. russellii and Z. uliginosa. Diversity 2021; 13:520 [View Article]
    [Google Scholar]
  13. Kirchman DL. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 2002; 39:91–100 [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. Alain K, Intertaglia L, Catala P, Lebaron P. Eudoraea adriatica gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2008; 58:2275–2281 [View Article] [PubMed]
    [Google Scholar]
  16. Wang Q, Liu F, Zhang D-C. Pelagihabitans pacificus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount. Int J Syst Evol Microbiol 2020; 70:4569–4575 [View Article] [PubMed]
    [Google Scholar]
  17. Kim I, Kim J, Chhetri G, Seo T. Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. J Microbiol 2019; 57:1079–1085 [View Article] [PubMed]
    [Google Scholar]
  18. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. Kumar S, Stecher G, Li M, Knyaz C, Tamura K et al. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
    [Google Scholar]
  23. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article]
    [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. 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]
  26. 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]
  27. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013; 20:714–737 [View Article] [PubMed]
    [Google Scholar]
  28. Okonechnikov K, Golosova O, Fursov M, Team U. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012; 28:1166–1167 [View Article] [PubMed]
    [Google Scholar]
  29. Yoon S-H, Ha S-M, 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] [PubMed]
    [Google Scholar]
  30. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–14 [View Article]
    [Google Scholar]
  31. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  32. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
    [Google Scholar]
  33. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  34. Zhang D-F, Cui X-W, Zhao Z, Zhang A-H, Huang J-K et al. Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie van Leeuwenhoek 2020; 113:1523–1530 [View Article] [PubMed]
    [Google Scholar]
  35. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 2004; 5:1–19
    [Google Scholar]
  36. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
    [Google Scholar]
  37. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article] [PubMed]
    [Google Scholar]
  38. Lee SD. Tamlana crocina gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae, isolated from beach sediment in Korea. Int J Syst Evol Microbiol 2007; 57:764–769 [View Article]
    [Google Scholar]
  39. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article]
    [Google Scholar]
  40. Wang H, Yang A, Zhang G, Ma B, Meng F et al. Enhancement of carotenoid and bacteriochlorophyll by high salinity stress in photosynthetic bacteria. Int Biodeterior Biodegr 2017; 121:91–96 [View Article]
    [Google Scholar]
  41. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101 Newark, DE: MIDI inc; 1990
    [Google Scholar]
  42. Athayle M, Schaal A, Parlett J. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233241Saitou [View Article]
    [Google Scholar]
  43. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  44. 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]
  45. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
    [Google Scholar]
  46. Li M, Hou L-Z, Xu X-H, Wang X-X, Zheng M-C et al. Phylogenomic analyses of a clade within the family Flavobacteriaceae suggest taxonomic reassignments of species of the genera Algibacter, Hyunsoonleella, Jejuia, and Flavivirga, and the proposal of Pseudalgibacter gen. nov. and Pseudalgibacter alginicilyticus comb. nov. Curr Microbiol 2021; 78:3277–3284 [View Article] [PubMed]
    [Google Scholar]
  47. Choi J, Lee D, Jang JH, Cha S, Seo T. Aestuariibaculum marinum sp. nov., a marine bacterium isolated from seawater in South Korea. J Microbiol 2018; 56:614–618 [View Article] [PubMed]
    [Google Scholar]
  48. Kwon KK, Lee H-S, Jung H-B, Kang J-H, Kim S-J. Yeosuana aromativorans gen. nov., sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae, isolated from estuarine sediment of the South Sea, Korea. Int J Syst Evol Microbiol 2006; 56:727–732 [View Article]
    [Google Scholar]
  49. Hameed A, Shahina M, Lin S-Y, Sridhar KR, Young L-S et al. Siansivirga zeaxanthinifaciens gen. nov., sp. nov., a novel zeaxanthin-producing member of the family Flavobacteriaceae isolated from coastal seawater of Taiwan. FEMS Microbiol Lett 2012; 333:37–45 [View Article] [PubMed]
    [Google Scholar]
  50. Nedashkovskaya OI, Kim SB, Kwak J, Mikhailov VV, Bae KS. Mariniflexile gromovii gen. nov., sp. nov., a gliding bacterium isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 2006; 56:1635–1638 [View Article] [PubMed]
    [Google Scholar]
  51. Park S, Park J-M, Kang C-H, Yoon J-H. Aestuariivivens insulae gen. nov., sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2015; 65:1883–1888 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006107
Loading
/content/journal/ijsem/10.1099/ijsem.0.006107
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