1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 12

sp. nov. and sp. nov., two novel species belonging to the family No Access

Abstract

Two Gram-stain-negative, chemoheterotrophic, aerobic bacteria, designated IC7 and JM2-8, were isolated from seawater of the Yellow Sea of China and rhizosphere soil of mangroves in Xiamen, Fujian, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that these two novel strains belonged to the family . Strain IC7 formed a coherent lineage within the genus , showing 98.05 % 16S rRNA gene sequence similarity to Y-2. Strain JM2-8 was most closely related to members of the genus , showing 96.51 and 96.73 % 16S rRNA gene sequence similarities to NH52F and KHS03, respectively. The two novel strains contained Q-10 as the major quinone, and phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol and phosphatidylcholine as the principal polar lipids. The main fatty acid of strain IC7 was C cyclo 8, while the fatty acid profile JM2-8 was dominated by summed feature 8 containing C 7 and/or C 6. The average nucleotide identity and digital DNA–DNA hybridization values between these two novel isolates and their closely related species were below the cut-off values of 95–96 and 70 %, respectively. The combined genotypic and phenotypic data show that strain IC7 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain IC7 (=MCCC 1A02763=KCTC 82844), and strain JM2-8 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain JM2-8 (=MCCC 1A17756=KCTC 82846).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Pseudodonghicola flavimaris sp. nov. , rhizosphere soil of mangroves , seawater , Sedimentitalea xiamensis sp. nov. and taxonomy
Funding
This study was supported by the:
  • National Infrastructure for Microbiological Resources (Award No. NMRC-2023-9)
    • Principle Award Recipient: ZongzeShao
  • Scientific Research Foundation of Third Institute of Oceanography, MNR (Award No. 2019021)
    • Principle Award Recipient: ZongzeShao
  • Scientific Research Foundation of Third Institute of Oceanography, MNR (Award No. 2019027)
    • Principle Award Recipient: LipingWang
  • National Natural Science Foundation of China (Award No.42030412)
    • Principle Award Recipient: ZongzeShao
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006192
2023-12-05
2024-05-08
Loading full text...

Full text loading...

References

  1. Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the “Roseobacter clade” into a novel family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12:683109 [View Article] [PubMed]
     [Google Scholar]
  2. Brinkhoff T, Giebel H-A, Simon M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 2008; 189:531–539 [View Article] [PubMed]
     [Google Scholar]
  3. Moran MA, Belas R, Schell MA, González JM, Sun F et al. Ecological genomics of marine Roseobacters. Appl Environ Microbiol 2007; 73:4559–4569 [View Article] [PubMed]
     [Google Scholar]
  4. Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol 2005; 71:5665–5677 [View Article] [PubMed]
     [Google Scholar]
  5. Yoon JH, Kang SJ, Oh TK. Donghicola eburneus gen. nov., sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 2007; 57:73–76 [View Article] [PubMed]
     [Google Scholar]
  6. Tan T, Wang B, Shao Z. Donghicola xiamenensis sp. nov., a marine bacterium isolated from seawater of the Taiwan Strait in China. Int J Syst Evol Microbiol 2009; 59:1143–1147 [View Article] [PubMed]
     [Google Scholar]
  7. Hameed A, Shahina M, Lin S-Y. Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007. Int J Syst Evol Microbiol 2014; 64:2729–2737 [View Article] [PubMed]
     [Google Scholar]
  8. Mostafa YS, Alrumman SA, Alamri SA, Otaif KA, Mostafa MS et al. Bioplastic (poly-3-hydroxybutyrate) production by the marine bacterium Pseudodonghicola xiamenensis through date syrup valorization and structural assessment of the biopolymer. Sci Rep 2020; 10:8815 [View Article] [PubMed]
     [Google Scholar]
  9. Sun F, Wang B, Liu X, Lai Q, Du Y et al. Leisingera nanhaiensis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2010; 60:275–280 [View Article] [PubMed]
     [Google Scholar]
  10. Breider S, Scheuner C, Schumann P. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front Microbiol 2014; 5:416
     [Google Scholar]
  11. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2014; 64:3603–3606 [View Article]
     [Google Scholar]
  12. Kim HS, Hyun D-W, Lee J-Y, Kim PS, Whon TW et al. Sedimentitalea todarodis sp. nov., isolated from the intestinal tract of a Japanese flying squid. Int J Syst Evol Microbiol 2016; 66:3293–3298 [View Article] [PubMed]
     [Google Scholar]
  13. Oren A, Garrity GM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 66, part 9, of the IJSEM. Int J Syst Evol Microbiol 2016; 66:4921–4923 [View Article] [PubMed]
     [Google Scholar]
  14. Skerman VBD. A Guide to the Identification of the Genera of Bacteria. 2nd edn Baltimore: Williams & Wilkins; 1967
     [Google Scholar]
  15. Dong X-Z, Cai M-Y. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
     [Google Scholar]
  16. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual, 2nd edn Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989
     [Google Scholar]
  17. Sasser M. Identification of bacteria by gas chromatography of cellular fatty Acids. In MIDI Technical Note vol 101 Newark, DE: MIDI; 1990
     [Google Scholar]
  18. 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 2010; 58:507–512 [View Article] [PubMed]
     [Google Scholar]
  19. 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 Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  20. Cui H-L, Gao X, Yang X. Halolamina pelagica gen. nov., sp. nov., a new member of the family Halobacteriaceae. Int J Syst Evol Microbiol 2011; 61:1617–1621 [View Article] [PubMed]
     [Google Scholar]
  21. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  22. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
     [Google Scholar]
  23. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  26. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 2021; 49:9077–9096 [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; 14:60 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. 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]
  33. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  34. Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K et al. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 2022; 10:33 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006192
Loading
Pseudodonghicola flavimaris sp. nov. and Sedimentitalea xiamensis sp. nov., two novel species belonging to the family Roseobacteraceae
Int J Syst Evol Microbiol 73, 006192 (2023); https://doi.org/10.1099/ijsem.0.006192
/content/journal/ijsem/10.1099/ijsem.0.006192
/content/journal/ijsem/10.1099/ijsem.0.006192
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