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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 11

sp. nov., isolated from the sediment on the surface of plastics and proposal of a novel genus gen. nov. based on the genome-based phylogeny of the family No Access

Abstract

A Gram-stain-negative, rod-shaped and orange-pigmented bacterial strain designated 10MBP4-2-1 was isolated from the sediment on the surface of a plastic straw collected from oyster-farming areas in Quanzhou Bay, PR China. Catalase activity and oxidase activity were positive. Flexirubin-type pigment was absent. The 16S rRNA gene of strain 10MBP4-2-1 showed highest sequence similarity to YM8-076 of 98.3 %. Phylogenetic analysis based on 16S rRNA gene sequences and 120 conserved concatenated proteins indicated that strain 10MBP4-2-1 was affiliated to the genus and formed a monophyletic clade with YM8-076. The digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between strain 10MBP4-2-1 and YM8-076 were estimated to be 17.7, 70.4 and 70.3 %, respectively. The respiratory quinone was menaquinone 7. The major fatty acid composition was iso-C, iso-C 3-OH and summed feature 3 (C 7 and/or C 6). The draft genome size was 5 191 941 bp with DNA G+C content of 39.2 %. Based on phylogenetic analyses and whole genomic comparisons, strain 10MBP4-2-1 represents a novel species, for which the name sp. nov. is proposed. The type strain is 10MBP4-2-1 (=MCCC 1K07073=KCTC 92101). Additionally, phylogeny and whole genomic comparison of the family placed and the remaining (currently comprising 11 species) in two clearly distinguishable clades recognized at the genus level. Thus, a novel genus named gen. nov. is proposed to accommodate the 11 species. Our study provides a taxonomic framework for the family based on genomic data.

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  • Accepted:
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Keyword(s): Lewinella , Neolewinella , phylogeny , polyphasic taxonomy and Portibacter
Funding
This study was supported by the:
  • Key Laboratory of Marine Biological Genetic Resources (Award HY202101)
    • Principle Award Recipient: QiliangLai
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100900)
    • Principle Award Recipient: QiliangLai
  • Fujian Provincial Department of Science and Technology (Award 2020N0032)
    • Principle Award Recipient: QiufangZhang
© 2022 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.005561
2022-11-02
2024-04-19
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References

  1. Yoon J, Matsuo Y, Kasai H, Yokota A. Portibacter lacus gen. nov., sp.nov., a new member of the family Saprospiraceae isolated from a saline lake. J Gen Appl Microbiol 2012; 58:191–197 [View Article] [PubMed]
     [Google Scholar]
  2. Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M et al. Genome-based taxonomic classification of Bacteroidetes. Front Microbiol 2016; 7:2003 [View Article] [PubMed]
     [Google Scholar]
  3. Bowman JP, Bernardet JF, Frandsen Lau E. International committee on systematics of prokaryotes: subcommittee on the taxonomy of aerobic Bacteroidetes (formerly Flavobacterium and Cytophaga-like bacteria). Int J Syst Evol Microbiol 2020; 70:6017–6020 [View Article] [PubMed]
     [Google Scholar]
  4. 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]
  5. Oren A, Garrity G. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2020; 70:4061–4090 [View Article] [PubMed]
     [Google Scholar]
  6. DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci U S A 1992; 89:5685–5689 [View Article] [PubMed]
     [Google Scholar]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  12. Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007; 23:127–128 [View Article] [PubMed]
     [Google Scholar]
  13. 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] [PubMed]
     [Google Scholar]
  14. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  15. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  16. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  17. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  18. 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]
  19. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019btz848 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Kim I, Chhetri G, Kim J, Kang M, Seo T. Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:6180–6187 [View Article] [PubMed]
     [Google Scholar]
  22. Park S, Won SM, Yoon JH. Lewinella litorea sp. nov., isolated from marine sand. Int J Syst Evol Microbiol 2020; 70:246–250 [View Article] [PubMed]
     [Google Scholar]
  23. Kang H, Kim H, Joung Y, Joh K. Lewinella maritima sp. nov., and Lewinella lacunae sp. nov., novel bacteria from marine environments. Int J Syst Evol Microbiol 2017; 67:3603–3609 [View Article]
     [Google Scholar]
  24. Sly LI, Taghavi M, Fegan M. Phylogenetic heterogeneity within the genus Herpetosiphon: transfer of the marine species Herpetosiphon cohaerens, Herpetosiphon nigricans and Herpetosiphon persicus to the genus Lewinella gen. nov. in the Flexibacter-Bacteroides-Cytophaga phylum. Int J Syst Bacteriol 1998; 48 Pt 3:731–737 [View Article] [PubMed]
     [Google Scholar]
  25. Khan ST, Fukunaga Y, Nakagawa Y, Harayama S. Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov. Int J Syst Evol Microbiol 2007; 57:2946–2951 [View Article] [PubMed]
     [Google Scholar]
  26. Lee SD. Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment. Int J Syst Evol Microbiol 2007; 57:2814–2818 [View Article] [PubMed]
     [Google Scholar]
  27. Oh HM, Lee K, Cho JC. Lewinella antarctica sp. nov., a marine bacterium isolated from Antarctic seawater. Int J Syst Evol Microbiol 2009; 59:65–68 [View Article] [PubMed]
     [Google Scholar]
  28. Sung HR, Lee JM, Kim M, Shin KS. Lewinella xylanilytica sp. nov., a member of the family Saprospiraceae isolated from coastal seawater. Int J Syst Evol Microbiol 2015; 65:3433–3438 [View Article] [PubMed]
     [Google Scholar]
  29. Jung YT, Lee JS, Yoon JH. Lewinella aquimaris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:3989–3994 [View Article] [PubMed]
     [Google Scholar]
  30. Chen Z, Lei X, Lai Q, Li Y, Zhang B et al. Phaeodactylibacter xiamenensis gen. nov., sp. nov., a member of the family Saprospiraceae isolated from the marine alga Phaeodactylum tricornutum. Int J Syst Evol Microbiol 2014; 64:3496–3502 [View Article] [PubMed]
     [Google Scholar]
  31. Lei X, Li Y, Wang G, Chen Y, Lai Q et al. Phaeodactylibacter luteus sp. nov., isolated from the oleaginous microalga Picochlorum sp. Int J Syst Evol Microbiol 2015; 65:2666–2670 [View Article] [PubMed]
     [Google Scholar]
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Portibacter marinus sp. nov., isolated from the sediment on the surface of plastics and proposal of a novel genus Neolewinella gen. nov. based on the genome-based phylogeny of the family Lewinellaceae
Int J Syst Evol Microbiol 72, 005561 (2022); https://doi.org/10.1099/ijsem.0.005561
/content/journal/ijsem/10.1099/ijsem.0.005561
/content/journal/ijsem/10.1099/ijsem.0.005561
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