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Abstract

A novel Gram-reaction-negative, aerobic, motile, rod-shaped, grey bacterium, strain P4.10X, was isolated from plastic debris sampled from shallow waters in the Mediterranean Sea (Valencia, Spain). P4.10X was catalase- and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA gene sequences revealed that P4.10X was closely related to DSM 19524 and E6 (98.25 and 98.03 % sequence similarity, respectively). The DNA G+C content of the genome sequence of P4.10X was 53.66 %. The genomic indexes average nucleotide identity by (ANIb) and digital DNA–DNA hybridization (dDDH) confirmed its classification as representing a novel species of the genus . The predominant fatty acids were summed feature 8 (Cω7/Cω6) and C ω 11-methyl. The results of this polyphasic study confirm that P4.10X represents a novel species of the genus , for which the name sp. nov. is proposed (type strain P4.10X=CECT 30306 = DSM 112386).

Funding
This study was supported by the:
  • Ministerio de Ciencia, Innovación y Universidades (Award FPU17/04184)
    • Principle Award Recipient: EstherMolina-Menor
  • Ministerio de Ciencia, Innovación y Universidades (Award FPU18/02578)
    • Principle Award Recipient: ÀngelaVidal-Verdú
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-01-17
2024-12-12
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References

  1. Hwang CY, Cho KD, Yih W, Cho BC. Maritalea myrionectae gen. nov., sp. nov., isolated from a culture of the marine ciliate Myrionecta rubra. Int J Syst Evol Microbiol 2009; 59(3):609–614 [View Article]
    [Google Scholar]
  2. 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]
  3. Xu HY, Chen LP, Fu SZ, Fan HX, Zhou YG et al. Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater. Int J Syst Evol Microbiol 2009; 59:2297–2301 [View Article]
    [Google Scholar]
  4. Fukui Y, Abe M, Kobayashi M, Ishihara K, Oikawa H et al. Maritalea porphyrae sp. nov., isolated from a red alga (Porphyra yezoensis), and transfer of Zhangella mobilis to Maritalea mobilis comb. nov. Int J Syst Evol Microbiol 2012; 62:43–48 [View Article]
    [Google Scholar]
  5. Vidal-Verdú À, Latorre-Pérez A, Molina-Menor E, Baixeras J, Peretó J et al. Living in a bottle: bacteria from sediment-associated Mediterranean waste and potential growth on polyethylene terephthalate. Microbiologyopen 2022; 11:e1259 [View Article]
    [Google Scholar]
  6. Bernardet JF, Nakagawa Y, Holmes B. 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]
    [Google Scholar]
  7. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark: DE: MIDI; 1990
    [Google Scholar]
  8. MIDI Sherlock Microbial Identification System Operating Manual, version 6.1 Newark, DE: MIDI Inc; 2008
    [Google Scholar]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  10. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1897; 4:406–425
    [Google Scholar]
  11. 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]
    [Google Scholar]
  12. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  13. Andrews S. Fastqc: a quality control tool for high throughput sequence data. Available online 2010 http://www.bioinformatics.babraham.ac.uk/projects/fastqc
    [Google Scholar]
  14. 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]
    [Google Scholar]
  15. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article]
    [Google Scholar]
  18. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
    [Google Scholar]
  22. Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O. PathogenFinder - distinguishing friend from foe using bacterial whole genome sequence data. PLoS ONE 2013; 8:e77302 [View Article]
    [Google Scholar]
  23. 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]
  24. Gaytán I, Sánchez-Reyes A, Burelo M, Vargas-Suárez M, Liachko I et al. Degradation of recalcitrant polyurethane and xenobiotic additives by a selected landfill microbial community and its biodegradative potential revealed by proximity ligation-based metagenomic analysis. Front Microbiol 2019; 10:2986 [View Article]
    [Google Scholar]
  25. Ndahebwa Muhonja C, Magoma G, Imbuga M, Makonde HM. Molecular characterization of Low-Density Polyethene (LDPE) degrading bacteria and fungi from Dandora Dumpsite, Nairobi, Kenya. Int J Microbiol 2018; 2018:4167845 [View Article]
    [Google Scholar]
  26. Billig S, Oeser T, Birkemeyer C, Zimmermann W. Hydrolysis of cyclic poly(ethylene terephthalate) trimers by a carboxylesterase from Thermobifida fusca KW3. Appl Microbiol Biotechnol 2010; 87:1753–1764 [View Article] [PubMed]
    [Google Scholar]
  27. Furukawa M, Kawakami N, Tomizawa A, Miyamoto K. Efficient degradation of poly(ethylene terephthalate) with Thermobifida fusca cutinase exhibiting improved catalytic activity generated using mutagenesis and additive-based approaches. Sci Rep 2019; 9:16038 [View Article]
    [Google Scholar]
  28. Yoshida S, Hiraga K, Takehana T, Taniguchi I, Yamaji H et al. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science 2016; 351:1196–1199 [View Article] [PubMed]
    [Google Scholar]
  29. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  30. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
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