1887

Abstract

A Gram-stain-positive, aerobic, non-sporulating, yellow-pigmented and rod or cocci-shaped bacterium, designated Arc0846-15, was isolated from the kelp . Strain Arc0846-15 was found to grow at 16–35 °C (optimum, 28 °C), at pH 6.0–9.5 (optimum, 7.0) and in the presence of 0–6 % (w/v) NaCl (optimum, 2 %). Cells were positive for catalase and negative for oxidase activity. Phylogenetic analyses, based on 16S rRNA gene sequence comparisons, revealed that the nearest phylogenetic neighbour strains of strain Arc0846-15 were 01 Gi-040 (96.2 %), K22-20 (96.1 %) and HKI 0124 (95.2 %). Based on phylogenomic analysis, the average nucleotide identity values between strain Arc0846-15 and the neighbour strains were 69.8, 69.7 and 69.8 %, respectively; the digital DNA–DNA hybridization values between strain Arc0846-15 and its three closest neighbour strains were 18.8, 19.1 and 19.3 %, respectively. The predominant menaquinone was MK-8 (H). The dominant cellular fatty acids were C 8, iso-C, iso-C and C. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipid, one unidentified aminolipid and four unidentified lipids. The DNA G+C content of strain Arc0846-15 was 61.6 mol% based on the whole genome sequence. Based on the phylogenetic and phenotypic characteristics, strain Arc0846-15 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed, with Arc0846-15 (=KCTC 49655=MCCC 1K06093) as the type strain.

Funding
This study was supported by the:
  • State Key Laboratory of Microbial Technology Open Projects Fund (Award M2020-03)
    • Principle Award Recipient: Wen-RuiCao
  • Fundamental Research Funds for Central Universities of the Central South University (Award 2019HW022)
    • Principle Award Recipient: Ying-JieLi
  • National Natural Science Foundation of China (Award 41976202)
    • Principle Award Recipient: Ming-YuJiang
  • Strategic Priority Research Program of the Chinese Academy of Sciences (Award XDB42000000)
    • Principle Award Recipient: NotApplicable
  • Open Fund of the Key Laboratory of Marine Geology and Environment, Chinese Academy of Sciences (Award MGE2020KG14)
    • Principle Award Recipient: Wen-RuiCao
  • Natural Science Foundation of Shandong Province (Award ZR2020MD088)
    • Principle Award Recipient: Wen-RuiCao
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005187
2022-01-19
2022-05-18
Loading full text...

Full text loading...

References

  1. Groth I, Schumann P, Weiss N, Schuetze B, Augsten K et al. Ornithinimicrobium humiphilum gen. nov., sp. nov., a novel soil actinomycete with L-ornithine in the peptidoglycan. Int J Syst Evol Microbiol 2001; 51:81–87 [View Article]
    [Google Scholar]
  2. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article] [PubMed]
    [Google Scholar]
  3. Fang X-M, Du H-J, Bai J-L, He W-N, Li J et al. Ornithinimicrobium cerasi sp. nov., isolated from the fruit of Cerasus pseudocerasus and emended description of the genus Ornithinimicrobium . Int J Syst Evol Microbiol 2020; 70:1691–1697 [View Article] [PubMed]
    [Google Scholar]
  4. Fang X-M, Yan D, Bai J-L, Su J, Liu H-Y et al. Ornithinimicrobium flavum sp. nov., isolated from the leaf of Paris polyphylla . Int J Syst Evol Microbiol 2017; 67:4541–4545 [View Article] [PubMed]
    [Google Scholar]
  5. Guo Q, Wang B, Zhou Z, Ke X, Zhang L et al. Ornithinimicrobium pratense sp. nov., isolated from meadow soil. Int J Syst Evol Microbiol 2020; 70:6450–6457 [View Article] [PubMed]
    [Google Scholar]
  6. Huo Y, Kang JP, Ahn JC, Yang DU, Yang DC. Ornithinimicrobium panacihumi sp. nov., antagonistic bacteria against root rot fungal pathogens, isolated from cultivated ginseng soil. Curr Microbiol 2019; 76:22–28 [View Article] [PubMed]
    [Google Scholar]
  7. Kämpfer P, Glaeser SP, Schäfer J, Lodders N, Martin K et al. Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds. Int J Syst Evol Microbiol 2013; 63:119–123 [View Article] [PubMed]
    [Google Scholar]
  8. Liu L-Z, Liu Y, Chen Z, Liu H-C, Zhou Y-G et al. Ornithinimicrobium tianjinense sp. nov., isolated from a recirculating aquaculture system. Int J Syst Evol Microbiol 2013; 63:4489–4494 [View Article] [PubMed]
    [Google Scholar]
  9. Liu XY, Wang BJ, Jiang CY, Liu SJ. Ornithinimicrobium pekingense sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2008; 58:116–119 [View Article] [PubMed]
    [Google Scholar]
  10. Mayilraj S, Saha P, Suresh K, Saini HS. Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas. Int J Syst Evol Microbiol 2006; 56:1657–1661 [View Article] [PubMed]
    [Google Scholar]
  11. Ramaprasad EVV, Sasikala C, Ramana CV. Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva . Int J Syst Evol Microbiol 2015; 65:4627–4631 [View Article]
    [Google Scholar]
  12. Zhang L-Y, Ming H, Meng X-L, Fang B-Z, Jiao J-Y et al. Ornithinimicrobium cavernae sp. nov., an actinobacterium isolated from a karst cave. Antonie van Leeuwenhoek 2019; 112:179–186 [View Article] [PubMed]
    [Google Scholar]
  13. Atlas RM. Handbook of Microbiological Media Boca Raton, FL: CRC Press; 1993
    [Google Scholar]
  14. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
  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. 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]
  21. Lowe TM. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Cao W-R, Lu D-C, Sun X-K, Sun Y-Y, Saren G et al. Seonamhaeicola maritimus sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2020; 70:902–908 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. 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]
  27. Fitch WM. On the problem of discovering the most parsimonious tree. The American Naturalist 1977; 111:223–257 [View Article]
    [Google Scholar]
  28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  31. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
    [Google Scholar]
  32. Smibert RM, Krieg NR. Phenotypic characteristics In. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Biology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  33. Jorgensen JH, Turnidge JD, Washington JA. Antibacterial susceptibility tests: dilution and disk diffusion methods In. In Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolken RH. eds Manual of Clinical Microbiology Washington, DC: American Society for Microbiology; 1999 pp 1526–1543
    [Google Scholar]
  34. 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]
  35. 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 Meth 1984; 2:233–241 [View Article]
    [Google Scholar]
  36. Kroppenstedt RM. Separation of Bacterial Menaquinones by HPLC Using Reverse Phase (RP18) and a Silver Loaded Ion Exchanger as Stationary Phases. J Liq Chromat 2006; 5:2359–2367 [View Article]
    [Google Scholar]
  37. Tindall B, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM. eds Methods for General and Molecular Microbiology, 3rd. edn Washington, DC: American Society for Microbiology; 2007 pp 330–393 [View Article]
    [Google Scholar]
  38. Schumann P. 5-Peptidoglycan sStructure. In Rainey F, Oren A. eds Methods in Microbiology Academic Press; 2011 pp 101–129
    [Google Scholar]
  39. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 vol 2001 Newark, Del: Microbial ID, Inc;
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005187
Loading
/content/journal/ijsem/10.1099/ijsem.0.005187
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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