1887

Abstract

Two novel Gram-stain-positive bacteria, designated as SCSIO 52909 and SCSIO 52915, were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 °C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3α (-Lys-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909 and of 4.42 Mbp with G+C content of 69.1 % in SCSIO 52915. The two novel strains encoded genes for metabolism that are absent in most other species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0 % pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized species, respectively. In the phylogenetic analysis, strains SCSIO 52909 and SCSIO 52915 were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus . Based on the data presented here, these two strains should be recognized as two new species in the genus , for which the names sp. nov., with the type strain SCSIO 52909 (=KCTC 49412=CGMCC 1.13853), and sp. nov., with the type strain SCSIO 52915 (=KCTC 49411=CGMCC 1.13852), are proposed.

Funding
This study was supported by the:
  • Xin-Peng Tian , Youth Innovation Promotion Association of the Chinese Academy of Sciences , (Award 2016307)
  • Xin-Peng Tian , National Natural Science Foundation of China , (Award 41576143)
  • Xin-Peng Tian , Strategic Priority Research Program of the Chinese Academy of Sciences , (Award XDA19060301)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004449
2020-09-17
2020-12-01
Loading full text...

Full text loading...

References

  1. Suzuki K-ichiro, Collins MD, Iljima E, Komagata K. Chemotaxonomic characterization of a radiotolerant bacterium, Arthrobacter radiotolerans : description of Rubrobacter radiotolerans gen. nov., comb. nov. FEMS Microbiol Lett 1988; 52:33–39 [CrossRef]
    [Google Scholar]
  2. Albuquerque L, Johnson MM, Schumann P, Rainey FA, da Costa MS. Description of two new thermophilic species of the genus Rubrobacter, Rubrobacter calidifluminis sp. nov. and Rubrobacter naiadicus sp. nov., and emended description of the genus Rubrobacter and the species Rubrobacter bracarensis. Syst Appl Microbiol 2014; 37:235–243 [CrossRef][PubMed]
    [Google Scholar]
  3. Saito T, Terato H, Yamamoto O. Pigments of Rubrobacter radiotolerans . Arch Microbiol 1994; 162:414–421 [CrossRef]
    [Google Scholar]
  4. Norman JS, King GM, Friesen ML. Rubrobacter spartanus sp. nov., a moderately thermophilic oligotrophic bacterium isolated from volcanic soil. Int J Syst Evol Microbiol 2017; 67:3597–3602 [CrossRef][PubMed]
    [Google Scholar]
  5. Chen M-Y, Wu S-H, Lin G-H, Lu C-P, Lin Y-T et al. Rubrobacter taiwanensis sp. nov., a novel thermophilic, radiation-resistant species isolated from hot springs. Int J Syst Evol Microbiol 2004; 54:1849–1855 [CrossRef][PubMed]
    [Google Scholar]
  6. Carreto L, Moore E, Nobre MF, Wait R, Riley PW et al. Rubrobacter xylanophilus sp. nov., a new thermophilic species isolated from a thermally polluted effluent. Int J Syst Bacteriol 1996; 46:460–465 [CrossRef]
    [Google Scholar]
  7. Kämpfer P, Glaeser SP, Busse H-J, Abdelmohsen UR, Hentschel U. Rubrobacter aplysinae sp. nov., isolated from the marine sponge Aplysina aerophoba . Int J Syst Evol Microbiol 2014; 64:705–709 [CrossRef][PubMed]
    [Google Scholar]
  8. Jurado V, Miller AZ, Alias-Villegas C, Laiz L, Saiz-Jimenez C. Rubrobacter bracarensis sp. nov., a novel member of the genus Rubrobacter isolated from a biodeteriorated monument. Syst Appl Microbiol 2012; 35:306–309 [CrossRef][PubMed]
    [Google Scholar]
  9. Chen R-W, Wang K-X, Wang F-Z, He Y-Q, Long L-J et al. Rubrobacter indicoceani sp. nov., a new marine actinobacterium isolated from Indian Ocean sediment. Int J Syst Evol Microbiol 2018; 68:3487–3493 [CrossRef][PubMed]
    [Google Scholar]
  10. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Microbiology Washington, DC USA: American Society for Microbiology; 1994 pp 611–654
    [Google Scholar]
  11. Xu X-W, Ren P-G, Liu S-J, Wu M, Zhou P-J. Natrinema altunense sp. nov., an extremely halophilic archaeon isolated from a salt lake in Altun Mountain in Xinjiang, China. Int J Syst Evol Microbiol 2005; 55:1311–1314 [CrossRef][PubMed]
    [Google Scholar]
  12. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 2007; 57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  13. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [CrossRef][PubMed]
    [Google Scholar]
  14. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [CrossRef][PubMed]
    [Google Scholar]
  15. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW, Arlington VA. (editors) Actinomycete Taxonomy Society for Industrial Microbiology; 1980 pp 227–291
    [Google Scholar]
  16. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Microbiol 1979; 47:87–95
    [Google Scholar]
  17. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [CrossRef]
    [Google Scholar]
  18. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
    [Google Scholar]
  19. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [CrossRef][PubMed]
    [Google Scholar]
  20. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [CrossRef][PubMed]
    [Google Scholar]
  21. 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 [CrossRef][PubMed]
    [Google Scholar]
  22. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [CrossRef][PubMed]
    [Google Scholar]
  23. Dhakal D, Pokhrel AR, Shrestha B, Sohng JK. Marine rare actinobacteria: isolation, characterization, and strategies for harnessing bioactive compounds. Front Microbiol 2017; 8:1106 [CrossRef][PubMed]
    [Google Scholar]
  24. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:1–10 [CrossRef]
    [Google Scholar]
  25. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [CrossRef][PubMed]
    [Google Scholar]
  26. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  27. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  28. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES science gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE New Orleans, LA: IEEE; 2010 pp 1–8
    [Google Scholar]
  29. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  30. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431:980–984 [CrossRef][PubMed]
    [Google Scholar]
  31. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. megaX: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [CrossRef][PubMed]
    [Google Scholar]
  32. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evol 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  33. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  34. 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 [CrossRef][PubMed]
    [Google Scholar]
  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  36. 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 [CrossRef][PubMed]
    [Google Scholar]
  37. 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 [CrossRef][PubMed]
    [Google Scholar]
  38. Schabereiter-Gurtner C, Piñar G, Vybiral D, Lubitz W, Rölleke S. Rubrobacter-related bacteria associated with rosy discolouration of masonry and lime wall paintings. Arch Microbiol 2001; 176:347–354 [CrossRef][PubMed]
    [Google Scholar]
  39. Tait AW, Gagen EJ, Wilson SA, Tomkins AG, Southam G. Microbial populations of stony meteorites: substrate controls on first colonizers. Front Microbiol 2017; 8:1227 [CrossRef][PubMed]
    [Google Scholar]
  40. Brown MV, Bowman JP. A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiol Ecol 2001; 35:267–275 [CrossRef][PubMed]
    [Google Scholar]
  41. Köchling T, Lara-Martín P, González-Mazo E, Amils R, Sanz JL. Microbial community composition of anoxic marine sediments in the Bay of Cadiz. Int Microbiol 2011; 14:143–154 [CrossRef][PubMed]
    [Google Scholar]
  42. Keshri J, Yousuf B, Mishra A, Jha B. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea. Microbiol Res 2015; 175:57–66 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004449
Loading
/content/journal/ijsem/10.1099/ijsem.0.004449
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