1887

Abstract

A Gram-stain-positive, aerobic bacterium, designated GW1C4-4, was isolated from the seawater sample from the tidal zone of Guanyinshan Coast, Xiamen, Fujian Province, PR China. The strain was reddish-orange, rod-shaped and non-motile. Cells of strain GW1C4-4 were oxidase-negative and catalase-positive. The strain could grow at 10–42 °C (optimum, 32–35 °C), pH 5–9 (optimum, pH 6) and with 0–10 % NaCl (w/v; optimum, 1 %). Phylogenetic analysis based on the 16S rRNA sequences indicated that strain GW1C4-4 belonged to the genus , having the highest similarity to HNM0687 (98.5 %), followed by DSM 43247 (98.4 %). The G+C DNA content was 66.5 mol %. Average nucleotide identity and digital DNA–DNA hybridization values between strain GW1C4-4 and HNM0687 were 85.8 and 30.0 %, respectively. The principal fatty acids of strain GW1C4-4 were C, C 10-methyl (TBSA) and summed feature 3 (C 7/C 6). MK-9 (H) was the sole respiratory quinone. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified lipid. Based on its phylogenetic, phenotypic, chemotaxonomic and genomic characteristics, it is proposed that strain GW1C4-4 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is GW1C4-4 (=MCCC 1A18727=KCTC 49729).

Funding
This study was supported by the:
  • the Scientific Research Foundation of Third Institute of Oceanography (Award 2020009)
    • Principle Award Recipient: ZongzeShao
  • the Scientific Research Foundation of Third Institute of Oceanography (Award 2019021)
    • Principle Award Recipient: ZongzeShao
  • Guangdong Pearl River Talents Program (Award 2017BT01Z134)
    • Principle Award Recipient: ZhiqiangYu
  • National Natural Science Foundation of China (Award 42030412)
    • Principle Award Recipient: ZongzeShao
  • National Natural Science Foundation of China (Award 91851203)
    • Principle Award Recipient: ZongzeShao
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2022-12-15
2024-05-09
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References

  1. Tsukamura M. Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 1971; 68:15–26 [View Article]
    [Google Scholar]
  2. Stackebrandt E, Smida J, Collins MD. Evidence of phylogenetic heterogeneity within the genus Rhodococcus: revival of the genus Gordona (Tsukamura). J Gen Appl Microbiol 1988; 34:341–348 [View Article]
    [Google Scholar]
  3. Klatte S, Rainey FA, Kroppenstedt RM. Transfer of Rhodococcus aichiensis tsukamura 1982 and Nocardia amarae Lechevalier and Lechevalier 1974 to the genus Gordona as Gordona aichiensis comb. nov. and Gordona amarae comb. nov. Int J Syst Bacteriol 1994; 44:769–773 [View Article]
    [Google Scholar]
  4. Kageyama A, Iida S, Yazawa K, Kudo T, Suzuki S-I et al. Gordonia araii sp nov. and Gordonia effusa sp. nov., isolated from patients in Japan. Int J Syst Evol Microbiol 2006; 56:1817–1821 [View Article]
    [Google Scholar]
  5. Kang YQ, Ming H, Gonoi T, Chen Y, Cao Y et al. Gordonia iterans sp. nov., isolated from a patient with pneumonia. Int J Syst Evol Microbiol 2014; 64:3520–3525 [View Article] [PubMed]
    [Google Scholar]
  6. Stackebrandt E, Smida J, Collins MD. Evidence of phylogenetic heterogeneity within the genus Rhodococcus: revival of the genus Gordona (Tsukamura). J Gen Appl Microbiol 1988; 34:341–348 [View Article]
    [Google Scholar]
  7. Cha JH, Cha CJ. Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment. Int J Syst Evol Microbiol 2013; 63:327–331 [View Article] [PubMed]
    [Google Scholar]
  8. Kummer C, Schumann P, Stackebrandt E. Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int J Syst Bacteriol 1999; 49 Pt 4:1513–1522 [View Article] [PubMed]
    [Google Scholar]
  9. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50 Pt 6:2031–2036 [View Article] [PubMed]
    [Google Scholar]
  10. Suriyachadkun C, Ngaemthao W, Pujchakarn T, Chunhametha S. Gordonia asplenii sp. nov., isolated from humic soil on bird’s nest fern (Asplenium nidus L. Int J Syst Evol Microbiol 2019; 71:004746
    [Google Scholar]
  11. Kim SB, Brown R, Oldfield C, Gilbert SC, Goodfellow M. Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete. Int J Syst Bacteriol 1999; 49 Pt 4:1845–1851 [View Article] [PubMed]
    [Google Scholar]
  12. Park S, Kang SJ, Kim W, Yoon JH. Gordonia hankookensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:3172–3175 [View Article] [PubMed]
    [Google Scholar]
  13. Kämpfer P, Young C-C, Chu J-N, Frischmann A, Busse H-J et al. Gordonia humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:65–70 [View Article]
    [Google Scholar]
  14. Kim YS, Roh SG, Kim SB. Gordonia insulae sp. nov., isolated from an island soil. Int J Syst Evol Microbiol 2020; 70:2079–2083 [View Article] [PubMed]
    [Google Scholar]
  15. Xie Y, Zhou S, Xu Y, Wu W, Xia W et al. Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan. Int J Syst Evol Microbiol 2020; 70:4537–4543 [View Article] [PubMed]
    [Google Scholar]
  16. Brandão PF, Maldonado LA, Ward AC, Bull AT, Goodfellow M. Gordonia namibiensis sp. nov., a novel nitrile metabolising actinomycete recovered from an African sand. Syst Appl Microbiol 2001; 24:510–515 [View Article] [PubMed]
    [Google Scholar]
  17. Sangkanu S, Suriyachadkun C, Phongpaichit S. Gordonia sediminis sp. nov., an actinomycete isolated from mangrove sediment. Int J Syst Evol Microbiol 2019; 69:1814–1820 [View Article] [PubMed]
    [Google Scholar]
  18. Luo H, Gu Q, Xie J, Hu C, Liu Z et al. Gordonia shandongensis sp. nov., isolated from soil in China. Int J Syst Evol Microbiol 2007; 57:605–608 [View Article] [PubMed]
    [Google Scholar]
  19. Maldonado LA, Stainsby FM, Ward AC, Goodfellow M. Gordonia sinesedis sp. nov., a novel soil isolate. Antonie van Leeuwenhoek 2003; 83:75–80 [View Article] [PubMed]
    [Google Scholar]
  20. Shen FT, Goodfellow M, Jones AL, Chen YP, Arun AB et al. Gordonia soli sp. nov., a novel actinomycete isolated from soil. Int J Syst Evol Microbiol 2006; 56:2597–2601 [View Article] [PubMed]
    [Google Scholar]
  21. Srinivasan S, Park G, Yang H, Hwang S, Bae Y et al. Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant. Int J Syst Evol Microbiol 2012; 62:2703–2709 [View Article] [PubMed]
    [Google Scholar]
  22. Drzyzga O, Navarro Llorens JM, Fernández de Las Heras L, García Fernández E, Perera J. Gordonia cholesterolivorans sp. nov., a cholesterol-degrading actinomycete isolated from sewage sludge. Int J Syst Evol Microbiol 2009; 59:1011–1015 [View Article] [PubMed]
    [Google Scholar]
  23. Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y et al. Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:3718–3723 [View Article]
    [Google Scholar]
  24. Soddell JA, Stainsby FM, Eales KL, Seviour RJ, Goodfellow M. Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam. Int J Syst Evol Microbiol 2006; 56:2265–2269 [View Article] [PubMed]
    [Google Scholar]
  25. Yassin AF, Shen FT, Hupfer H, Arun AB, Lai WA et al. Gordonia malaquae sp. nov., isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2007; 57:1065–1068 [View Article] [PubMed]
    [Google Scholar]
  26. Kämpfer P, Martin K, Dott W. Gordonia phosphorivorans sp. nov., isolated from a wastewater bioreactor with phosphorus removal. Int J Syst Evol Microbiol 2013; 63:230–235 [View Article] [PubMed]
    [Google Scholar]
  27. Jin D, Kong X, Jia M, Yu X, Wang X et al. Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2017; 67:5128–5133 [View Article] [PubMed]
    [Google Scholar]
  28. Kim KK, Lee CS, Kroppenstedt RM, Stackebrandt E, Lee ST. Gordonia sihwensis sp. nov., a novel nitrate-reducing bacterium isolated from a wastewater-treatment bioreactor. Int J Syst Evol Microbiol 2003; 53:1427–1433 [View Article] [PubMed]
    [Google Scholar]
  29. Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y et al. Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:3718–3723 [View Article]
    [Google Scholar]
  30. de Menezes CBA, Afonso RS, de Souza WR, Parma M, de Melo IS et al. Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp. Antonie van Leeuwenhoek 2016; 109:297–303 [View Article] [PubMed]
    [Google Scholar]
  31. Zhang G, Huang Y, Yang J, Lai X-H, Jin D et al. Gordonia jinghuaiqii sp nov. and Gordonia zhaorongruii sp. nov., isolated from Tibetan Plateau wildlife. Int J Syst Evol Microbiol 2021; 71:4897 [View Article]
    [Google Scholar]
  32. Arenskötter M, Bröker D, Steinbüchel A. Biology of the metabolically diverse genus Gordonia. Appl Environ Microbiol 2004; 70:3195–3204 [View Article] [PubMed]
    [Google Scholar]
  33. Shintani M, Sugiyama K, Sakurai T, Yamada K, Kimbara K. Biodegradation of A-fuel oil in soil samples with bacterial mixtures of Rhodococcus and Gordonia strains under low temperature conditions. J Biosci Bioeng 2019; 127:197–200 [View Article]
    [Google Scholar]
  34. Chatterjee S, Dutta TK. Metabolism of butyl benzyl phthalate by Gordonia sp. strain MTCC 4818. Biochem Biophys Res Commun 2003; 309:36–43 [View Article]
    [Google Scholar]
  35. Sowani H, Kulkarni M, Zinjarde S. Harnessing the catabolic versatility of Gordonia species for detoxifying pollutants. Biotechnol Adv 2019; 37:382–402 [View Article] [PubMed]
    [Google Scholar]
  36. Linos A, Berekaa MM, Steinbüchel A, Kim KK, Sproer C et al. Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete. Int J Syst Evol Microbiol 2002; 52:1133–1139 [View Article] [PubMed]
    [Google Scholar]
  37. Liu CL, Shao ZZ. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 2005; 55:1181–1186 [View Article] [PubMed]
    [Google Scholar]
  38. Park S-C, Won S. Evaluation of 16S rRNA databases for taxonomic assignments using mock community. Genomics Inform 2018; 16:e24 [View Article]
    [Google Scholar]
  39. 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]
    [Google Scholar]
  40. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  41. 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]
  42. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
    [Google Scholar]
  43. Yoon SH, Ha SM, Lim JM, Kwon SJ, 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]
  44. 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]
    [Google Scholar]
  45. 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]
    [Google Scholar]
  46. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article]
    [Google Scholar]
  47. Dong XZ, Cai MY. Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001 pp 370–398
    [Google Scholar]
  48. 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]
  49. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  50. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  51. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990
    [Google Scholar]
  52. Takeuchi M, Hatano K. Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere. Int J Syst Bacteriol 1998; 48 Pt 3:907–912 [View Article] [PubMed]
    [Google Scholar]
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