1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 7

sp. nov., isolated from the production water of a water-flooded oil reservoir in PR China Free

Abstract

A novel, moderately thermophilic, Gram-stain-negative bacterium, designated strain J18, was isolated from a water-flooded oil reservoir. Cells were aerobic, oxidase- and catalase-positive, with a polar flagellum. Growth occurred at 35–60 °C and at pH 6–8.5. The respiratory quinones were ubiquinone 8 and ubiquinone 9. The dominant cellular fatty acids were C, C cyclo, C cyclo 8 and summed feature 8 (C 7/C 6). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and an unidentified aminophospholipid. The strain showed the highest 16S rRNA gene sequence similarities to DSM 15129 (98.6 %), DSM 15512 (98.4 %) and DSM 27220 (98.1 %), respectively, and the similarity to other species was lower than 93 %. In the phylogenetic trees, it constituted a unique sub-cluster within the genus . The DNA G+C content of strain J18 was 64.44 mol%. As compared with the type strains, the genome-to-genome distances of strain J18 were 34.7–40 %. These results confirmed the separate species status of J18 with its close relatives. On the basis of physiological, chemotaxonomic and phylogenetic analyses along with the low levels of identity at the whole-genome level, it can be concluded that strain J18 represents a new species of the genus , for which the name sp. nov. is proposed. The type strain of is J18 (=CGMCC 1.16800=LMG 31400).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , genome , oil reservoir , polyphasic taxonomy and Tepidiphilus olei sp. nov.
Funding
This study was supported by the:
  • PetroChina Company Limited (Award LHYT-KTKFYJY-2019-JS-849)
    • Principle Award Recipient: Xiao-Tong Wang
  • National Natural Science Foundation of China (Award 180 41977198)
    • Principle Award Recipient: Lei Wang
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004297
2020-06-24
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4364.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004297&mimeType=html&fmt=ahah

References

  1. Manaia CM, Nogales B, Nunes OC. Tepidiphilus margaritifer gen. nov., sp. nov., isolated from a thermophilic aerobic digester. Int J Syst Evol Microbiol 2003; 53:1405–1410 [View Article][PubMed]
     [Google Scholar]
  2. Salinas MB, Fardeau M-L, Cayol J-L, Casalot L, Patel BKC et al. Petrobacter succinatimandens gen. nov., sp. nov., a moderately thermophilic, nitrate-reducing bacterium isolated from an Australian oil well. Int J Syst Evol Microbiol 2004; 54:645–649 [View Article][PubMed]
     [Google Scholar]
  3. Poddar A, Lepcha RT, Das SK. Taxonomic study of the genus Tepidiphilus: transfer of Petrobacter succinatimandens to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov., emended description of the genus Tepidiphilus and description of Tepidiphilus thermophilus sp. nov., isolated from a terrestrial hot spring. Int J Syst Evol Microbiol 2014; 64:228–235 [View Article][PubMed]
     [Google Scholar]
  4. Wang X, Li X, Yu L, Huang L, Xiu J et al. Characterizing the microbiome in petroleum reservoir flooded by different water sources. Sci Total Environ 2019; 653:872–885 [View Article][PubMed]
     [Google Scholar]
  5. Zhang F, She Y-H, Li H-M, Zhang X-T, Shu F-C et al. Impact of an Indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir. Appl Microbiol Biotechnol 2012; 95:811–821 [View Article]
     [Google Scholar]
  6. Wang X, Li X, Yu L, Li Y, Huang L et al. Distinctive microbial communities imply the main mechanism in a MEOR trial in high pour-point reservoir. J Petrol Sci Eng 2019; 175:97–107 [View Article]
     [Google Scholar]
  7. Ming H, Nie G-X, Jiang H-C, Yu T-T, Zhou E-M et al. Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 2012; 102:297–305 [View Article]
     [Google Scholar]
  8. Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  9. Leifson E. Atlas of Bacterial Flagellation. Atlas of Bacterial Flagellation London: Academic Press; 1960
     [Google Scholar]
  10. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article][PubMed]
     [Google Scholar]
  11. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria . J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  12. 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]
  13. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
     [Google Scholar]
  14. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  15. Collins MD, JONES D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  16. Liu Y-H, Guo J-W, Salam N, Li L, Zhang Y-G et al. Culturable endophytic bacteria associated with medicinal plant Ferula songorica: molecular phylogeny distribution and screening for industrially important traits. 3 Biotech 2016; 6:209
     [Google Scholar]
  17. 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 [View Article][PubMed]
     [Google Scholar]
  18. Imhoff JF, Pfennig N. Thioflavicoccus mobilis gen. nov., sp. nov., a novel purple sulfur bacterium with bacteriochlorophyll b. Int J Syst Evol Microbiol 2001; 51:105–110 [View Article][PubMed]
     [Google Scholar]
  19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  20. Chun J, Lee J-H, Jung Y, Kim M, Kim S et al. Eztaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Rzhetsky A, Nei M. Theoretical Foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article][PubMed]
     [Google Scholar]
  23. Felsenstein J. Phylogenies from restriction sites: a maximum-likelihood approach. Evolution 1992; 46:159–173 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  26. 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]
  27. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article][PubMed]
     [Google Scholar]
  28. Lowe TM, Eddy SR. 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]
  29. 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 [View Article][PubMed]
     [Google Scholar]
  30. 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]
  31. 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 [View Article][PubMed]
     [Google Scholar]
  32. 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]
  33. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
     [Google Scholar]
  34. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  35. Pikuta E, Cleland D, Tang J. Aerobic growth of Anoxybacillus pushchinoensis K1T: emended descriptions of A. pushchinoensis and the genus Anoxybacillus . Int J Syst Evol Microbiol 2003; 53:1561–1562 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004297
Loading
Tepidiphilus olei sp. nov., isolated from the production water of a water-flooded oil reservoir in PR China
Int J Syst Evol Microbiol 70, 4364 (2020); https://doi.org/10.1099/ijsem.0.004297
/content/journal/ijsem/10.1099/ijsem.0.004297
/content/journal/ijsem/10.1099/ijsem.0.004297
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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