1887

Abstract

A rod-shaped, spore-forming, thermophilic, chemoorganotrophic, aerobic or facultatively anaerobic bacterial strain, 1017, was isolated from production water sampled at the Dagang oilfield (PR China), and was characterized by using a polyphasic approach. The strain is capable of anaerobic glucose fermentation. Nitrate is reduced to nitrite. Optimal growth was observed at 60–65 °C, at pH between pH 7.0 and 7.5, and with 1–2 % (w/v) NaCl. The major cellular fatty acids were iso-C17 : 0, anteiso-C17 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. The predominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analysis based on the 16S rRNA, gyrB and parE gene sequences indicated that the isolate belonged to the genus Geobacillus and was most closely related to Geobacillus thermoleovorans KCTC 3570 (99.5, 96.1 and 97.9 % sequence similarity, respectively). Genome sequencing revealed a genome size of 3.57495 Mb and a DNA G+C content of 51.8 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain 1017 and G. thermoleovorans KCTC 3570 were 95.9 and 64.9 %, respectively. Results of phylogenomic metrics analysis of the genome and 1172 core genes of strain 1017 and its physiological and biochemical characteristics confirmed that strain 1017 represented a novel species of the genus Geobacillus , for which the name Geobacillus proteiniphilus sp. nov. is proposed. The type strain is 1017 (=VKM B-3132=KCTC 33986).

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2019-05-30
2019-08-19
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References

  1. Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA et al. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Int J Syst Evol Microbiol 2001;51: 433– 446 [CrossRef] [PubMed]
    [Google Scholar]
  2. Ash C, Farrow JAE, Wallbanks S, Collins MD. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 1991;13: 202– 206 [CrossRef]
    [Google Scholar]
  3. Zeigler DR. Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus. Int J Syst Evol Microbiol 2005;55: 1171– 1179 [CrossRef] [PubMed]
    [Google Scholar]
  4. Meintanis C, Chalkou KI, Kormas KA, Lymperopoulou DS, Katsifas EA et al. Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus. Lett Appl Microbiol 2008;46: 395– 401 [CrossRef] [PubMed]
    [Google Scholar]
  5. Weng FY, Chiou CS, Lin PH, Yang SS. Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus species. J Appl Microbiol 2009;107: 452– 464 [CrossRef] [PubMed]
    [Google Scholar]
  6. Kapralou S, Fabbretti A, Garulli C, Gualerzi CO, Pon CL et al. Characterization of Bacillus stearothermophilus infA and of its product IF1. Gene 2009;428: 31– 35 [CrossRef] [PubMed]
    [Google Scholar]
  7. Kuisiene N, Raugalas J, Chitavichius D. Phylogenetic, inter, and intraspecific sequence analysis of spo0A gene of the genus Geobacillus. Curr Microbiol 2009;58: 547– 553 [CrossRef] [PubMed]
    [Google Scholar]
  8. Tourova TP, Korshunova AV, Mikhailova EM, Sokolova DS, Poltaraus AB et al. Application of gyrB and parE sequence similarity analyses for differentiation of species within the genus Geobacillus. Microbiology 2010;79: 356– 369 [CrossRef]
    [Google Scholar]
  9. Dinsdale AE, Halket G, Coorevits A, van Landschoot A, Busse HJ et al. Emended descriptions of Geobacillus thermoleovorans and Geobacillus thermocatenulatus. Int J Syst Evol Microbiol 2011;61: 1802– 1810 [CrossRef] [PubMed]
    [Google Scholar]
  10. Zarilla KA, Perry JJ. Bacillus thermoleovorans, sp. nov., a species of obligately thermophilic hydrocarbon utilizing endospore-forming bacteria. Syst Appl Microbiol 1987;9: 258– 264 [CrossRef]
    [Google Scholar]
  11. Miñana-Galbis D, Pinzón DL, Lorén JG, Manresa A, Oliart-Ros RM. Reclassification of Geobacillus pallidus (Scholz et al. 1988) Banat et al. 2004 as Aeribacillus pallidus gen. nov., comb. nov. Int J Syst Evol Microbiol 2010;60: 1600– 1604 [CrossRef] [PubMed]
    [Google Scholar]
  12. Coorevits A, Dinsdale AE, Halket G, Lebbe L, De Vos P et al. Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G. stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly 'thermoglucosidasius'); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov. Int J Syst Evol Microbiol 2012;62: 1470– 1485 [CrossRef] [PubMed]
    [Google Scholar]
  13. Bryanskaya AV, Rozanov AS, Slynko NM, Shekhovtsov SV, Peltek SE. Geobacillus icigianus sp. nov., a thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2015;65: 864– 869 [CrossRef] [PubMed]
    [Google Scholar]
  14. Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P. Phylogenomic re-assessment of the thermophilic genus Geobacillus. Syst Appl Microbiol 2016;39:527–523. [Corrigendum. Syst Appl Microbiol 2018;41: 529– 530
    [Google Scholar]
  15. Nazina TN, Sokolova DSh, Grigoryan AA, Shestakova NM, Mikhailova EM et al. Geobacillus jurassicus sp. nov., a new thermophilic bacterium isolated from a high-temperature petroleum reservoir, and the validation of the Geobacillus species. Syst Appl Microbiol 2005;28: 43– 53 [CrossRef] [PubMed]
    [Google Scholar]
  16. Tourova TP, Sokolova DS, Semenova EM, Shumkova ES, Korshunova AV et al. Detection of n-alkane biodegradation genes alkB and ladA in thermophilic hydrocarbon-oxidizing bacteria of the genera Aeribacillus and Geobacillus. Microbiology 2016;85: 693– 707 [CrossRef]
    [Google Scholar]
  17. Nazina TN, Grigor'yan AA, Shestakova NM, Babich TL, Pavlova NK et al. MEOR study enhances production in a high-temperature reservoir. World Oil 2008; 97– 101
    [Google Scholar]
  18. Nazina TN, Shestakova NM, Semenova EM, Korshunova AV, Kostrukova NK et al. Diversity of metabolically active bacteria in water-flooded high-temperature heavy oil reservoir. Front Microbiol 2017;8: 707 [CrossRef] [PubMed]
    [Google Scholar]
  19. Pfennig N, Lippert KD. Uber das vitamin B12 – Bedurfnis phototropher Schweferelbakterien. Arch Microbiol 1966;55: 245– 256
    [Google Scholar]
  20. Pitt A, Schmidt J, Lang E, Whitman WB, Woyke T et al. Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica. Int J Syst Evol Microbiol 2018;68: 1975– 1985 [CrossRef] [PubMed]
    [Google Scholar]
  21. Kämpfer P. Limits and possibilities of total fatty acid analysis for classification and identification of Bacillus species. Syst Appl Microbiol 1994;17: 86– 98 [CrossRef]
    [Google Scholar]
  22. Manachini PL, Mora D, Nicastro G, Parini C, Stackebrandt E et al. Bacillus thermodenitrificans. sp. nov., nom. rev. Int J Syst Evol Microbiol 2000;50: 1331– 1337 [CrossRef] [PubMed]
    [Google Scholar]
  23. 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 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef]
    [Google Scholar]
  25. Kadnikov VV, Mardanov AV, Poltaraus AB, Sokolova DS, Semenova EM et al. Genome sequencing and annotation of Geobacillus sp. 1017, a hydrocarbon-oxidizing thermophilic bacterium isolated from a heavy oil reservoir (China). Genom Data 2017;11: 95– 97 https://doi.org/ [CrossRef] [PubMed]
    [Google Scholar]
  26. 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]
  27. 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– D214 [CrossRef] [PubMed]
    [Google Scholar]
  28. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016;428: 726– 731 [CrossRef] [PubMed]
    [Google Scholar]
  29. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008;9: 286– 298 [CrossRef] [PubMed]
    [Google Scholar]
  30. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33: 1870– 1874 [CrossRef] [PubMed]
    [Google Scholar]
  31. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010;26: 2460– 2461 [CrossRef] [PubMed]
    [Google Scholar]
  32. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016;6: 24373 [CrossRef] [PubMed]
    [Google Scholar]
  33. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002;30: 3059– 3066 [CrossRef] [PubMed]
    [Google Scholar]
  34. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015;32: 268– 274 [CrossRef] [PubMed]
    [Google Scholar]
  35. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017;14: 587– 589 [CrossRef] [PubMed]
    [Google Scholar]
  36. Minh BQ, Nguyen MA, von Haeseler A. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 2013;30: 1188– 1195 [CrossRef] [PubMed]
    [Google Scholar]
  37. Vandamme P, Peeters C. Time to revisit polyphasic taxonomy. Antonie van Leeuwenhoek 2014;106: 57– 65 [CrossRef] [PubMed]
    [Google Scholar]
  38. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005;102: 2567– 2572 [CrossRef] [PubMed]
    [Google Scholar]
  39. 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]
  40. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J Preprints 2016;4: e1900v1
    [Google Scholar]
  41. 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 [CrossRef] [PubMed]
    [Google Scholar]
  42. Burgess SA, Flint SH, Lindsay D, Cox MP, Biggs PJ. Insights into the Geobacillus stearothermophilus species based on phylogenomic principles. BMC Microbiol 2017;17: 140 [CrossRef] [PubMed]
    [Google Scholar]
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