Advertisement

Antonie van Leeuwenhoek

, Volume 106, Issue 6, pp 1259–1267 | Cite as

Oenococcus alcoholitolerans sp. nov., a lactic acid bacteria isolated from cachaça and ethanol fermentation processes

  • Fernanda Badotti
  • Ana Paula B. Moreira
  • Luciane A. Chimetto Tonon
  • Brígida T. Luckwu de Lucena
  • Fátima de Cássia O. Gomes
  • Ricardo Kruger
  • Cristiane C. Thompson
  • Marcos Antonio de MoraisJr.
  • Carlos A. Rosa
  • Fabiano L. Thompson
Original Paper

Abstract

Four strains of lactic acid bacteria isolated from cachaça and alcohol fermentation vats in Brazil were characterised in order to determine their taxonomic position. Phylogenetic analysis revealed that they belong to the genus Oenococcus and should be distinguished from their closest neighbours. The 16S rRNA gene sequence similarity against the type strains of the other two species of the genus was below 94.76 % (Oenococcus kitaharae) and 94.62 % (Oenococcus oeni). The phylogeny based on pheS gene sequences also confirmed the position of the new taxon. DNA–DNA hybridizations based on in silico genome-to-genome comparison, Average Amino Acid Identity, Average Nucleotide Identity and Karlin genomic signature confirmed the novelty of the taxon. Distinctive phenotypic characteristics are the ability to metabolise sucrose but not trehalose. The name Oenococcus alcoholitolerans sp. nov. is proposed for this taxon, with the type strain UFRJ-M7.2.18T ( = CBAS474T = LMG27599T). In addition, we have determined a draft genome sequence of the type strain.

Keywords

Oenococcus alcoholitolerans Cachaça Ethanol Genomic taxonomy 

Notes

Acknowledgments

Financial support came from Fundação de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG), Fundação de Amparo a Pesquisa do Estado de Pernambuco (FACEPE), Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).

Supplementary material

10482_2014_296_MOESM1_ESM.doc (48 kb)
Supplementary material 1 (DOC 48 kb)
10482_2014_296_MOESM2_ESM.doc (42 kb)
Supplementary material 2 (DOC 42 kb)
10482_2014_296_MOESM3_ESM.doc (70 kb)
Supplementary material 3 (DOC 71 kb)
10482_2014_296_MOESM4_ESM.pdf (302 kb)
Supplementary material 4 (PDF 303 kb)
10482_2014_296_MOESM5_ESM.pdf (430 kb)
Supplementary material 5 (PDF 431 kb)
10482_2014_296_MOESM6_ESM.pdf (185 kb)
Supplementary material 6 (PDF 186 kb)
10482_2014_296_MOESM7_ESM.pdf (257 kb)
Supplementary material 7 (PDF 257 kb)

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410PubMedCrossRefGoogle Scholar
  2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402PubMedCrossRefPubMedCentralGoogle Scholar
  3. Auch AF, Klenk H-P, Göker M (2010a) Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2(1):142–148. doi: 10.4056/sigs.541628 PubMedCrossRefPubMedCentralGoogle Scholar
  4. Auch AF, Klenk H-P, Göker M (2010b) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2(1):117–134. doi: 10.4056/sigs.531120 PubMedCrossRefPubMedCentralGoogle Scholar
  5. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9(1):75. doi: 10.1186/1471-2164-9-75 PubMedCrossRefPubMedCentralGoogle Scholar
  6. Badotti F, Gomes F, Rosa C (2012) Brazilian cachaça: fermentation and production. In: Hui YH, Evranuz EÖ, Hansen AS (eds) Handbook of plant-based fermented food and beverage technology, 2nd edn. CRC Press, Boca Raton, pp 639–648CrossRefGoogle Scholar
  7. Beckner M, Ivey ML, Phister TG (2011) Microbial contamination of fuel ethanol fermentations. Lett Appl Microbiol 53(4):387–394PubMedCrossRefGoogle Scholar
  8. Borneman AR, McCarthy JM, Chambers PJ, Bartowsky EJ (2012) Functional divergence in the genus Oenococcus as predicted by genome sequencing of the newly-described species, Oenococcus kitaharae. PLoS ONE 7(1):e29626PubMedCrossRefPubMedCentralGoogle Scholar
  9. Carvalho-Neto O, Rosa DD, Camargo LEA (2008) Identification of contaminant bacteria in cachaça yeast by 16S rDNA gene sequencing. Sci Agric 65:508–515CrossRefGoogle Scholar
  10. Chang IS, Kim BH, Shin PK, Lee WK (1995) Bacterial contamination and its effects on ethanol fermentation. J Microbiol Biotechnol 5(6):309–314Google Scholar
  11. Dicks LMT, Dellaglio F, Collins MD (1995) Proposal to reclassify Leuconostoc Oenos as Oenococcus Oeni [corrig] gen-nov, comb-nov. Int J Syst Evol Microbiol 45(2):395–397Google Scholar
  12. Endo A, Okada S (2006) Oenococcus kitaharae sp nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue. Int J Syst Evol Microbiol 56:2345–2348PubMedCrossRefGoogle Scholar
  13. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane-filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39(3):224–229CrossRefGoogle Scholar
  14. FAOSTAT (2013) http://www.faostat.fao.org/site/339/default.aspx. Accessed 15/Jul/2014
  15. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376PubMedCrossRefGoogle Scholar
  16. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791CrossRefGoogle Scholar
  17. Garvie EI (1967) Leuconostoc oenos sp. nov. J Gen Microbiol 48(3):431–438PubMedCrossRefGoogle Scholar
  18. Gomes FCO, Silva CLC, Vianna CR, Lacerda ICA, Borelli BM, Nunes AC, Franco GR, Mourao MM, Rosa CA (2010) Identification of lactic acid bacteria associated with traditional cachaca fermentations. Braz J Microbiol 41(2):486–492PubMedCrossRefPubMedCentralGoogle Scholar
  19. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57(Pt 1):81–91PubMedCrossRefGoogle Scholar
  20. Hallin PF, Binnewies TT, Ussery DW (2008) The genome BLASTatlas, Äîa GeneWiz extension for visualization of whole-genome homology. Mol BioSyst 4(5):363–371PubMedCrossRefGoogle Scholar
  21. Heist P (2009) Identifying, controlling the most common microbial contaminants. Ethanol Producer Magazine. http://www.ethanolproducer.com/articles/5464/ identifying-the-most-common-microbial-contaminants Accessed 15/Jul/2013
  22. Jukes T, Cantor C (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132CrossRefGoogle Scholar
  23. Karlin S, Mrázek J, Campbell AM. (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179(12):3899–913Google Scholar
  24. Karlin S. (1998) Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol 1(5):598–610Google Scholar
  25. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120PubMedCrossRefGoogle Scholar
  26. Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264PubMedCrossRefPubMedCentralGoogle Scholar
  27. Kunkee RE (1991) Some roles of malic-acid in the malolactic fermentation in wine-making. FEMS Microbiol Rev 88(1):55–72Google Scholar
  28. Labarre C, Guzzo J, Cavin J-F, Divies C (1996) Cloning and characterization of the genes encoding the malolactic enzyme and the malate permease of Leuconostoc oenos. Appl Environ Microbiol 62(4):1274–1282PubMedPubMedCentralGoogle Scholar
  29. Lane D (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175Google Scholar
  30. Lucena BTL, dos Santos BM, Moreira JLS, Moreira APB, Nunes AC, Azevedo V, Miyoshi A, Thompson FL, de Morais Junior MA (2010) Diversity of lactic acid bacteria of the bioethanol process. BMC Microbiol 10:298Google Scholar
  31. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380PubMedPubMedCentralGoogle Scholar
  32. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195(6):413–418. doi: 10.1007/s00203-013-0888-4 PubMedCrossRefGoogle Scholar
  33. Moreira JO, Mota R, Horta M, Teixeira S, Neumann E, Nicoli J, Nunes Å (2005) Identification to the species level of Lactobacillus isolated in probiotic prospecting studies of human, animal or food origin by 16S-23S rRNA restriction profiling. BMC Microbiol 5(1):15PubMedCrossRefPubMedCentralGoogle Scholar
  34. Narendranath NSB (2009) Bacterial contamination and control in ethanol production. In: WM I (ed) The alcohol textbook, vol 4. 5 edn. Nottingham University Press, Nottingham, pp 481–490Google Scholar
  35. Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K, Cleenwerck I, Vancanneyt M, Swings J (2007) Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 57(Pt 12):2777–2789PubMedCrossRefGoogle Scholar
  36. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New YorkGoogle Scholar
  37. Nielsen JC, Prahl C, LonvaudFunel A (1996) Malolactic fermentation in wine by direct inoculation with freeze-dried Leuconostoc oenos cultures. Am J Enol Vitic 47(1):42–48Google Scholar
  38. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302(1):205–217PubMedCrossRefGoogle Scholar
  39. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhou J, Zhang YZ (2014) A proposed genus boundary for the prokaryotes based on genomic insights. J bacteriol 196(12):2210–2215PubMedCrossRefGoogle Scholar
  40. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425PubMedGoogle Scholar
  41. Schwan RF, Mendonca AT, da Silva JJ, Rodrigues V, Wheals AE (2001) Microbiology and physiology of Cachaca (Aguardente) fermentations. Antonie Van Leeuwenhoek 79(1):89–96PubMedCrossRefGoogle Scholar
  42. Skinner KA, Leathers TD (2004) Bacterial contaminants of fuel ethanol production. J Ind Microbiol Biotechnol 31(9):401–408. doi: 10.1007/s10295-004-0159-0 PubMedCrossRefGoogle Scholar
  43. Stackebrandt E, Goebel B (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849Google Scholar
  44. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739PubMedCrossRefPubMedCentralGoogle Scholar
  45. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL (2013a) a Microbial genomic taxonomy. BMC Genom 14(1):913CrossRefGoogle Scholar
  46. Thompson CC, Silva GG, Vieira NM, Edwards R, Vicente ACP, Thompson FL (2013b) b Genomic Taxonomy of the Genus Prochlorococcus. Microb Ecol 66(4):752–762PubMedCrossRefGoogle Scholar
  47. Vandamme P, Pot B, Gillis M, De Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438PubMedPubMedCentralGoogle Scholar
  48. Versalovic J, Schneider M, de Bruijn FJ, Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5:25–40Google Scholar
  49. Waterhouse AM, Procter JB, Martin DM, Clamp Ml, Barton GJ (2009) Jalview version 2, a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191PubMedCrossRefPubMedCentralGoogle Scholar
  50. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Rosselló-Móra R (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12(9):635–645PubMedCrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Fernanda Badotti
    • 1
  • Ana Paula B. Moreira
    • 2
  • Luciane A. Chimetto Tonon
    • 2
  • Brígida T. Luckwu de Lucena
    • 3
  • Fátima de Cássia O. Gomes
    • 4
  • Ricardo Kruger
    • 5
  • Cristiane C. Thompson
    • 2
  • Marcos Antonio de MoraisJr.
    • 6
  • Carlos A. Rosa
    • 1
  • Fabiano L. Thompson
    • 7
  1. 1.Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB)Universidade Federal de Minas GeraisBelo HorizonteBrazil
  2. 2.Instituto de BiologiaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
  3. 3.Centro de Ciências Biológicas e Sociais AplicadasUniversidade Estadual da ParaíbaJoão PessoaBrazil
  4. 4.Departamento de QuímicaCentro Federal de Educação Tecnológica de Minas GeraisBelo HorizonteBrazil
  5. 5.Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de BiologiaUniversidade de BrasíliaBrasíliaBrazil
  6. 6.Departamento de GenéticaUniversidade Federal de PernambucoRecifeBrazil
  7. 7.Instituto de Biologia and Laboratório de Sistemas Avançados de Gestão da Produção - SAGE/ COPPEUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil

Personalised recommendations