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Applied and Environmental Microbiology, April 2009, p. 2079-2090, Vol. 75, No. 7
0099-2240/09/$08.00+0     doi:10.1128/AEM.02194-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Oenococcus oeni Genome Plasticity Is Associated with Fitness{triangledown} ,{dagger}

Elisabeth Bon,1,2,{ddagger} Arnaud Delaherche,1,3,{ddagger} Eric Bilhère,1,3 Antoine De Daruvar,1,4 Aline Lonvaud-Funel,1,3 and Claire Le Marrec1,3*

Université de Bordeaux, Bordeaux, France,1 Université Bordeaux 2-LaBRI (CNRS-Université Bordeaux 1), 351 Cours de la Libération, 33405 Talence Cedex, France,2 UMR INRA 1219-Institut des Sciences de la Vigne et du Vin (ISVV) (Université Victor Segalen Bordeaux 2-Université Bordeaux 1), 210 Chemin de Leysotte, 33882 Villenave d'Ornon Cedex, France,3 CBiB, Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France4

Received 22 September 2008/ Accepted 2 February 2009

Oenococcus oeni strains are well-known for their considerable phenotypic variations in terms of tolerance to harsh wine conditions and malolactic activity. Genomic subtractive hybridization (SH) between two isolates with differing enological potentials was used to elucidate the genetic bases of this intraspecies diversity and identify novel genes involved in adaptation to wine. SH revealed 182 tester-specific fragments corresponding to 126 open reading frames (ORFs). A large proportion of the chromosome-related ORFs resembled genes involved in carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis, and replication, recombination, and repair. Six regions of genomic plasticity were identified, and their analysis suggested that both limited recombination and insertion/deletion events contributed to the vast genomic diversity observed in O. oeni. The association of selected sequences with adaptation to wine was further assessed by screening a large collection of strains using PCR. No sequences were found to be specific to highly performing (HP) strains alone. However, there was a statistically significant positive association between HP strains and the presence of eight gene sequences located on regions 2, 4, and 5. Gene expression patterns were significantly modified in HP strains, following exposure to one or more of the common stresses in wines. Regions 2 and 5 showed no traces of mobile elements and had normal GC content. In contrast, region 4 had the typical hallmarks of horizontal transfer, suggesting that the strategy of acquiring genes from other bacteria enhances the fitness of O. oeni strains.

* Corresponding author. Mailing address: UMR INRA 1219 OEnologie, LMBA, UMR INRA 1219-Institut Supérieur de la Vigne et du Vin (ISVV) (Université Victor Segalen Bordeaux 2-Université Bordeaux 1), 210 Chemin de Leysotte, 33882 Villenave d'Ornon Cedex, France. Phone: 33 5 57 57 58 31. Fax: 33 5 57 57 58 13. E-mail: claire.le-henaff{at}u-bordeaux1.fr

{triangledown} Published ahead of print on 13 February 2009.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

{ddagger} E.B. and A.D. contributed equally to this work.

Applied and Environmental Microbiology, April 2009, p. 2079-2090, Vol. 75, No. 7
0099-2240/09/$08.00+0     doi:10.1128/AEM.02194-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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