16S-23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous

Zavaleta, Amparo I.; Martínez‐Murcia, Antonio; Rodrı́guez-Valera, Francisco

doi:10.1099/13500872-142-8-2105

Cited by 69 publications

(76 citation statements)

References 52 publications

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“…The extensive degree of conservation of the order of loci presented here supports the previously suggested homogeneous nature of O. oeni (Morse et al, 1996 ;Zavaleta et al, 1996Zavaleta et al, , 1997. As suggested by St.…”

Section: Discussionsupporting

confidence: 77%

“…O. oeni has a restricted ecological niche (wine and related habitats), a peculiar acidophilic nature and viability at high ethanol levels (Garvie, 1986) and, although its dissimilarity to other leuconostocs is fully accepted, there is some controversy regarding both the evolution rate of the species (Martı! nez-Murcia et al, 1993 ;Morse et al, 1996) and its diversity (Dicks et al, 1990 ;Zavaleta et al, 1996). Based on metabolic\physiological criteria, splitting of O. oeni into two species was once proposed (Peynaud & Domercq, 1968), but the levels of DNA-DNA homology (73-110 % ; Dicks et al, 1990) are in agreement with the genomic concept of bacterial species.…”

Section: Introductionsupporting

confidence: 51%

“…The precise location and opposite transcription direction of the two rrn operons (Zavaleta et al, 1996) was determined by Southern hybridization with rrs and rrl homologous probes, taking advantage of the fact that the sequence of these genes is cleaved by FseI and I-CeuI, respectively. The origin and terminus of replication of the O. oeni chromosome remains unknown.…”

Section: Discussionmentioning

confidence: 99%

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The Oenococcus oeni genome: physical and genetic mapping of strain GM and comparison with the genome of a ‘divergent’ strain, PSU-1

2000

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The physical and genetic maps of the Oenococcus oeni strains GM and PSU-1, which represent two genomic divergent groups on the basis of macrorestriction and ribotyping analysis, were compared. To achieve this comparison, the GM maps were constructed and the PSU-1 maps, already established, were improved. All the recognition sites of the restriction enzymes AscI, I-CeuI, FseI, NotI and SfiI were located in both chromosomes and the position of 26 genetic markers, including two rrn operons and 14 new putative oenococcal genes, were allocated to the restriction fragments generated by the five enzymes. The comparative analysis of O. oeni GM and PSU-1 genomes revealed extensive conservation of loci order. As for the differences encountered in the locations of restriction sites, they seem to be a reflection of the differences in restriction fragment sizes, explainable by insertion/deletion events and point mutations. No evidence for major genomic rearrangements was found. The genomic conservation between the two strains is in agreement and suggests homogeneity within the species, which was not unexpected in view of the restricted ecological niche of O. oeni. Further comparisons of physical maps, both of O. oeni strains and related species, will certainly help to assess whether O. oeni is really an homogeneous species and physical mapping is suitable for taxonomic purposes, both at the supra-and intraspecific levels.

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Section: Discussionsupporting

confidence: 77%

Section: Introductionsupporting

confidence: 51%

Section: Discussionmentioning

confidence: 99%

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The Oenococcus oeni genome: physical and genetic mapping of strain GM and comparison with the genome of a ‘divergent’ strain, PSU-1

2000

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“…This contributes to a high mutation rate, an excess of recombination, and a rapid genetic evolution and is characterized by a lack of certain genes and highly divergent sequences (19). However, several studies based on the sequencing of the 16S, 23S, and 16S-to-23S intergenic spacer region (ISR) sequences suggested that the species O. oeni is genetically homogenous (14,20,21,26). This was reinforced by the levels of DNA-DNA homology and by the similarities of genetic maps observed for various strains (8,27).…”

mentioning

confidence: 99%

Evidence of Distinct Populations and Specific Subpopulations within the SpeciesOenococcus oeni

Bridier

Claisse

Coton³

et al. 2010

Appl Environ Microbiol

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Among the lactic acid bacteria (LAB) present in the oenological microbial ecosystem, Oenococcus oeni, an acidophilic lactic acid bacterium, is essential during winemaking. It outclasses all other bacterial species during malolactic fermentation (MLF). Oenological performances, such as malic acid degradation rate and sensorial impact, vary significantly according to the strain. The genetic diversity of the O. oeni species was evaluated using a multilocus sequence typing (MLST) scheme. Seven housekeeping genes were sequenced for a collection of 258 strains that had been isolated all over the world (particularly Burgundy, Champagne, and Aquitaine, France, Chile, South Africa, and Italy) and in several wine types (red wines, white wines, and champagne) and cider. The allelic diversity was high, with an average of 20.7 alleles per locus, many of them being rare alleles. The collection comprised 127 sequence types, suggesting an important genotypic diversity. The neighbor-joining phylogenetic tree constructed from the concatenated sequence of the seven housekeeping genes showed two major phylogenetic groups, named A and B. One unique strain isolated from cider composed a third group, rooting the phylogenetic tree. However, all other strains isolated from cider were in group B. Eight phylogenetic subgroups were statistically differentiated and could be delineated by the analysis of only 32 mutations instead of the 600 mutations observed in the concatenated sequence of the seven housekeeping genes. Interestingly, in group A, several phylogenetic subgroups were composed mostly of strains coming from a precise geographic origin. Three subgroups were identified, composed of strains from Chile, South Africa, and eastern France.

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“…Methods for typing O. oeni strains include the study of patterns of total soluble cell proteins (11,13), ribotyping (58), 16S and 23S rRNA spacer region analysis (26,64), randomly amplified polymorphic DNA (RAPD)-PCR (3,17,43,62), pulsed-field gel electrophoresis (PFGE) (22,24,27,51,65), differential display PCR (25), and amplified fragment length polymorphism (AFLP) analysis (6). Being easy to use, RAPD and multiplex RAPD assays have been employed to study O. oeni population dynamics in wine and to check which strains really are responsible for MLF (43,44,54,62).…”

mentioning

confidence: 99%

Development of a Sequence-Characterized Amplified Region Marker-Targeted Quantitative PCR Assay for Strain-Specific Detection ofOenococcus oeniduring Wine Malolactic Fermentation

Solieri

Giudici

2010

Appl Environ Microbiol

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Control over malolactic fermentation (MLF) is a difficult goal in winemaking and needs rapid methods to monitor Oenococcus oeni malolactic starters (MLS) in a stressful environment such as wine. In this study, we describe a novel quantitative PCR (QPCR) assay enabling the detection of an O. oeni strain during MLF without culturing. O. oeni strain LB221 was used as a model to develop a strain-specific sequence-characterized amplified region (SCAR) marker derived from a discriminatory OPA20-based randomly amplified polymorphic DNA (RAPD) band. The 5 and 3 flanking regions and the copy number of the SCAR marker were characterized using inverse PCR and Southern blotting, respectively. Primer pairs targeting the SCAR sequence enabled strain-specific detection without cross amplification of other O. oeni strains or wine species of lactic acid bacteria (LAB), acetic acid bacteria (AAB), and yeasts. The SCAR-QPCR assay was linear over a range of cell concentrations (7 log units) and detected as few as 2.2 ؋ 10 2 CFU per ml of red wine with good quantification effectiveness, as shown by the correlation of QPCR and plate counting results. Therefore, the cultivation-independent monitoring of a single O. oeni strain in wine based on a SCAR marker represents a rapid and effective strain-specific approach. This strategy can be adopted to develop easy and rapid detection techniques for monitoring the implantation of inoculated O. oeni MLS on the indigenous LAB population, reducing the risk of unsuccessful MLF.Malolactic fermentation (MLF) is a secondary fermentation which decreases the acidity, enhances the sensorial properties, and increases the microbiological stability of wine (23). Often, this step occurs naturally after completion of alcoholic fermentation. However, when MLF is carried out by indigenous lactic acid bacteria (LAB), the process can be unpredictable and start randomly, many months after the end of alcoholic fermentation, leading to wine spoilage and the production of biogenic amines. Moreover, when Lactobacillus and Pediococcus species are responsible for spontaneous MLF, the wine quality decreases due to the production of off-flavor (8, 23).To overcome these drawbacks, Oenococcus oeni malolactic starters (MLS) were used owing to their ability to successfully withstand multiple adverse wine conditions and to produce well-balanced wine (8, 34). Although progress has been made in selecting and preparing MLS, the induction of malolactic fermentation (MLF) by direct inoculation with selected O. oeni strains is not always guaranteed (19). Several factors contribute to the unpredictable nature of inoculated MLF. O. oeni is known to be a fastidious, slow-growing bacterium (23), auxotrophic for several amino acids, while other amino acids are needed for optimal growth (19,23). This species is highly heterogeneous, with a considerable intraspecific variation in resistance to wine conditions (19,63). Furthermore, loss of vitality was observed when strains isolated from wines and then cultivated in the laboratory were ...

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16S-23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous

Cited by 69 publications

References 52 publications

The Oenococcus oeni genome: physical and genetic mapping of strain GM and comparison with the genome of a ‘divergent’ strain, PSU-1

The Oenococcus oeni genome: physical and genetic mapping of strain GM and comparison with the genome of a ‘divergent’ strain, PSU-1

Evidence of Distinct Populations and Specific Subpopulations within the SpeciesOenococcus oeni

Development of a Sequence-Characterized Amplified Region Marker-Targeted Quantitative PCR Assay for Strain-Specific Detection ofOenococcus oeniduring Wine Malolactic Fermentation

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