| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 UMR de Pathologie Végétale INRA INH UNIVERSITE, BP 57, 42 rue G. Morel, 49071 Beaucouzé, France
2 UMR 6078 CNRS and Université de Nice Sophia Antipolis, Laboratoire Jean Maetz, 06230 Villefranche sur Mer, France
Correspondence
Louis Gardan
gardan{at}angers.inra.fr
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
). The subspecies of E. carotovora were historically described as distinct species or subspecies on the basis of pathogenicity and host-plant origin. ‘Bacillus carotovorus’ was created for strains isolated from carrot and other vegetables (Jones, 1901). ‘Bacillus atrosepticus’ was created for the pathogen causing potato blackleg (van Hall, 1902) and was reduced to a subspecies of E. carotovora (Lelliott & Dickey, 1984). This classification, comprising two E. carotovora subspecies, was based on the exhaustive study of Dye (1969), who concluded that the many pathogens isolated from various hosts, such as arum, cabbage, carrot, celery, cotton, cucumber, cyclamen, delphinium, hyacinth, maize, potato, sugar cane and tobacco, represented a single species on the basis of their overall common biochemical characteristics. Three other pathogens were subsequently described as subspecies of E. carotovora: subsp. betavasculorum, responsible for vascular necrosis of sugar beet (Thomson et al., 1981), subsp. wasabiae, responsible for internal discoloration of rhizomes of wasabi (Goto & Matsumoto, 1987), and subsp. odorifera, responsible for slimy rot of witloof chicory (Gallois et al., 1992).
For the purposes of identification of E. carotovora subspecies, several studies have yielded reliable phenotypic criteria that differentiate two or more subspecies (Graham, 1972; Thomson et al., 1981; Verdonck et al., 1987; de Boer et al., 1987; Goto & Matsumoto, 1987; Alcorn et al., 1991; Gallois et al., 1992). Serological differentiation using the Ouchterlony double-diffusion method was effective for an E. carotovora subsp. atroseptica diagnosis, but not for E. carotovora subsp. carotovora, because of the large number of O serogroups (De Boer et al., 1979).
The natural relationships of Erwinia species have been studied by analysis of 16S rRNA sequences on the basis of evolutionary trees inferred only by neighbour-joining. Kwon et al. (1997) showed that Erwinia species formed four phyletic lines. Clade III comprised E. chrysanthemi and three subspecies of E. carotovora (carotovora, betavasculorum and wasabiae) clustered together. They noticed that the genus Erwinia was composed of taxa that displayed considerable heterogeneity and were intermixed with members of other genera belonging to the Enterobacteriaceae. Hauben et al. (1998) also divided the genus Erwinia into three phylogenetic groups. They united the members of clade II, including the five subspecies of Erwinia carotovora, Erwinia cacticida, Erwinia chrysanthemi and Erwinia cypripedii, in the genus Pectobacterium.
DNA-relatedness studies of soft-rot organisms were first initiated by Brenner et al. (1973), who showed that strains of Pectobacterium carotovorum and Pectobacterium chrysanthemi belonged to distinct DNA homology groups. Of all the soft-rot bacteria, only E. cacticida (=Pectobacterium cacticidum) (Alcorn et al., 1991) and E. carotovora subsp. odorifera (=P. carotovorum subsp. odoriferum) (Gallois et al., 1992) were described on the basis of DNA–DNA hybridization. Recently, using amplified fragment length polymorphism (AFLP) fingerprinting, Avrova et al. (2002) defined three clusters corresponding to P. carotovorum subspecies: cluster 1 (containing two subclusters, 1a for P. carotovorum subsp. carotovorum and 1b for P. carotovorum subsp. odoriferum), cluster 2 (containing two subclusters, 2a for P. carotovorum subsp. atrosepticum and 2b for P. carotovorum subsp. betavasculorum) and cluster 3 (for P. carotovorum subsp. wasabiae).
P. carotovorum is currently divided into five subspecies: atrosepticum, betavasculorum, carotovorum, odoriferum and wasabiae (Hauben et al., 1998). The purpose of this work was to clarify the taxonomy of the five subspecies by numerical taxonomy, DNA–DNA hybridization, phylogenetic analysis and serology. By using a genotypic approach, we have obtained evidence, presented here, that three subspecies of P. carotovorum should be elevated to species level.
|
METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
. Forty-two strains of the subspecies of P. carotovorum were selected from various host plants and locations all over the world. Ten strains of biovars and pathovars of P. chrysanthemi, including the type strain, and the type strain of P. cacticidum were included as reference strains.
|
. Native DNA of P. carotovorum subsp. atrosepticum CFBP 1526T, P. carotovorum subsp. betavasculorum CFBP 2122T, P. carotovorum subsp. carotovorum CFBP 2046T and P. carotovorum subsp. wasabiae CFBP 3304T was labelled in vitro by nick-translation with tritium-labelled nucleotides (Amersham). The S1 nuclease–trichloroacetic acid method was used for DNA–DNA hybridization (Crosa et al., 1973; Grimont et al., 1980). The thermal stability of reassociated DNA (Tm) was determined by using the method of Crosa et al. (1973).
Phenotypic tests.
Twenty-two conventional biochemical and physiological tests were performed for all 53 strains as indicated by Sutra et al. (2001). All tests were incubated at 28 °C except for growth at 36 and 39 °C in liquid King medium B.
In addition, to study the differentiation of strains by phenotypic tests, a selection of 38 strains, including 28 strains of the five subspecies of P. carotovorum and 10 reference strains of P. chrysanthemi and P. cacticidum, were tested for assimilation of 99 carbon sources, using Biotype 100 strips (bioMérieux). Results were recorded after 4 and 6 days incubation at 28 °C. A total of 121 characteristics were included in a numerical taxonomy analysis for the 38 strains. A distance matrix was calculated using the Jaccard coefficient and a cluster analysis was done using the UPGMA algorithm (Sneath & Sokal, 1973). Discriminatory tests were selected using the diagnostic ability coefficient deduced from the numerical analysis (Descamps & Véron, 1981).
Serology.
Antisera were produced in rabbits by injecting formalin-fixed whole bacterial cells. Precipitated antisera were tested by using the Ouchterlony double-diffusion method (Saunier et al., 1996) and gave a single, strong and diffuse band in agar gel, demonstrating a lipopolysaccharide reaction (De Boer et al., 1979).
Phylogenetic analysis.
The 16S rDNA sequences of P. carotovorum strains and related sequences were selected from a database of 40 000 previously aligned bacterial 16S rDNA sequences. Selection of sequences was based on previous phylogenetic analyses of the entire database and BLAST searches against the latest release of the European Bioinformatics Institute database. Phylogenetic trees were constructed using three different methods: neighbour joining (bioNJ), maximum likelihood (ML) and maximum parsimony (MP). For the NJ analysis, distance matrices were calculated using Kimura's two-parameter correction. bioNJ was applied according to Gascuel (1997), ML and MP were from the PHYLIP package (version 3.573c). For the final tree, 80 sequences of strains closely related to P. carotovorum were retained. Because of their close relationships, no evident homoplasy was detected, and almost the entire sequences corresponding to positions 52–1399 of sequence U80197 of P. carotovorum subsp. carotovorum were used for that analysis. Phylogenetic trees were drawn using NJPLOT (Perrière & Gouy, 1996). When several sequences were available for a type species, all sequences were included (they often differed by a few nucleotides).
|
RESULTS |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
. In all, four hybridization groups were delineated. DNA hybridization group 1 included the nine strains of P. carotovorum subsp. atrosepticum, which demonstrated 89–100 % relatedness to the type strain, CFBP 1526T (mean, 95·6 %; SD, 3·4 %). These strains constituted genomospecies 1. Strains of the other groups were 36–55 % related to CFBP 1526T.
|
DNA hybridization group 3 included the five strains of P. carotovorum subsp. wasabiae, which were 100 % related to the type strain, CFBP 3304T. These strains constituted genomospecies 3. Strains of the three other groups were 48–64 % related to CFBP 3304T, with 
Tm values ranging from 6·3 to 7·8 °C.
DNA hybridization group 4 included 14 of the 18 strains of P. carotovorum subsp. carotovorum, which were 62–100 % (76·8±8·5 %) related to the type strain, CFBP 2046T, with Tm values ranging from 3·1 to 4·9 °C, and two strains of P. carotovorum subsp. odoriferum (one of which, CFBP 3296, was misidentified, having been received as P. carotovorum subsp. betavasculorum) that were 70–75 % (72·5±3·5 %) related to strain CFBP 2046T, with a Tm value of 3·7 °C. These strains corresponded to genomospecies 4. The strains of the other unrelated groups were 42–62 % related to strain CFBP 2046T, with Tm values ranging from 7·5 to 9·0 °C.
The four remaining strains of P. carotovorum subsp. carotovorum did not fit with any other genomospecies described above, since they were 46–60 % related to P. carotovorum subsp. carotovorum CFBP 2046T (55±6·6 %), with Tm values ranging from 6·2 to 7·3 °C.
The type strain, CFBP 2048T, and seven reference strains of the biovars of P. chrysanthemi and the type strain of P. cacticidum were not closely related (7–30 %) to the type strains of the four P. carotovorum subspecies.
Phenotypic tests
The use of 22 biochemical and physiological tests confirmed the identity of the bacteria (Gallois et al., 1992) and the repartition in their respective genomic groups, with the exception of two strains: CFBP 5835, received as P. carotovorum subsp. atrosepticum, which was identified as P. carotovorum subsp. carotovorum; and CFBP 3296, received as P. carotovorum subsp. betavasculorum, which was reclassified as P. carotovorum subsp. odoriferum.
The dendrogram of phenotypic distances among the 38 strains is shown in Fig. 1. At a distance of 0·37, the strains were clustered in three groups: P. carotovorum, P. chrysanthemi and P. cacticidum. The criteria that distinguished these three groups were L(+)-arabinose, malonate, growth at 39 °C, indole, D(+)-malate, D(+)-trehalose and lecithinase. At a distance of 0·15, seven phenons and eight unclustered strains were observed.
|
Reference strains of the different biovars of P. chrysanthemi (two strains of bv. 4, CFBP 1451 and 3477T, are now named Brenneria paradisiaca) and P. cacticidum were clustered either in phenon 7 (CFBP 1200 and 2015) or as isolated strains.
The five subspecies of P. carotovorum constituted rather homogeneous phenotypic groups, except the aforementioned five strains of P. carotovorum subsp. betavasculorum. Phenotypic characteristics that differentiate the seven phenons and the reference strains of P. chrysanthemi were deduced from the diagnostic ability coefficient given by numerical taxonomy analysis (Table 3). Two to eight tests allowed phenons to be distinguished from one another.
|
). All strains of genomospecies 2 and phenons 5 and 6 (P. carotovorum subsp. betavasculorum) reacted with antiserum 413. The five strains of genomospecies 3 (P. carotovorum subsp. wasabiae) reacted with antiserum 411. The remaining strains of P. carotovorum subsp. odoriferum and P. carotovorum subsp. carotovorum showed wide serological diversity, since each antiserum only recognized one or two of the strains (Table 4). The three aforementioned subspecies of P. carotovorum constitute distinct but uniform serogroups. The correspondence with the serogroups of De Boer et al. (1979, 1987) is based upon control reactions of the serological references.
|
is a robust subset of a larger tree of 80 sequences. The topology shown is that of the bootstrap tree, as it has been demonstrated that this topology is often better than that of a simple NJ or MP analysis (Berry & Gascuel, 1996).
|
|
DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
By DNA–DNA hybridization, four genomospecies were delineated. DNA relatedness within genomospecies was 62–100 %, with Tm values ranging from 0 to 5·6 °C. Heterologous DNA relatedness among all genomospecies was 41–63 %, with Tm values of 6·2–9·0 °C. Thus, genomospecies 1–4 correspond to the phylogenetic definition of bacterial species of Wayne et al. (1987), taking account of both DNA–DNA relatedness of approximately 70 % or more and Tm values of 5 °C or less. Fourteen of 18 strains previously identified as P. carotovorum. subsp. carotovorum were grouped in genomospecies 4, including the type strain (CFBP 2046T). We consider these strains as representing genuine P. carotovorum, which we have better circumscribed by DNA–DNA hybridization. We demonstrated genomic heterogeneity among the strains of P. carotovorum subsp. carotovorum, since four strains identified as P. carotovorum subsp. carotovorum by classical phenotypic tests remained ungrouped by DNA–DNA hybridization. Further studies on additional strains would be necessary in order to establish the taxonomic position of these unclustered strains. The strains of P. carotovorum subsp. odoriferum were normally grouped among P. carotovorum, and its taxonomic status will remain unchanged (Gallois et al., 1992).
Reports on the genetic diversity of P. carotovorum have mainly concerned the subspecies atrosepticum and carotovorum, because of economic losses of potato crops due to soft rots. Several DNA probes were found to be specific for P. carotovorum subsp. atrosepticum (Darrasse et al., 1994a; Ward & De Boer, 1994) and PCR primers were proposed for the detection of the same subspecies on potatoes (De Boer & Ward, 1995; Frechon et al., 1998). P. carotovorum subsp. atrosepticum was also consistently considered rather uniform in terms of PCR-RFLP fingerprints using a pel gene (Darrasse et al., 1994b; Helias et al., 1998) and comparison of the recA gene (Waleron et al., 2001). By contrast, P. carotovorum subsp. carotovorum showed far greater diversity: almost 20 RFLP groups were described in the two gene PCR-RFLP studies. Using AFLP fingerprinting, Avrova et al. (2002) confirmed the subdivision of P. carotovorum into five subspecies, but they did not draw taxonomic conclusions from their results. These reports are consistent with our results, placing P. carotovorum subsp. atrosepticum, P. carotovorum subsp. betavasculorum and P. carotovorum subsp. wasabiae into individual species, and indicate extreme diversity within P. carotovorum subsp. carotovorum.
Our results allowed the strains clustered in genomospecies 1 (P. carotovorum subsp. atrosepticum), 2 (P. carotovorum subsp. betavasculorum) and 3 (P. carotovorum subsp. wasabiae) to be readily identified on the basis of biochemical tests and serological reactions. We did not find tests that distinguished P. carotovorum subsp. carotovorum strains of genomospecies 4 from the four genomically unclustered strains of this subspecies. P. carotovorum subsp. carotovorum strains demonstrated genomic heterogeneity that was not correlated to phenotypic properties. Similar discrepancies have already been observed for other groups of bacteria, e.g. among strains of Pseudomonas isolated from soil or the rhizosphere (Achouak et al., 2000; Bossis et al., 2000).
Among the 17 differentiating tests selected on the basis of numerical taxonomy by diagnostic ability coefficient, 12 were previously reported tests, confirmed in their ability to identify the subspecies of P. carotovorum (Dye, 1969; Graham, 1972; Thomson et al., 1981; Verdonck et al., 1987; De Boer et al., 1987; Goto & Matsumoto, 1987; Alcorn et al., 1991; Gallois et al., 1992). Of the five other tests, palatinose was already known but is too expensive to be used routinely. meso-Tartaric acid assimilation seemed specific for phenon 4 strains, D-(-)-tartaric acid for phenon 3 strains, absence of D-glucuronic acid assimilation for strains of phenons 3 and 5 and L-glutamic acid assimilation testing constantly negative for phenon 4 strains. These five tests represent new criteria useful for the identification of P. carotovorum subspecies.
The serological heterogeneity of P. carotovorum subsp. carotovorum was pointed out previously by De Boer et al. (1987), who described 37 O serogroups for this subspecies. In contrast, serology has long been considered useful for recognition of P. carotovorum subsp. atrosepticum (Graham, 1963; Vruggink & Maas-Geesteranus, 1975). Murray et al. (1990) demonstrated that three P. carotovorum subsp. betavasculorum strains isolated from sugar beet belonged to De Boer's serogroup XXXV. We confirmed this result with eight strains of the same subspecies isolated from three different host plants. Unless contraindicated by examination of a larger collection of strains, particularly of P. carotovorum subsp. wasabiae, we conclude that antisera can be useful for rapid identification of the three subspecies atrosepticum, betavasculorum and wasabiae.
The phylogenetic analysis revealed that not all subspecies of P. carotovorum were grouped in a single, robust clade identified by all methods. This was not a definitive conclusion, but a strong indication that the different subspecies of P. carotovorum could indeed belong to different species; the DNA–DNA hybridization data presented above confirmed this speculation. Detailed scrutiny of the results given by each phylogenetic method showed that all P. carotovorum subspecies formed a clade according to the NJ method (32 % bootstrap), while they formed two paraphyletic clusters according to MP and ML methods; these clusters corresponded to the two branches identified by NJ. Such a result is very often observed in phylogenetic analyses when the numbers of derived characters are rather small compared with the numbers of sequences analysed. Therefore, a phylogenetic analysis of 16S rDNA sequences alone is insufficient to determine whether all of these species can be placed in a single genus or not. DNA–DNA hybridization values around 50 % and strong phenotypic similarities are then decisive. A similar conclusion can be reached for P. cacticidum, which can be included (NJ, 34 % bootstrap) or excluded from the genus (paraphyletic: MP and ML). By contrast, P. chrysanthemi and P. cypripedii should be excluded from the genus (all methods) according to 16S rDNA phylogenetic analyses.
Using only NJ for inferring evolutionary trees, Hauben et al. (1998) grouped the five subspecies of E. carotovora in a unique genus, Pectobacterium. The results presented above using two other methods (ML and MP) showed that the subspecies of P. carotovorum formed two paraphyletic clusters. Phylogenetic analysis of 16S rDNA sequences alone is insufficient to split the P. carotovorum subspecies into two genera. Therefore, we propose that these five subspecies of P. carotovorum be maintained in the genus Pectobacterium first proposed by Waldee (1945). The taxonomic status of P. cacticidum, P. chrysanthemi and P. cypripedii should be revised later.
The taxonomy of soft-rot erwinias has evolved and has been debated over the last four decades. The taxonomic status of P. carotovorum was, successively, species (Burkholder, 1957), variety (Dye, 1969) and species again divided into three subspecies, carotovorum, atrosepticum and betavasculorum (Lelliott & Dickey, 1984). Except for P. carotovorum subsp. odoriferum, these taxonomic proposals were based on biochemical and physiological characteristics only.
Although the species and subspecies of Pectobacterium have usually been named according to the host from which each was first isolated, their expanded host range means that pathogenicity is not a determinative test for these taxa. For instance, P. carotovorum subsp. betavasculorum has been isolated from hosts other than sugar beet (sunflower, potato and artichoke) and P. carotovorum subsp. odoriferum has been isolated from witloof chicory and hyacinth (this study revealed the true identity of the hyacinth strain) as well as from celery, leek (Gallois et al., 1992) and sugar beet (R. Samson, unpublished).
Our results on DNA–DNA hybridization and phenotypic characteristics and serological reactions are in accordance with the bacterial definition of species of Wayne et al. (1987). We consider that the three subspecies of P. carotovorum subsp. atrosepticum, betavasculorum and wasabiae should be elevated to species level. We therefore propose the names Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. for these taxa.
P. carotovorum subsp. carotovorum and subsp. odoriferum share some characteristics with the three novel species described below that differentiate them from P. chrysanthemi and P. cacticidum: they do not possess lecithinase or arginine dihydrolase, they grow in the presence of 5 % NaCl, they assimilate D-mannitol, sucrose, trehalose, L(+)-arabinose, 
-L-rhamnose, D-saccharate, mucate and L-serine and they do not assimilate malonate, L(+)-tartrate, cis-aconitate or 4-aminobutyrate. There is no growth at 39°C and no indole production.
Description of Pectobacterium atrosepticum (van Hall 1902) Hauben et al. 1999 sp. nov.
Basonym: Pectobacterium carotovorum subsp. atrosepticum (van Hall 1902) Hauben et al. 1999.
Does not grow at 36 °C, produces reducing compounds from sucrose, produces acid from -methylglucoside, lactose, melibiose, cellobiose and raffinose, does not produce acid from inulin, sorbitol or D(+)-arabitol, assimilates palatinose, lactulose, L-alanine, 1-O-methyl 
-galactopyranoside and D-glucuronate and does not assimilate meso-tartrate, D(-)-tartrate or L-alanine. Causes blackleg of potato and soft rot of potato tubers during storage, and is casually isolated from tomato (Barzic et al., 1976). The G+C content of the DNA ranges from 51·3 to 53·1 mol% (Hauben et al., 1998). The type strain is CFBP 1526T (=LMG 2386T =NCPPB 549T =ICMP 1526T).
Description of Pectobacterium betavasculorum (Thomson et al. 1981) Hauben et al. 1999 sp. nov.
Basonym: Pectobacterium carotovorum subsp. betavasculorum (Thomson et al. 1981) Hauben et al. 1999.
Grows at 36 °C, produces reducing compounds from sucrose, does not possess gelatinase, produces acid from methyl -glucoside, inulin, lactose and raffinose, does not produce acid from sorbitol or D(+)-arabitol, assimilates palatinose and L-alanine and does not assimilate meso-tartrate, D(-)-tartrate or citrate. Causes root vascular necroses of sugar beet and is casually isolated from sunflower, artichoke and potato. The G+C content of the DNA ranges from 54·1 to 54·6 mol% (Hauben et al., 1998). The type strain is CFBP 2122T (=LMG 2464T =NCPPB 2795T =ICMP 4226T).
Emended description of Pectobacterium carotovorum (Jones 1901) Waldee 1945
The description is based on the results of our phenotypic study (Table 3
) and those of Hauben et al. (1998). Strains grow at 36 °C and possess gelatinase. Strains utilize lactose, -D(+)-melibiose, D(+)-cellobiose, raffinose and L-glutamate and do not utilize inulin or meso-tartrate. The type strain is CFBP 2046T (=LMG 2404T =NCPPB 312T =ICMP 5702T).
Emended description of Pectobacterium carotovorum subsp. carotovorum (Jones 1901) Hauben et al. 1999
Grows at 36 °C, does not produce reducing compounds from sucrose, possesses gelatinase, produces acid from lactose, melibiose, raffinose and cellobiose, does not produce acid from methyl -glucoside, inulin, sorbitol or D(+)-arabitol, assimilates 1-O-methyl -galactopyranoside, 1-O-methyl -galactopyranoside and L-glutamate and does not assimilate palatinose, meso-tartrate or L-alanine. Strains cause soft rot in a wide range of host plants. The G+C content of the DNA of the type strain is 52·1 mol% (Starr & Mandel, 1969). The type strain is CFBP 2046T (=LMG 2404T =NCPPB 312T =ICMP 5702T).
Emended description of Pectobacterium carotovorum subsp. odoriferum (Gallois et al. 1992) Hauben et al. 1999
The description is given by Gallois et al. (1992), and some additional tests are listed in Table 3. Produces volatile flavouring compounds. Strains cause soft rot of witloof chicory during forcing and decay of other plants such as leek, celery and hyacinth. The type strain is CFBP 1878T (=NCPPB 3839T =ICMP 11533T).
Description of Pectobacterium wasabiae (Goto & Matsumoto 1987) Hauben et al. 1999 sp. nov.
Basonym: Pectobacterium carotovorum subsp. wasabiae (Goto & Matsumoto 1987) Hauben et al. 1999.
Does not grow at 36 °C, does not produce reducing compounds from sucrose, possesses gelatinase, does not produce acid from methyl -glucoside, inulin, lactose, melibiose, raffinose, sorbitol or D(+)-arabitol, assimilates meso-tartrate and D-glucuronate and does not assimilate palatinose, 1-O-methyl -galactopyranoside, lactulose, L-alanine, 1-O-methyl -galactopyranoside or L-glutamate. Causes discoloured rhizomes and fibrous rot of Japanese horseradish (Eutrema wasabi). The G+C content of the DNA ranges from 51·4 to 51·7 mol% (Hauben et al., 1998). The type strain is CFBP 3304T (=LMG 8404T =NCPPB 3701T =ICMP 9121T).
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
Alcorn, S. M., Orum, T. V., Steigerwalt, A. G., Foster, J. L. M., Fogleman, J. C. & Brenner, D. J. (1991). Taxonomy and pathogenicity of Erwinia cacticida sp. nov. Int J Syst Bacteriol 41, 197–212.
Avrova, A. O., Hyman, L. H., Toth, R. L. & Toth, I. K. (2002). Application of amplified fragment length polymorphism fingerprinting for taxonomy and identification of the soft rot bacteria Erwinia carotovora and Erwinia chrysanthemi. Appl Environ Microbiol 68, 1499–1508.
Barzic, M. R., Samson, R. & Trigalet, A. (1976). Pourriture bactérienne de la tomate cultivée en serre. Ann Phytopathol 8, 4.
Berry, V. & Gascuel, O. (1996). Interpretation of bootstrap trees: threshold of clade selection and induced gain. Mol Biol Evol 13, 999–1011.
Bossis, E., Lemanceau, P., Latour, X. & Gardan, L. (2000). The taxonomy of Pseudomonas fluorescens and Pseudomonas putida: current status and need for revision. Agronomie 20, 51–63.
Brenner, D. J., Steigerwalt, A. G., Miklos, G. V. & Fanning, G. R. (1973). Deoxyribonucleic acid relatedness among erwiniae and other Enterobacteriaceae: the soft-rot organisms (genus Pectobacterium Waldee). Int J Syst Bacteriol 23, 205–216.
Brenner, D. J., McWhorter, A. C., Knutson, J. K. & Steigerwalt, A. G. (1982). Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J Clin Microbiol 15, 1133–1140.
Burkholder, W. H. (1957). Genus VI. Erwinia Winslow et al. 1917. In Bergey's Manual of Determinative Bacteriology, 7th edn, pp. 349–359. Edited by R. S. Breed, E. G. D. Murray & N. R. Smith. Baltimore: Williams & Wilkins.
Crosa, J. H., Brenner, D. J. & Falkow, S. (1973). Use of a single-strand-specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J Bacteriol 115, 904–911.
Darrasse, A., Priou, S., Kotoujansky, A. & Bertheau, Y. (1994). PCR and restriction fragment length polymorphism of a pel gene as a tool to identify Erwinia carotovora in relation to potato diseases. Appl Environ Microbiol 60, 1437–1443.
De Boer, S. H. & Ward, L. J. (1995). PCR detection of Erwinia carotovora subsp. atroseptica associated with potato tissue. Phytopathology 85, 854–858.[CrossRef]
De Boer, S. H., Copeman, R. J. & Vruggink, H. (1979). Serogroups of Erwinia carotovora potato strains determined with diffusible somatic antigens. Phytopathology 69, 316–319.[CrossRef]
De Boer, S. H., Verdonck, L., Vruggink, H., Harju, P., Bang, H. O. & De Ley, J. (1987). Serological and biochemical variation among potato strains of Erwinia carotovora subsp. atroseptica and their taxonomic relationship to other E. carotovora strains. J Appl Bacteriol 63, 487–495.
Descamps, P. & Véron, M. (1981). A method to select diagnostic criteria from Bayes' theorem and information theory. Ann Microbiol (Paris) 132B, 157–170 (in French).
Dye, D. W. (1969). A taxonomic study of the genus Erwinia. II. The "Carotovora" group. N Z J Sci 12, 81–97.
Frechon, D., Exbrayat, P., Helias, V. & 7 other authors (1998). Evaluation of a PCR kit for the detection of Erwinia carotovora subsp. atroseptica on potato tubers. Potato Res 41, 163–173.[CrossRef]
Gallois, A., Samson, R., Ageron, E. & Grimont, P. A. D. (1992). Erwinia carotovora subsp. odorifera subsp. nov., associated with odorous soft rot of chicory (Cichorium intybus L.). Int J Syst Bacteriol 42, 582–588.
Gascuel, O. (1997). bioNJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14, 685–695.[Abstract]
Goto, M. & Matsumoto, K. (1987). Erwinia carotovora subsp. wasabiae subsp. nov. isolated from diseased rhizomes and fibrous roots of Japanese horseradish (Eutrema wasabi Maxim.). Int J Syst Bacteriol 37, 130–135.
Graham, D. C. (1963). Serological diagnosis of potato blackleg and tuber soft rot. Plant Pathol 12, 142–144.[CrossRef]
Graham, D. C. (1972). Identification of soft rot coliform bacteria. In Proceedings of the 3rd International Conference on Plant Pathogenic Bacteria, pp. 273–279. Edited by H. P. Maas Geesteranus. Wageningen: Pudoc.
Grimont, P. A. D., Popoff, M. Y., Grimont, F., Coynault, C. & Lemelin, M. (1980). Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr Microbiol 4, 325–330.
Hauben, L., Moore, E. R. B., Vauterin, L., Steenackers, M., Mergaert, J., Verdonck, L. & Swings, J. (1998). Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol 21, 384–397.[Medline]
Helias, V., Le Roux, A. C., Bertheau, Y., Andrivon, D., Gauthier, J. P. & Jouan, B. (1998). Characterisation of Erwinia carotovora subspecies and detection of Erwinia carotovora subsp. atroseptica in potato plants, soil and water extracts with PCR-based methods. Eur J Plant Pathol 104, 685–699.[CrossRef]
Jones, L. R. (1901). A soft rot of carrot and other vegetables caused by Bacillus carotovorus. Vt Agric Exp Stn Annu Rep 13, 299–332.
Kwon, S.-W., Go, S.-J., Kang, H.-W., Ryu, J.-C. & Jo, J.-K. (1997). Phylogenetic analysis of Erwinia species based on 16S rRNA gene sequences. Int J Syst Bacteriol 47, 1061–1067.
Lelliott, R. A. & Dickey, R. S. (1984). Genus VII. Erwinia Winslow, Broadhurst, Buchanan, Krumwiede, Rogers and Smith 1920, 209AL. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 469–476. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
Murray, J., Fixter, L. M., Hamilton, I. D., Pérombelon, M. C. M., Quinn, C. E. & Graham, D. C. (1990). Serogroups of potato pathogenic Erwinia carotovora strains: identification by lipopolysaccharide electrophoretic patterns. J Appl Bacteriol 68, 231–240.
Perrière, G. & Gouy, M. (1996). WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364–369.[Medline]
Saunier, M., Malandrin, L. & Samson, R. (1996). Distribution of Pseudomonas syringae pathovars into twenty-three O serogroups. Appl Environ Microbiol 62, 2360–2374.[Abstract]
Sneath, P. H. A. & Sokal, R. R. (1973). Numerical Taxonomy: the Principles of Numerical Classification. San Francisco: W. H. Freeman.
Starr, M. P. & Mandel, M. (1969). DNA base composition and taxonomy of phytopathogenic and other enterobacteria. J Gen Microbiol 56, 113–123.
Sutra, L., Christen, R., Bollet, C., Simoneau, P. & Gardan, L. (2001). Samsonia erythrinae gen. nov., sp. nov., isolated from bark necrotic lesions of Erythrina sp., and discrimination of plant-pathogenic Enterobacteriaceae by phenotypic features. Int J Syst Evol Microbiol 51, 1291–1304.[Abstract]
Thomson, S. V., Hildebrand, D. C. & Schroth, M. N. (1981). Identification and nutritional differentiation of the Erwinia sugarbeet pathogen from members of Erwinia carotovora and Erwinia chrysanthemi. Phytopathology 71, 1037–1042.[CrossRef]
Van Hall, C. J. J. (1902). Bijdragen tot de Kennis der Bakteriele Plantenziekten. Inaugural dissertation, University of Amsterdam (in Dutch).
Verdonck, L., Mergaert, J., Rijckaert, C., Swings, J., Kersters, K. & De Ley, J. (1987). Genus Erwinia: numerical analysis of phenotypic features. Int J Syst Bacteriol 37, 4–18.
Vruggink, H. & Maas-Geesteranus, H. P. (1975). Serological recognition of Erwinia carotovora var. atroseptica, the causal organism of potato blackleg. Potato Res 18, 546–555.[CrossRef]
Waldee, E. L. (1945). Comparative studies of some peritrichous phytopathogenic bacteria. Iowa State J Sci 19, 435–484.
Waleron, M., Waleron, K. & Lojkowska, E. (2001). Application of recA PCR-RFLP for differentiation of Erwinia carotovora subsp. carotovora and Erwinia carotovora subsp. atroseptica. In Plant Pathogenic Bacteria, Proceedings of the 10th International Conference on Plant Pathogenic Bacteria, pp. 385–388. Charlottetown, PEI, Canada, 23–27 July 2000. Edited by S. H. De Boer. Dordrecht: Kluwer.
Ward, L. J. & De Boer, S. H. (1994). Specific detection of Erwinia carotovora subsp. atroseptica with a digoxigenin-labeled DNA probe. Phytopathology 84, 180–186.[CrossRef]
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
Young, J. M., Saddler, G. S., Takikawa, Y., De Boer, S. H., Vauterin, L., Gardan, L., Gvozdyak, R. I. & Stead, D. (1996). Names of plant pathogenic bacteria 1864–1995. Rev Plant Pathol 75, 721–863.
This article has been cited by other articles:
|
|
 |
|
  H.-S. Kim, B. Ma, N. T. Perna, and A. O. Charkowski Phylogeny and Virulence of Naturally Occurring Type III Secretion System-Deficient Pectobacterium Strains Appl. Envir. Microbiol., July 1, 2009; 75(13): 4539 - 4549. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Stoczko, J.-M. Frere, G. M. Rossolini, and J.-D. Docquier Functional Diversity among Metallo-{beta}-Lactamases: Characterization of the CAR-1 Enzyme of Erwinia carotovora Antimicrob. Agents Chemother., July 1, 2008; 52(7): 2473 - 2479. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Latour, S. Diallo, S. Chevalier, D. Morin, B. Smadja, J.-F. Burini, D. Haras, and N. Orange Thermoregulation of N-Acyl Homoserine Lactone-Based Quorum Sensing in the Soft Rot Bacterium Pectobacterium atrosepticum Appl. Envir. Microbiol., June 15, 2007; 73(12): 4078 - 4081. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Samson, J. B. Legendre, R. Christen, M. F.-L. Saux, W. Achouak, and L. Gardan Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int J Syst Evol Microbiol, July 1, 2005; 55(4): 1415 - 1427. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. S. Bell, M. Sebaihia, L. Pritchard, M. T. G. Holden, L. J. Hyman, M. C. Holeva, N. R. Thomson, S. D. Bentley, L. J. C. Churcher, K. Mungall, et al. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors PNAS, July 27, 2004; 101(30): 11105 - 11110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M.-N. Yap, J. D. Barak, and A. O. Charkowski Genomic Diversity of Erwinia carotovora subsp. carotovora and Its Correlation with Virulence Appl. Envir. Microbiol., May 1, 2004; 70(5): 3013 - 3023. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
