Changing Concepts in the Taxonomy of Plant Pathogenic Bacteria

Young, J. M.; Takikawa, Yuichi; Gardan, and L; Stead, D. E.

doi:10.1146/annurev.py.30.090192.000435

Cited by 104 publications

(74 citation statements)

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“…Dickeya chrysanthemi (formerly Erwinia chrysanthemi) is the causal agent of tuber soft rot and blackleg-like symptoms in many potato growing areas of the world (Young et al 1992, Toth et al 2011, Tsror et al 2012). However, our study found D. dadantii subsp.…”

Section: Discussionmentioning

confidence: 99%

Pectinolytic bacteria associated with potato soft rot and blackleg in South Africa and Zimbabwe

et al. 2012

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Section: Discussionmentioning

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Pectinolytic bacteria associated with potato soft rot and blackleg in South Africa and Zimbabwe

et al. 2012

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Section: International Journal Of Systematic and Evolutionary Microbimentioning

confidence: 99%

“…by, 1997). One expectation of modern systematics has been that the increasing numbers of methods and sophisticated tools for analysis would form congruent circumscriptions of taxa ; that, in future, genera, species and, perhaps, higher taxa would be more precisely and clearly circumscribed and that methods would be available for allocation of isolates to those groups (Murray et al, 1990 ;Young et al, 1992 ; Goodfellow & O'Donnell, 1993 ;Vandamme et al, 1996 ;Goodfellow et al, 1997 J. M. Young taxa, with a trend towards subdivision of previously published genera. This is indicated by the fact that, by January 2001, an estimated 4518 species in 998 genera (4n5 species per genus) had been validly described (Euze!…”

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confidence: 99%

“…It is at the generic level and above that single-character tests are found to be inadequate when more extensive data are included. Multiple-character tests [also called polyphasic tests by Young et al (1992) and including chemotaxonomic tests], such as comparisons of cell wall composition, fatty acid and protein profiling, isoprenoid quinone and DNA composition and DNA and RNA sequences when considered as part of the bacterial phenotype, have the advantage that large components of a phenotype could be compared directly. Some multiple-character tests can also be analysed and interpreted by quantitative, numerical methods (Sneath, 1985 ;Kersters, 1985).…”

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“…There is no phenotypic basis for the differentiation of the plant-pathogenic genera Brenneria or Pectobacterium from Erwinia. Young et al (1992) noted the need for a comprehensive revision of the Enterobacteriaceae, which has not yet been accomplished.(v) In a revision of Rhizobium, the new genus Sinorhizobium was proposed for Sinorhizobium fredii and Sinorhizobium xinjiangense by Chen et al (1988) on the basis of nutritional and biochemical tests. The validity of the genus was questioned by Jarvis et al (1992) on the basis of partial 16S rDNA analysis and on the interpretation of numerical data.…”

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Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy.

Young¹

2001

International Journal of Systematic and Evolutionary Microbiology

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Following the publication of the Approved Lists, there has been a tendency to regard all subsequent revisions of classification as providing improved nomenclature, to be accepted without question. This takes no account of the fact that such revisions may be based on one of three alternative concepts, phenetic, phylogenetic or polyphasic classification, sometimes leading to different, valid, but incompatible nomenclature, or that some investigations are based only on subsets of relevant taxa and on limited data, leading to incomplete and sometimes confusing revisions of nomenclature. The polyphasic approach to classification has widespread support, although there appears to be a tendency to allow comparative sequence analyses of 16S rDNA to determine classification contrary to the indications of other data. In some cases, classification is based solely on 16S rDNA data. Examples are considered. Consideration is given to the criteria by which taxa are circumscribed, particularly at the level of genus and species. It is suggested that there is a need for reconciliation of the criteria by which taxa at these levels are circumscribed. Recent studies demonstrating the widespread occurrence of horizontal gene transfer suggest that there is a need for caution in monophyletic interpretations, especially when these are based on the analysis of single sequences. Keywords : phenetic, phylogenetic, polyphasic, bacterial systematics IntroductionAlthough Staley & Krieg (1984) wrote that ' bacterial classifications are devised for microbiologists, not for the entities being classified ', bacteriologists do not necessarily agree about the aims of classification. The several systems of bacterial classification that are in vogue at present are incompatible, sometimes leading to different classifications and to different schemes of bacterial nomenclature. Unless the principles underlying different classifications are understood, these different applications of names cause bewilderment. The thrust of this article is to show that no one system of classification is supreme, each offering a different perspective on evolutionary processes and serving different purposes in systematics. One problem that particularly besets discussions on bacterial taxonomy is that some terms derived elsewhere and often in the distant past are poorly defined or are used in different ways by different writers. For example, see the history of the usage of ' polyphasic ' described below. Ambiguity and lack of precision of usage are real causes of confusion. In attempting to maintain simplicity without confusion, terms are referred to Cowan (1978) and Lincoln et al. (1998) unless further explanation is felt necessary. Terms used here are not inconsistent with Tindall (1997).In 1980, the Approved Lists (Skerman et al., 1980) recorded 1792 validly published species names in 290 genera (6n2 species per genus) (Euze! by, 1997). One expectation of modern systematics has been that the increasing numbers of methods and sophisticated tools for analysis would form co...

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