Deoxyribonucleic Acid Relatedness among Members of the Genus Frankia

Fernández, María P.; Meugnier, H.; Grimont, Patrick A. D.; Bardin, R.

doi:10.1099/00207713-39-4-424

Cited by 146 publications

(120 citation statements)

References 30 publications

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“…The second group of Alnus-infective strains (which does not include Alnus-infective, non-nitrogen-fixing strain AgB1-9) (19) is made up of at least three strains, two of which belong to different genomic species (14). This group is not well defined, as indicated by the differences in topology observed with the method which we used, and the data probably reflect the large distances that exist between the strains.…”

Section: Derrnatophilus-congolensismentioning

confidence: 78%

Molecular Phylogeny of the Genus Frankia and Related Genera and Emendation of the Family Frankiaceae

Normand

Orso

Cournoyer

et al. 1996

International Journal of Systematic Bacteriology

314

249

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The members of the actinomycete genus Frankia are nitrogen-fixing symbionts of many species of woody dicotyledonous plants belonging to eight families. Several strains isolated from diverse actinorhizal plants growing in different geographical areas were used in this study. The phylogenetic relationships of these organisms and uncharacterized microsymbionts that are recalcitrant to isolation in pure culture were determined by comparing complete 16s ribosomal DNA sequences. The resulting phylogenetic tree revealed that there was greater diversity among the Alnus-infective strains than among the strains that infect other host plants. The four main subdivisions of the genus Frankia revealed by this phylogenetic analysis are (i) a very large group comprising Frankia alni and related organisms (including Alnus rugosa Sp+ microsymbionts that are seldom isolated in pure culture), to which Casuarina-infective strains, a Myrica nagi microsymbiont, and other effective Alnus-infective strains are related; (ii) unisolated microsymbionts of Dryas, Coriaria, and Dutisca species; (iii) Elaeagnus-infective strains; and (iv) "atypical" strains (a group which includes an Anus-infective, non-nitrogen-fixing strain). Taxa that are related to this well-defined, coherent Frankia cluster are the genera Geodermatophilus, "Blastococcus," Sporichthya, Acidothermus, and Actinoplanes. However, the two genera whose members have multilocular sporangia (the genera Frankia and Geodermatophilus) did not form a coherent group. For this reason, we propose that the family Frankiaceae should be emended so that the genera Geodermatophilus and "Blastococcus" are excluded and only the genus Frankia is retained.The slowly growing members of the actinomycete genus Frankia are root symbionts that nodulate a wide range of perennial woody dicotyledonous plants. This nitrogen-fixing symbiosis is known to occur in more than 200 species of plants belonging to 24 genera and eight families that are called actinorhizal (6). The first Frankia strain was isolated in 1956 by Pommer (43), but this strain was subsequently lost. In 1978, Callaham et al. (8) isolated an infective Frankia strain from Comptonia peregrirza, and since then hundreds of isolates have been obtained from a number of plant species growing in many geographical areas.Becking (5) was unsuccessful in isolating the causative agent of actinorhizal nodules despite numerous attempts. He suggested that this organism was an "obligate symbiont" and devised a classification scheme based on cross-inoculation groups and on the morphology of the endosymbiont. This scheme was subsequently found to be erroneous when pure cultures became available (8). Nonetheless, Becking ( 5 ) correctly perceived the bacterial nature of the microsymbiont, named it Frankia sp., and classified it as the only member of the family Frankiaceae in the order Actinomycetales.The members of the genus Frankia can now be clearly distinguished from other bacterial genera on the basis of their host specificity, their morphology (hyphae, ...

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Section: Derrnatophilus-congolensismentioning

confidence: 78%

Molecular Phylogeny of the Genus Frankia and Related Genera and Emendation of the Family Frankiaceae

Normand

Orso

Cournoyer

et al. 1996

International Journal of Systematic Bacteriology

314

249

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“…and members of the Myricaceae or by isolates obtained from members of the Casuarinaceae. These LFRFA findings lend weight to the conclusions of Lalonde et al (46), the conclusions of the DNA-DNA relatedness studies (31), and some of the 16s ribosomal DNA sequence data (66) which indicated that the host plant of origin is an important element in defining species. The results of the LFRFA study also confirmed the finding of Nazaret et al (66) that the type strain of "F. alni subsp.…”

mentioning

confidence: 72%

“…In contrast, using a specific PCR-amplified, 268-bp DNA segment of the 16s rRNA gene (E. coli positions 921 to 1189), Nazaret et al (66) compared frankiae representing the nine genomic species of Fernandez et al determined by DNA-DNA relatedness (31). With one exception, the data showed that strains belonging to the same genomic species had identical sequences and that they differed from the other genomic species.…”

mentioning

confidence: 80%

Taxonomy of the Genus Frankia (Actinomycetales)

Lechevalier

1994

International Journal of Systematic Bacteriology

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Members of the genus Frankiu have been classified in the orderActinomycetales on the basis of morphology, cell chemistry, and 16s rRNA sequences and catalogs. This genus, which is presently defined by morphology, cell chemistry, the ability to fix nitrogen, and infectivity for and ability to enter into symbiotic relationships with certain plant hosts, may be heterogeneous. Frankiu species groups have been difficult to delineate by classical phenotypic methods. The recent use of DNA-DNA pairing and low-frequency restriction fragment analysis, as well as probes composed of certain sequences from the nif (nitrogen fixation) genes or the variable regions of 16s rRNA, has contributed to substantial progress in developing species concepts. In this review I trace the taxonomic history of the genus and outline some of the problems to be resolved in the future.Frankiae are nitrogen-fixing actinomycete symbionts that cause the formation of perennial nodules on the roots of a botanically diverse group of bushes and small trees belonging to eight families, 25 genera, and well over 200 species. The association is referred to as "actinorhizal." A number of good recent reviews (9,10,15) provide an overview of the Frankia-plant interaction. The frankiae themselves are relative newcomers to laboratory research, and their taxonomy is still developing.From an evolutionary standpoint, actinorhizal associations are quite old; there is fossil evidence of actinomycetecontaining nodules on alders in the late Pleistocene era (5). As early as 1866 (52, 100) it was hypothesized that the endophyte is microbial, but this was proven only after the introduction of electron microscopy and the actual isolation and maintenance of a pure culture in 1978 (21).In 1970, despite his lack of success in growing a single strain in vitro, and believing the organisms to be obligate symbionts, J. H. Becking (11) proposed that the name Frankia should be resurrected for these organisms. The name had been first proposed by Brunchorst in 1886 (20) to honor A. B. Frank, a Swiss microbiologist who coined the word symbiosis, but had fallen into disuse. Becking correctly discerned the actinomycetic nature of the endophytes and placed them in the family Frankiaceae in the order Actinomycetales. Following the lead of Rhizobium taxonomists, he created 10 species on the basis of host plant specificity, which he determined by using crushed nodules as inocula.Following the successful propagation of the first isolate, more and more strains became available, and problems of nomenclature and taxonomy became a matter of concern, especially as Becking's host compatibility data were not always found to be correct (49). The slow growth and nutritional fastidiousness of Frankia isolates made it difficult to pursue classical phenotypic approaches to the taxonomy of these organisms, and molecular methods have proven to be increasingly useful. Indeed, from a methodological point of view, the current taxonomic research on Frankia isolates might be said to be a paradigm for microb...

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“…This approach used on Frankia isolates yielded at least nine genomic species (10), with three, including F. alni, in the Alnus infectivity group, five in the Elaeagnus infectivity group, and one in the Casuarina infectivity group.…”

mentioning

confidence: 99%

“…In this study, a rapid and reproducible protocol based on DNA amplification and double-strand sequencing of the resulting partial 16S ribosomal DNA (rDNA) sequences was used to estimate the phylogenetic relationships among the genomic species defined by our group (10).…”

mentioning

confidence: 99%