Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae

Abstract

The genus Frankia is at present the sole genus in the family Frankiaceae and encompasses filamentous, sporangia-forming actinomycetes principally isolated from root nodules of taxonomically disparate dicotyledonous hosts named actinorhizal plants. Multiple independent phylogenetic analyses agree with the division of the genus Frankia into four well-supported clusters. Within these clusters, Frankia strains are well defined based on host infectivity range, mode of infection, morphology, and their behaviour in culture. In this study, phylogenomics, overall genome related indices (OGRI), together with available data sets for phenotypic and host-plant ranges available for the type strains of Frankia species, were considered. The robustness and the deep radiation observed in Frankia at the subgeneric level, fulfilling the primary principle of phylogenetic systematics, were strengthened by establishing genome criteria for new genus demarcation boundaries. Therefore, the taxonomic elevation of the Frankia clusters to the rank of the genus is proposed. The genus Frankia should be revised to encompass cluster 1 species only and three novel genera, Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov., are proposed to accommodate clusters 2, 3, and 4 species, respectively. New combinations for validly named species are also provided.

High Frankia abundance and low diversity of microbial community are associated with nodulation specificity and stability of sea buckthorn root nodule

“…In addition, we also analyzed the differences in the abundance of all 19 Frankia species contained in RN at different sites ( Supplementary Table S8 ). These 19 Frankia species were distributed in different Frankia clusters ( Hong et al., 2012 ; Nouioui et al., 2019 ; Gtari, 2022 ). We observed that most of the Frankia species in the RN microbial community did not differ significantly between the different sites, but their relative abundance was very low.…”

Streptantibioticus silvisoli sp. nov., acidotolerant actinomycetes from pine litter, reclassification of Streptomyces cocklensis, Streptomyces ferralitis, Streptomyces parmotrematis and Streptomyces rubrisoli as Actinacidiphila cocklensis comb. nov., Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov., and emended descriptions of the genus Streptantibioticus, the family Streptomycetaceae and Streptomyces iconiensis

“…The outcome of the whole-genome sequence analysis provides further evidence that much better resolution is found between actinomycetes in phylogenomic trees than in corresponding 16S rRNA gene and MLSA trees as the former are based on millions not hundreds of unit characters [4,5]. It is evident from the phylogenomic tree (Fig.…”

“…The outcome of the whole-genome sequence analysis provides further evidence that much better resolution is found between actinomycetes in phylogenomic trees than in corresponding 16S rRNA gene and MLSA trees as the former are based on millions not hundreds of unit characters [4, 5]. It is evident from the phylogenomic tree () that the isolates form a distinct lineage within a clade that includes the type strains of Streptantibioticus cattleyicolor , Streptomyces ferralitis , S. parmotrematis and S.…”

“…Classifications based on phylogenomic characteristics, notably digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI) and percentages of conserved proteins (POCP) [1, 2] are clarifying relationships between complex groups of filamentous actinomycetes of biotechnological and ecological importance [3–8]. A case in point is the family Streptomycetaceae Waksman and Henrici [9], which until recently was composed of actinomycetes classified in the genera Allostreptomyces [10], Kitasatospora [11, 12], Streptacidiphilus [13] and Streptomyces [14], the type genus [9]; all of these taxa share a combination of chemotaxonomic, morphological and 16S rRNA signatures [10, 15].…”

The impact of Elaeagnus angustifolia root exudates on Parafrankia soli NRRL B-16219 exoproteome

“…Parafrankia is a bacterial genus classified within the Frankiaceae family, alongside the genera Frankia, Protofrankia, and Pseudofrankia 1 , 2 . Parafrankia strains are known for their ability to form symbiotic relationships with actinorhizal plants of the Elaeagnaceae , Colletieae ( Rhamnaceae ), Morella ( Myricaceae ), and Gynmnostoma ( Casuarinaceae ) species.…”