Abstract
Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156T and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of Geodermatophilaceae and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, Geodermatophilus, is not monophyletic, hence the arrangement of the genera of Geodermatophilaceae must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within Geodermatophilus. In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, Klenkia, with the type species Klenkia marina sp. nov. and harboring four species formerly assigned to Geodermatophilus, G. brasiliensis, G. soli, G. taihuensis, and G. terrae. Emended descriptions of all species of Geodermatophilaceae are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.
Highlights
The order Geodermatophilales (Sen et al, 2014) comprises the sole family Geodermatophilaceae, which was initially proposed by Normand et al (1996), no type genus was designated at that time, confirmed later by Stackebrandt et al (1997), formally described by Normand (2006) and later emended by Zhi et al (2009)
The phylogenetic tree based on the whole proteomes of the sequenced type strains placed, with maximum support, the group formed by the strain YIM M13156T, G. brasiliensis DSM 44526T, G. soli DSM 45843T and G. taihuensis DSM 45962T as a sister-group of all other Geodermatophilaceae genera (Figure 1)
The unconstrained phylogenetic tree based on 16S rRNA gene sequences was not well resolved at its backbone but when applying the constraint derived from the genome BLAST Distance Phylogeny (GBDP) tree, Modestobacter, Blastoccocus and the two distinct groups of Geodermatophilus appeared as monophyletic (Figure 2); support for their monophyly was strong except in the case of Blastococcus
Summary
The order Geodermatophilales (Sen et al, 2014) comprises the sole family Geodermatophilaceae, which was initially proposed by Normand et al (1996), no type genus was designated at that time, confirmed later by Stackebrandt et al (1997), formally described by Normand (2006) and later emended by Zhi et al (2009). Taxonomic Rearrangement of Geodermatophilaceae (Ahrens and Moll, 1970; Skerman et al, 1980; Hezbri et al, 2016b), Modestobacter (Mevs et al, 2000) and the type genus Geodermatophilus (Luedemann, 1968; Skerman et al, 1980). Geodermatophilus was historically poorly studied due to difficulties in culturing novel isolates (Urzì et al, 2004). Overcoming those technical difficulties, the number of validly named species within the genus dramatically increased from a single species, G. obscurus, in 2011 to twenty-one species at the time of writing (Parte, 2014). Species belonging to the genus are mainly isolated from arid soils and characterized by tolerance against oxidative stress (Gtari et al, 2012; Montero-Calasanz et al, 2013a, 2014b, 2015; Hezbri et al, 2015a, 2016a) some isolates from rhizospheric soils and lake sediments have been classified within the genus
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