Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

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.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

“…It is also difficult to unravel the internal structure of complex actinobacterial genera using data acquired from polyphasic taxonomic studies, notable examples include Actinomyces (Schaal and Yassin, 2012a ), Amycolatopsis (Tan and Goodfellow, 2012 ), Arthrobacter (Busse et al, 2012 ), Micromonospora (Carro et al, 2018 ), Nocardioides (Evtushenko et al, 2012 ), Rhodococcus (Jones and Goodfellow, 2012 ), and Streptomyces (Labeda et al, 2012 ). Polyphasic studies as currently conducted largely depend on the 16S rRNA gene (Montero-Calasanz et al, 2017 ) but despite its usefulness for resolving taxonomic questions in the past, the gene contains only a limited number of characters and thus, much like any other single gene, can yield trees with many statistically unsupported branches (Klenk and Göker, 2010 ; Breider et al, 2014 ).…”

“…In contrast, trees based on a few thousand nucleotides (Tang et al, 2016 ) tend to have branches with low bootstrap values; the same limitation applies, albeit to a lesser extent, to multi-locus sequence analyses of conserved housekeeping genes (Glaeser and Kämpfer, 2015 ), which can hardly be called genome-scale (Klenk and Göker, 2010 ). Phylogenomic methods have already been applied to elucidate the classification of complex actinobacterial taxa, such as the genera Amycolatopsis, Micromonospora, Rhodococcus , and Salinispora (Sangal et al, 2016 ; Tang et al, 2016 ; Jensen, 2017 ; Carro et al, 2018 ), and in some cases has led to marked reclassification (Montero-Calasanz et al, 2017 ). However, a comprehensive analysis of the phylum Actinobacteria based on truly genome-scale methods has not been undertaken.…”

Genome-Based Analysis Reveals the Taxonomy and Diversity of the Family Idiomarinaceae

“…Presently, the integration of genomic information into microbial systematics, in addition to physiological and chemotaxonomic parameters as taxonomic criteria, is strongly recommended in the post-genomic era ( Chun and Rainey, 2014 ). Numerous genome-based approaches have been developed and applied for species delineation, for example pan-genome analysis ( Medini et al, 2005 ; Beukes et al, 2017 ), average nucleotide identity (ANI) analysis ( Konstantinidis and Tiedje, 2005 ; Riesco et al, 2018 ), and digital DNA–DNA hybridization (dDDH) analysis ( Meier-Kolthoff et al, 2013 ; Montero-Calasanz et al, 2017 ). The concept of the pan-genome was first introduced in 2005, and includes the core genome composed of genes shared by all strains, a dispensable genome made of genes present in a subset of the strains, and finally strain-specific genes ( Medini et al, 2005 ; Vernikos et al, 2015 ).…”

Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile

“…Christensen [66] and nitrate reduction following Schaal et al [67]. The tolerance tests were carried out in triplicate and incubated for 3 weeks at 28°C, apart from the temperature tests.…”