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. 2017 Dec 19:8:2501.
doi: 10.3389/fmicb.2017.02501. eCollection 2017.

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

Maria Del Carmen Montero-Calasanz  1   2 , Jan P Meier-Kolthoff  2 , Dao-Feng Zhang  3 , Adnan Yaramis  1   4 , Manfred Rohde  5 , Tanja Woyke  6 , Nikos C Kyrpides  6 , Peter Schumann  2 , Wen-Jun Li  3 , Markus Göker  2
Affiliations

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

Maria Del Carmen Montero-Calasanz et al. Front Microbiol. .

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.

Keywords: Blastococcus; GBDP; GGDC; Geodermatophilus; Klenkia; Modestobacter; phylogenetic systematics; polyphasic taxonomy.

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Figures

FIGURE 1
FIGURE 1
Phylogenomic tree inferred with GBDP. The tree was inferred with FastME from GBDP distances calculated from whole proteomes. The numbers above branches are GBDP pseudo-bootstrap support values from 100 replications. Tip colors indicate chemotaxonomic characters that provide apomorphies for groups of interest, genome sizes and the exact G+C content as calculated from the genome sequences (see the embedded legend for details). B., Blastococcus; C., Cryptosporangium; G., Geodermatophilus; M., Modestobacter; S., Sporichthya; NA, not applicable.
FIGURE 2
FIGURE 2
Maximum likelihood phylogenetic tree inferred from 16S rRNA gene sequences, showing the phylogenetic position of the strain YIM M13156T relative to the type strains within Geodermatophilaceae. The branches are scaled in terms of the expected number of substitutions per site (see size bar). Support values from maximum-likelihood constrained (first), maximum-parsimony constrained (second), maximum-likelihood unconstrained (third) and maximum-parsimony unconstrained (fourth) bootstrapping are shown above the branches if equal to or larger than 60%.
FIGURE 3
FIGURE 3
Polar lipids profile of strain YIM M13156T (a), G. soli DSM 45843T (b), G. taihuensis DSM 45962T (c) and G. terrae DSM 45844T (d) after separation by two-dimensional TLC using the solvents chloroform:methanol:water (65:25:4; v:v:v) in the first dimension and chloroform:methanol:acetic acid:water (80:12:15:4; v:v:v:v) in the second one. Plates were sprayed with molybdatophosphoric acid (3.5%; MerckTM) for detection of the total polar lipids. DPG, diphosphatidylglycerol; PG, phosphatidylglycerol; PE, phosphatidylethanolamine; OH-PE, hydroxyphosphatidylethanolamine; PI, phosphatidylinositol; GPI, glycophosphatidylinositol; GPL, unidentified glycophospholipid; AL, aminolipid; L1-7, unidentified lipids. All data are from this study.
FIGURE 4
FIGURE 4
Fatty-acids dendrogram estimated from the logit-transformed percent values as measured with the MIDI system using the Ward algorithm for agglomerative hierarchical clustering and euclidean distances using the pvclust package for the R statistical environment. Approximately unbiased (AU, left) and bootstrapping (BP, right) support values are shown above the branches.
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