Genotype–phenotype correlations within the Geodermatophilaceae

Abstract

The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype–phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.

Blastococcus brunescens sp. nov., a member of the Geodermatophilaceae isolated from sandstone collected from the Sahara Desert in Tunisia

“…The colonies exhibited a pink-orange hue on GYM Streptomyces , showcasing irregularities with a dry surface. A diffusible pink pigment was observed on medium 5322 (ISP7), while a distinctive brown pigment was observed on medium 5006, a characteristic not reported for other Blastococcus type strains [2–10] (Fig. S1A, available in the online version of this article).…”

“…The genus Blastococcus [1] encompasses 15 species with validly published names sourced from diverse environments. Blastococcus species have been identified in habitats as varied as the seawater of the Baltic Sea ( Blastococcus aggregatus [1]), monument samples (including Blastococcus saxobsidens [2], Blastococcus capsensis [3], Blastococcus colisei [4], Blastococcus xanthinilyticus [5], Blastococcus tunisiensis [6], and Blastococcus carthaginensis [7]), as well as desert soils and sands (with representatives such as Blastococcus aurantiacus [8], Blastococcus haudaquaticus [8], Blastococcus mobilis [8], Blastococcus atacamensis [9], and Blastococcus deserti [10]). While their ecological roles in these demanding conditions are still being unravelled, this recognition underscores their potential as valuable assets with significant biotechnological applications.…”

Lactiplantibacillus brownii sp. nov., a novel psychrotolerant species isolated from sauerkraut

“…The presence of putative folP, folC and dfrA genes (RA086_12815, 09200 and 07270) encoding dihydropteroate synthase (EC 2.5. The detection of a putative murE gene (RA086_03955) encoding a UDP-N-acetylmuramoyl-l-alanyl-d-glutamate−2,6diaminopimelate ligase (EC 6.3.2.13) but not the UDP-N-acetylmuramoyl-l-alanyl-d-glutamate−l-lysine ligase (EC 6.3.2.7 [62]) suggested that strain WILCCON 0030 T might contain Dpm-type peptidoglycan. This was deduced from a sequence similarity analysis, which found >90 % sequence similarity between the MurE variant of strain WILCCON 0030 T (MDQ7936800) with those of the other type strains of the genus Lactiplantibacillus, including L. plantarum DSM 20174 T (KRL35199) and L. pentosus DSM 20314 T (KRK27067).…”

Blastococcus carthaginiensis sp. nov., isolated from a monument sampled in Carthage, Tunisia

“…While the type species, Blastococcus aggregatus , was discovered in the seawater of the Baltic Sea [1], other species were mainly isolated from monument samples, including Blastococcus saxobsidens [12], Blastococcus capsensis [13], Blastococcus colisei [14], Blastococcus xanthinilyticus [15] and Blastococcus tunisiensis [16], and from desert soils and sands, including Blastococcus aurantiacus [17], Blastococcus haudaquaticus [17], Blastococcus mobilis [17], Blastococcus atacamensis [18] and Blastococcus deserti [19]. Lastly, Blastococcus jejuensis was isolated from sand sediment of a beach [20], Blastococcus litoris from sea tidal flat sediment [21], and Blastococcus fimeti from seepage water in a landfill [17].…”

“…Lastly, Blastococcus jejuensis was isolated from sand sediment of a beach [20], Blastococcus litoris from sea tidal flat sediment [21], and Blastococcus fimeti from seepage water in a landfill [17].…”