Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb

Abstract

The taxonomic status of two actinomycetes isolated from the wall of a hypogean Roman catacomb was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Amycolatopsis. They also shared a range of chemical, molecular and phenotypic markers which served to separate them from representatives of recognized Amycolatopsis species. The new isolates formed a branch in the Amycolatopsis 16S rRNA gene sequence tree with Amycolatopsis minnesotensis NRRL B-24435 T , but this association was not supported by a particularly high bootstrap value or by the product of the maximum-parsimony tree-making algorithm. The organisms were distinguished readily from closely related Amycolatopsis species based on a combination of phenotypic properties and from all Amycolatopsis strains by their characteristic menaquinone profiles, in which tetra-hydrogenated menaquinones with 11 isoprene units predominated. The combined genotypic and phenotypic data indicate that the isolates merit recognition as representing a novel species of the genus Amycolatopsis. The name proposed for this novel species is Amycolatopsis nigrescens sp. nov., with type strain CSC17Ta-90 T (=HKI 0330 T =DSM 44992 T =NRRL B-24473 T ).The genus Amycolatopsis Lechevalier et al. 1986 is a member of the family Pseudonocardiaceae Embley et al. 1988 (as circumscribed by Warwick et al., 1994). Members of this family are characterized by the presence of meso-diaminopimelic acid, arabinose and galactose in whole-cell hydrolysates (wall chemotype IV sensu Lechevalier & Lechevalier, 1970), fatty acids that mainly consist of iso-and anteisobranched components and N-acetylated muramic acid and by the lack of mycolic acids (Takahashi, 2001). Amycolatopsis strains can be separated from members of the other genera classified within the family Pseudonocardiaceae by using a range of chemotaxonomic and morphological markers (Kim & Goodfellow, 1999) and by genus-specific oligonucleotide primers based on 16S rRNA gene sequences (Tan et al., 2006).Members of the genus Amycolatopsis are Gram-positive, non-acid-fast, non-motile actinomycetes that form branched vegetative hyphae that undergo fragmentation into rod-like and squarish elements. If present, aerial hyphae may be sterile or differentiate into squarish to ovoid sporelike structures (Chun et al., 1999). The genus encompasses alkaliphilic, mesophilic, thermophilic and pathogenic species, which can be distinguished from one another by using a range of phenotypic properties (SaintpierreBonaccio et al., 2005;Lee, 2006;Lee et al., 2006). At the time of writing, the genus Amycolatopsis comprised 32 recognized species and subspecies, although there is compelling evidence that the genus is grossly underspeciated and that Amycolatopsis fastidiosa should be classified within a different taxon (Tan et al., 2006). The present polyphasic study was designed to determine the taxonomic position of two Amycolatopsis-like strains that had been isolated from a h...

Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis

“…The genus Amycolatopsis is one of the well-defined taxa in the family Pseudonocardiaceae, based on chemotaxonomic characteristics (Lechevalier et al, 1986;Kim & Goodfellow, 1999;Yassin et al, 1993;Groth et al, 2007) and phylogenetic evidence based on the comparison of 16S rRNA gene sequences (Lee et al, 2000;Tan et al, 2006). In the recently emended genus description (Groth et al, 2007), some species contain MK-11(H 4 ), instead of MK-9(H 4 ), as the predominant menaquinone.…”

“…In the recently emended genus description (Groth et al, 2007), some species contain MK-11(H 4 ), instead of MK-9(H 4 ), as the predominant menaquinone. At the time of writing, the genus consists of 38 recognized species and many novel species have been described from diverse environments such as soil, vegetation, human and animal clinical sources, fresh water, rock and subterranean sites.…”

Elucidation of the zinc‐dependent regulation in Amycolatopsis japonicum enabled the identification of the ethylenediamine‐disuccinate ([S,S]‐EDDS) genes

“…As expected, no [ S,S ]‐EDDS production could be detected after cultivation of A. azurea . Furthermore, representatives of the phylogenetic clades C and D, namely Amycolatopsis balhimycina DSM 5908 (Nadkarni et al ., ; Wink et al ., ), Amycolatopsis mediterranei DSM 43304 (Margalith and Beretta, ) and Amycolatopsis nigrescens DSM 44992 (Groth et al ., ), do not produce [ S,S ]‐EDDS (http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13159/suppinfo).…”

Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L.

“…Tseng et al 2006;Groth et al 2007;Bian et al 2009;Tamura et al 2010;Albarracín et al 2010;Duangmal et al 2011). At present, there is only one record of the isolation of a new species belonging to the genus Amycolatopsis from the endophytic environment (Duangmal et al 2011).…”