Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl.

Three novel actinomycete strains, designated as DR6-1(T), DR6-2 and DR6-4, isolated from the roots of Dendrobium heterocarpum Lindl in Thailand were studied using a polyphasic taxonomic approach. The strains grew at 20-37 degrees C, at pH 5-10 and with 5% (w/v) NaCl. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and MK-9(H-4) was a major menaquinone. Arabinose and galactose were the major sugars in the cell wall. The predominant cellular fatty acids were iso-C-16:0 and iso-C-15:0. The detected polar lipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. Strains DR6-1(T), DR6-2 and DR6-4 shared 99.9-100% 16S rRNA gene sequence similarity and were closely related to Amycolatopsis echigonensis JCM 21831(T) (98.7-98.8%). The approximate genome size of strain DR6-1(T) was 9.6 Mb with a G+C content of 69.6 mol%. The ANIb and dDDH values between genomic sequences of strain DR6-1(T) and Amycolatopsis echigonensis JCM21831(T), Amycolatopsis rubida JCM 10871(T) and Amycolatopsis nivea KCTC 39515(T) were 90.55, 92.25, 92.60%. and 47.20. 52.10 and 52.50%, respectively. Based on the phenotypic, chemotaxonomic and genotypic characteristics, it has been concluded that strains DR6-1(T), DR6-2 and DR6-4 represent a novel species of the genus Amycolatopsis for which the name Amycolatopsis dendrobii sp. nov. is proposed. The type strain is DR6-1(T) (=JCM 33742(T)=KCTC 49546(T)=TISTR 2840(T)).

Automated summary

Three novel actinomycete strains were isolated from the roots of Dendrobium heterocarpum Lindl in Thailand and were characterized as a new species of the genus Amycolatopsis, named Amycolatopsis dendrobii sp. nov. The strains showed high similarity in genetic sequences and shared phenotypic and chemotaxonomic characteristics. The proposed type strain is DR6-1(T) with specific genomic features distinguishing it from closely related strains.