Streptomyces coffeae sp. nov., an endophytic actinomycete isolated from the root of Coffea arabica (L.)

An endophytic actinobacterium, designated strain CA1R205(T), was isolated from the surface-sterilized root of Coffea arabica L. collected from Ratchaburi province, Thailand. The taxonomic position of this strain was evaluated using a polyphasic approach. The strain produced light yellowish brown to dark brownish black substrate mycelium and greyish white aerial mycelium. The spiral spore chains were produced directly on aerial mycelium. CA1R205(T) was found to have LL-diaminopimelic acid in the cell peptidoglycan, galactose, glucose, mannose and ribose as whole-cell reducing sugars, MK-10(H-4), MK-9(H-6), MK-10(H-2), MK-9(H-4), MK-10(H-6) and MK-10(H-8) as menaquinones and iso-C-15:0, anteiso-C-15:0, iso-C-16:0 and C-16:0 as major fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were detected in the cells. These characteristics were consistent the typical chemotaxonomic properties of members the genus Streptomyces. The taxonomic affiliation at the genus level of this strain could be confirmed using its 16S rRNA gene sequence data. CA1R205(T) showed the highest 16S rRNA gene sequence similarity value to Streptomyces rapamycinicus NRRL B-5491(T) (98.9%), followed by Streptomyces iranensis HM 35(T) (98.8 %). Digital DNA-DNA hybridization and average nucleotide identity-by blast (ANIb) values between CA1R205(T) and S. rapamycinicus NRRL B-5491(T) were 27.2 and 81.5%, respectively. The DNA G+C content of genomic DNA was 70.7 mol%. Due to the differences in physiological, biochemical and genotypic data, CA1R205(T) could be discriminated from its closest neighbour. Thus, CA1R205(T) should be recognized as representing a novel species of the genus Streptomyces, for which the name Streptomyces coffeae sp. nov. is proposed. The type strain is CA1R205(T) (=TBRC 11244(T)=NBRC 114295(T)).