Microbispora clausenae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f

Abstract

An endophytic actinobacterium, strain CLES2^T, was discovered from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f., collected from the Phujong-Nayoa National Park, Ubon Ratchathani Province, Thailand. The results of a polyphasic taxonomic study identified this strain as a member of the genus Microbispora and a Gram-stain-positive, aerobic actinobacterium. It had well-developed substrate mycelia, which were non-motile and possessed paired spores. A phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Streptosporangiaceae, being most closely related to Microbispora bryophytorum NEAU-TX2-2^T (99.4 %), Microbispora camponoti 2C-HV3^T (99.2 %), Microbispora catharanthi CR1-09^T (99.2 %) and Microbispora amethystogenes JCM 3021^T and Microbispora fusca NEAU-HEGS1-5^T (both at 99.1 %). The major cellular fatty acid of this strain was iso-C_{16 : 0} and major menaquinone was MK-9(H₄). The polar lipid profile of strain CLES2^T contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylinositol dimannosides. These chemotaxonomic data confirmed the affiliation of strain CLES2^T to the genus Microbispora. The DNA G+C content of this strain was 70 mol%. Digital DNA-DNA hybridization and average nucleotide identity blast values between strain CLES2^T and M. catharanthi CR1-09^T were 62.4 and 94.0 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain CLES2^T from its closest species with valid names. The name proposed for the new species is Microbispora clausenae sp. nov. The type strain is CLES2^T (=DSM 101759^T=NRRL B-65340^T).

Keywords: Microbispora clausenae; endophyte; genome; polyphasic taxonomy.

Fig. 1.

16S rRNA gene-based neighbour-joining tree showing the phylogenetic relationships between Microbispora clausenae CLES2^T and related strains with valid names belonging to the genus Microbispora . Nonomuraea cavernae SYSU K10005^T was used as an outgroup. Sequence length was 1423 bp. Bootstrap values (>50 %) based on 1000 replicates are shown at the branch nodes and asterisks (*) indicate clades that were conserved in the maximum-likelihood and neighbour-joining trees. The scale bar represents 0.005 changes per nucleotide.

Fig. 2.

Phylogenomic tree based on TYGS results showing the relationship between strain CLES2^T and its related type strains. The numbers above branches are GBDP pseudo-bootstrap support values >60 % from 100 replications, with an average branch support of 98.2 %. The tree was rooted at the midpoint [43]. Leaf labels are annotated by affiliation to species and subspecies clusters, genomic G+C content, δ values and overall genome sequence length, number of proteins, and the kind of strain [24].