Streptomyces tirandamycinicus sp. nov., a Novel Marine Sponge-Derived Actinobacterium With Antibacterial Potential Against Streptococcus agalactiae

Abstract

A novel actinobacterium, strain HNM0039^T, was isolated from a marine sponge sample collected at the coast of Wenchang, Hainan, China and its polyphasic taxonomy was studied. The isolate had morphological and chemical characteristics consistent with the genus Streptomyces. Based on the 16S rRNA gene sequence analysis, strain HNM0039^T was closely related to Streptomyces wuyuanensis CGMCC 4.7042^T (99.38%) and Streptomyces spongiicola HNM0071^T (99.05%). The organism formed a well-delineated subclade with S. wuyuanensis CGMCC 4.7042^T and S. spongiicola HNM0071^T in the Streptomyces 16S rRNA gene tree. Multi-locus sequence analysis (MLSA) based on five house-keeping gene alleles (atpD, gyrB, rpoB, recA, trpB) further confirmed their relationship. DNA-DNA relatedness between strain HNM0039^T and its closest type strains, namely S. wuyuanensis CGMCC 4.7042^T and S. spongiicola HNM0071^T, were 46.5 and 45.1%, respectively. The average nucleotide identity (ANI) between strain HNM0039^T and its two neighbor strains were 89.65 and 91.44%, respectively. The complete genome size of strain HNM0039^T was 7.2 Mbp, comprising 6226 predicted genes with DNA G+C content of 72.46 mol%. Thirty-one putative secondary metabolite biosynthetic gene clusters were also predicted in the genome of strain HNM0039^T. Among them, the tirandamycin biosynthetic gene cluster has been characterized completely. The crude extract of strain HNM0039^T exhibited potent antibacterial activity against Streptococcus agalactiae in Nile tilapia. And tirandamycins A and B were further identified as the active components with MIC values of 2.52 and 2.55 μg/ml, respectively. Based on genotypic and phenotypic characteristics, it is concluded that strain HNM0039^T represents a novel species of the genus Streptomyces whose name was proposed as Streptomyces tirandamycinicus sp. nov. The type strain is HNM0039^T (= CCTCC AA 2018045^T = KCTC 49236^T).

Keywords: Streptococcus agalactiae; Streptomyces tirandamycinicus; antibacterial; marine sponge; tirandamycins.

FIGURE 1

Neighbor-joining phylogenetic tree of strain HNM0039^T based on complete 16S rRNA gene sequences (1523 nucleotides). Asterisks indicate that the conserved branches were also recovered using maximum-parsimony and maximum-likelihood tree-making algorithms. Bootstrap values based on 1000 replications are listed as percentages; only values > 50% are given. Bar: 0.01 substitutions per nucleotide position.

FIGURE 2

Neighbor-Joining tree based on concatenated five house-keeping genes (atpD, gyrB, rpoB, recA, and trpB) showing the position of strain HNM0039^T amongst its phylogenetic neighbors. Percentages at the nodes represent levels of bootstrap support from 1000 replications datasets. Only values > 50% are given. Bar: 0.05 substitutions per nucleotide position.

FIGURE 3

Scanning electron micrograph showing spiral spore chains of strain HNM0039^T after growth on ISP7 medium at 28°C for 3 weeks. Bars: 10 μm.

FIGURE 4

Circular genome map of strain HNM0039^T. The genome map was made using Circos ver. 0.64 (Krzywinski et al., 2009). The outer scale is numbered in intervals of 0.1 Mbp; Circles 1 and 2 display the distribution of genes related to COG categories in the forward strand and in the backward strand respectively; Circle 3 displays the tRNA genes and rRNA genes; Circle 4 displays the GC percentage plot (red above average, blue below average); Circle 5 displays the GC skew (lime red above average, light green below average).

FIGURE 5

Structure of tirandamycins A (1) and B (2) from strain HNM0039^T.