AUTHOR=Zhou Shuangqing , Zhou Yifan , Li Chengui , Wu Wenqiang , Xu Yun , Xia Wei , Huang Dongyi , Huang Xiaolong 

TITLE=Identification and genomic analyses of a novel endophytic actinobacterium Streptomyces endophytica sp. nov. with potential for biocontrol of yam anthracnose

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1139456

DOI=10.3389/fmicb.2023.1139456

ISSN=1664-302X

ABSTRACT=<p>Anthracnose disease caused by <italic>Colletotrichum gloeosporioides</italic> is one of the devastating diseases of yams (<italic>Dioscorea</italic> sp.) worldwide. In this study, we aimed to isolate endophytic actinobacteria from yam plants and to evaluate their potential for the control of yam anthracnose based on bioassays and genomic analyses. A total of 116 endophytic actinomycete strains were isolated from the surface-sterilized yam tissues from a yam orchard in Hainan Province, China. In total, 23 isolates showed antagonistic activity against <italic>C. gloeosporioides</italic>. An endophytic actinomycete, designated HNM0140<sup>T</sup>, which exhibited strong antifungal activities, multiple biocontrol, and plant growth-promoting (PGP) traits was subsequently selected to colonize in the tissue-cultured seedlings of yam and was tested for its <italic>in vivo</italic> biocontrol potential on yam anthracnose. The results showed that treatment with strain HNM0140<sup>T</sup> markedly reduced the severity and incidence of yam anthracnose under greenhouse conditions. Morphological and chemotaxonomic analyses showed that strain HNM0140<sup>T</sup> was assigned to the genus <italic>Streptomyces</italic>. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain HNM0140<sup>T</sup> formed a separate cluster together with <italic>Streptomyces lydicus</italic> ATCC 25470<sup>T</sup> (99.45%), <italic>Streptomyces chattanoogensis</italic> NRRL ISP-5002<sup>T</sup> (99.45%), and <italic>Streptomyces kronopolitis</italic> NEAU-ML8<sup>T</sup> (98.97%). The phylogenomic tree also showed that strain HNM0140<sup>T</sup> stably clustered with <italic>Streptomyces lydicus</italic> ATCC 25470<sup>T</sup>. The ANI and dDDH between strain HNM0140<sup>T</sup> and its closest related-type species were well below the recommended thresholds for species demarcation. Hence, based on the phylogenetic, genomic, and phenotypic analyses, strain HNM0140<sup>T</sup> should represent a new streptomycete species named <italic>Streptomyces endophytica</italic> sp. nov. Genomic analysis revealed that strain HNM0140<sup>T</sup> harbored 18 putative BGCs for secondary metabolites, some PGP-related genes, and several genes coding for antifungal enzymes. The presented results indicated that strain HNM0140<sup>T</sup> was a promising biocontrol agent for yam anthracnose.</p>