Identification, antifungal and plant growth promoting activities of endophytic actinomycetes from orchids

Abstract

Sixty-two endophytic actinomycetes were isolated from 15 Thai orchids. They were identified as Streptomyces (34 isolates), Micromonospora (21 isolate), Streptosporangium (2 isolates), Actinomadura (1 isolates), Amycolatopsis (3 isolates) and Pseudonocardia (1 isolates) based on their phenotypic, chemotaxonomic and genotypic characteristics. The antimicrobial activity screening revealed that Streptomyces (18 isolates), Micromonospora (12 isolates) and Streptosporangium (1 isolate) exhibited antimicrobial activity against Bacillus subtilis ATCC 6633, Kocuria rhizophila ATCC 9341, Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853 and Candida albicans ATCC 10231. Strain DR2-2 could inhibit all tested pathogens. Based on 16S rRNA gene sequencing, strain DR6-1 was closely related to Amycolatopsis nivea KCTC 39515T with 99.06%, average nucleotide identity (ANI) with 93.8 % and digital DNA-DNA hybridization (dDDH) with 52.50 %. Therefore, strain DR6-1T was a new actinomycete species and was proposed as Amycolatopsis dendrobii. Based on 16S rRNA gene sequencing, strain DR5-3 was closely related to Micromonospora yasonensis DSM 45980T (98.96%), Therefore, strain DR5-3T was a new actinomycete species and was proposed as Micromonospora dendrobii. Strains DR5-1, DR7-3, DR8-5, and DR8-8 showed inhibitory activity against five phytopathogenic fungi including Fusarium oxysporum SA01, Fusarium solani SA02, Alternaria alternata SA01, Curcuria oryzae SA04, and Colletotrichum gloeosporioides SA03. Strain DR7-3 exhibited a broad-spectrum antifungal activity against five fungi, especially C. oryzae SA04. The analysis of secondary metabolites from ethyl acetate extract of strain DR7-3 using the gas chromatography-mass spectrometry, fifteen identified compounds were found. Eicosane, phenol-2,4-bis(1,1-dimethylethyl), hexadecane, and hexadecanoic acid-methyl ester showed antifungal activity. Screening for plant-growth promoting activity, endophytic actinomycetes could produce Indole-3-acetic acid (IAA) ranged from 0.04±0.36 to 294.10±12.17 µg/mL. Strain DR1-2 showed maximum IAA of 489.73±8.90 µg/mL, when optimized using 0.5% L-tryptophan, pH 6, with incubation at 30°C for 7 days. The IAA of strain DR1-2 enhanced the root length, shoot length, the number of roots, and fresh weight of rice seedlings (Oryza sativa L. cv. RD49). Results indicated that actinomycetes from Thai orchids were promising sources of antimicrobial compounds and plant hormones for agricultural applications.