Abstract
Microbial-based eco-friendly biological substances are needed to protect crops from phytopathogenic fungi and replace toxic chemical fungicides that cause serious environmental issues. This study screened for soil antifungal Streptomyces strains, which produce rich, diverse, and valuable bioactive metabolites in the soil environment. Bioassay-based antifungal screening of approximately 2,400 Streptomyces strains led to the isolation of 149 strains as tentative antifungal producers. One Streptomyces strain showing the most potent antifungal activities against Candida albicans and Fusarium oxysporum was identified as a putative anti-phytopathogenic soil isolate that is highly homologous to Streptomyces rubrisoli (named S. rubrisoli Inha 501). An in vitro antifungal assay, pot-test, and field-test against various phytopathogenic fungi confirmed that S. rubrisoli Inha 501 is a potential novel phytopathogenic fungicide producer to protect various crops in the soil environment. Whole-genome sequencing of S. rubrisoli Inha 501 and an anti-SMASH genome mining approach revealed an approximately 150-kb polyene biosynthetic gene cluster (BGC) in the chromosome. The target compound isolation and its BGC analysis confirmed that the giant linear polyene compound exhibiting the anti-phytopathogenic activity in S. rubrisoli Inha 501 was highly homologous to the previously reported compound, neotetrafibricin A. These results suggest that a bioassay-based screening of a novel antifungal Streptomyces strain followed by its genome mining for target compound BGC characterization would be an efficient approach to isolating a novel candidate phytopathogenic fungicide that can protect crops in the soil environment.
Highlights
For a long time in traditional agriculture, chemical fungicides have been used to control phytopathogenic fungi, such as Fusarium, Botrytis, and Colletotrichum, which cause severe damage in crop production (Dean et al, 2012; Parnell et al, 2016)
A total of 2,419 Streptomyces culture extracts provided from the actinomycetes cell collection center in the Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Korea was screened to isolate the strains showing antifungal activities against C. albicans and F. oxysporum (Figure 2 and Supplementary Figure 1). 149 antifungal culture extracts exhibiting antifungal activity were first selected, followed by the additional selection of 51 antifungal strains showing a typical polyene spectrum assayed by 2-dimensional high-performance liquid chromatography (HPLC) analysis (Figure 2, Guo et al, 2000)
Among the 51 strains tested, one Streptomyces sp. isolated from organic green tea fields in Jeolla Province in Korea (34◦51 31.7 N 127◦08 48.1 E) was selected as a final candidate to control phytopathogenic fungi, showing the strongest antifungal activities against C. albicans and F. oxysporum. 16s rRNA sequence-based phylogenetic analysis showed that the strain isolated above exhibited 98.9% similarity of S. rubrisoli FXJ1.725 (KC137300) and was called S. rubrisoli Inha501 (Figure 3A)
Summary
For a long time in traditional agriculture, chemical fungicides have been used to control phytopathogenic fungi, such as Fusarium, Botrytis, and Colletotrichum, which cause severe damage in crop production (Dean et al, 2012; Parnell et al, 2016). Alternative methods are being pursued to protect crops from phytopathogenic fungi using soil-rich microorganisms, such as Pseudomonas, Bacillus, and Streptomyces species, to minimize these toxic compounds in the soil environment. Many Streptomyces species present in plant roots have shown beneficial effects on crops by controlling phytopathogenic fungi or the secretion of plant growth hormones and increasing the possibility of agricultural applications (Shi et al, 2018; Kim et al, 2019)
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