New Streptomyces rochei FE-3-1 Genome Reveals Strong Antifungal Potential Against Rice Blast Pathogen Pyricularia oryzae

A newly isolated bacterium from rice rhizosphere soil—Streptomyces rochei FE-3-1—has emerged as a promising biocontrol agent against the devastating rice blast pathogen Pyricularia oryzae, according to a detailed genomic study published in PLOS ONE.

Rice blast remains one of the world’s most destructive fungal diseases, and the need for safer, sustainable alternatives to chemical fungicides is increasing. In this study, researchers isolated strain FE-3-1 using gradient dilution techniques and confirmed its identity via morphological, microscopic, and 16S rRNA-based phylogenetic analysis, placing it closest to Streptomyces rochei NRRL B-2410.

Potent Inhibition of Pyricularia oryzae

The strain showed 73.33% inhibition of the rice blast pathogen on PDA plates, strongly reducing fungal colony growth compared to the control. This antagonistic effect indicates that FE-3-1 produces active metabolites capable of suppressing P. oryzae.

High-Quality Whole Genome Sequencing

The research team generated a complete genome assembly of 8.25 Mb and 72.51% GC content, identifying:

7,158 genes, including
- 67 tRNAs
- 18 rRNAs
- 84 sRNAs
14 genomic islands
Extensive functional categories spanning transcription, metabolism, signal transduction, and membrane transport.

This robust dataset provides a critical foundation for understanding functional traits linked to plant growth promotion and biocontrol.

31 Biosynthetic Gene Clusters with Antimicrobial Relevance

Using antiSMASH, the study identified 31 biosynthetic gene clusters, at least four matching potent antimicrobial pathways, including:

Candicidin (antifungal)
Streptothricin (broad-spectrum antibiotic)
Albaflavenone (antibacterial)
Lipopeptide 8D1-1 / 8D1-2 (implicated in anti-P. oryzae activity)

Many clusters showed similarity to metabolites such as isorenieratene, melanin, desferrioxamine, ectoine, hopene, and more—highlighting this strain as a rich metabolic resource.

Plant Growth-Promoting Traits and Heavy Metal Resistance

Genome mining also revealed genes associated with:

Nitrogen, phosphorus, and potassium metabolism
Siderophore biosynthesis
Chitinase, protease, lipase, and catalase (linked to pathogen suppression)
Resistance to cadmium, arsenic, zinc, and copper

These features suggest FE-3-1 can both enhance plant health and persist in polluted soils, strengthening its value as a biofertilizer or biopesticide candidate.

Comparative Genomics Confirms Species Identity and Unique Capabilities

ANI and AAI values confirmed FE-3-1 belongs to Streptomyces rochei. Comparative analysis with eight related strains revealed 244 unique gene clusters present only in FE-3-1, many involved in stress tolerance, secondary metabolism, and nutrient cycling.

A Strong Candidate for Next-Generation Biocontrol Solutions

The combination of strong antifungal activity, diverse secondary metabolites, and plant-beneficial traits provides a compelling basis for developing FE-3-1 into a commercial biopesticide or biofertilizer. The authors highlight that further characterization of key lipopeptide compounds (8D1-1 and 8D1-2) will guide future applications.

Reference

Du D, Yi Z, Shan S, Gao S, Yu M, Wang B (2025) Isolation, identification, and whole-genome sequencing of Streptomyces rochei FE-3-1 against Pyricularia oryzae. PLoS One 20(10): e0331386. https://doi.org/10.1371/journal.pone.0331386