An antibiotic produced by Pseudomonas fluorescens CFBP2392 with antifungal activity against Rhizoctonia solani

Abstract

<i>Pseudomonas fluorescens</i> CFBP2392 has been recognized as a potential biocontrol agent due to its ability to suppress damping-off and root rot disease. This isolate has antibacterial activity <i>in vitro</i> as many other strains from the <i>Pseudomonas fluorescens</i> complex. In this work, the antibacterial and antifungal activity of the strain were explored. Dual culture assays evidenced the antifungal activity of the strain against different phytopathogens: <i>Alternaria</i> sp., <i>Pythium ultimun</i>, <i>Fusarium oxysporum</i>, and <i>Rhizoctonia solani</i>. Purification of an antifungal fraction was performed by preparative HPLC from the chemical extraction of growth media. The fraction showed altered <i>R. solani</i> growth and ultrastructure. Transmission electron microscopy revealed the purified compound <i>induced</i> hypertrophied mitochondria, membranous vesicles, and a higher number of vacuoles in <i>R. salani</i> cytoplasm. In addition, co-cultivation of <i>P. fluorescens</i> CFBP2392 with <i>R. solani</i> resulted in an enlarged and deformed cell wall. To gain genomic insights on this inhibition, the complete genome of <i>P. fluorescens</i> CFBP2392 was obtained with Oxford Nanopore technology. Different biosynthetic gene clusters (BGCs) involved in specialized metabolites production including a lokisin-like and a koreenceine-like cluster were identified. In accordance with the putative BGCs identified, sequence phylogeny analysis of the MacB transporter in the lokisin-like cluster further supports the similarity with other transporters from the amphisin family. Our results give insights into the cellular effects of the purified microbial metabolite in <i>R. solani</i> ultrastructure and provide a genomic background to further explore the specialized metabolite potential.