Mineração genômica e prospecção de moléculas de Streptomyces spp. isolados de sedimentos de rios amazônicos

Abstract

Global agricultural production has been impacted by a wide range of diseases caused by phytopathogens, responsible for 42% of losses in crops, and the use of chemical pesticides remains the primary method used in agriculture for disease control. Therefore, the search for alternatives such as biological control becomes important, which presents the advantage of minimal or no residual toxicity and environmental contamination. Microorganisms producing antifungal molecules, such as bacteria of the genus Streptomyces, can be a natural resource used in biological control, as well as a source of new molecules applied to agriculture. The selection of microorganisms with antagonistic activity against phytopathogens, combined with in silico analyses of complete genomes by bioinformatics tools, has facilitated the characterization of potential biocontrol agents and the prospecting of natural products through the identification of genes involved in secondary metabolism pathways, known as biosynthetic gene clusters (BGCs). In this context, the objective of this work was to evaluate four Streptomyces isolates for their potential antagonistic activity against agricultural pathogens, cytotoxic activity and to prospect secondary metabolites through genomic mining. Phylogenomic analysis of isolates MPUR-31.3 and SOL 159 based on dDDH values revealed that both have dDDH lower than 70% and represent new species, while isolates MPUR-28.3 belong to the species Streptomyces glomeratus (dDDH 87.9%) and MPUR-51.7 Streptomyces albidoflavus (dDDH 88.2%). The in vitro antagonistic activity against 13 phytopathogens indicated that isolate MPUR-28.3 inhibited all phytopathogens, with the highest inhibition against Colletotrichum guaranicola INPA 2939 (85.2%). Isolates MPUR-31.3 and MPUR-51.7 inhibited 10 out of 13 phytopathogens, with the highest inhibition against Rhizoctonia sp. INPA 2943 (90.2%) and Colletotrichum scovillei INPA 2910 (65.9%), respectively. While SOL-159 inhibited only 5 out of the 13 evaluated phytopathogens, with the best inhibition against Colletotrichum guaranicola INPA 2939 (42%). Preliminary tests of cytotoxic activity of extracts obtained from the four Streptomyces isolates against human colon carcinoma (HCT116) and human hepatocellular carcinoma (HepG2) cell lines showed results below 75%, not considered promising. Genomic mining identified 39 BGCs in S. limosus (MPUR-28.3) and 45 BGCs in S. albidoflavus (MPUR-51.7), while 55 BGCs were identified in the new species lineage MPUR-31.3 and 24 BGCs in SOL-159. Based on the BGCs, it was possible to predict the biosynthesis of several biomolecules with broad activities, highlighting anticancer, antifungal, antibacterial, antioxidant activities, which are of industrial, agricultural, environmental, medical, veterinary, and food importance.