Freshwater Actinobacteria from sediments of the deep and ancient Lake Baikal (Russia) and their genetic potential as producers of secondary metabolites

Abstract

Actinobacteria from terrestrial and marine environments produce a variety of natural products that mediate interand intraspecies interactions. In contrast, the potential of freshwater Actinobacteria for secondary metabolite production remains underexplored. Large lakes with a long evolutionary history might contain microflora subjected to unique environmental conditions that favor the evolution of unique metabolic capabilities. One such lake is Lake Baikal (Russia), the deepest lake on earth as well as one of the oldest. In this study, we investigated the genetically encoded secondary metabolic potential of 24 Actinobacteria strains isolated from Lake Baikal sediments. PCR-based screening for genes encoding type I and type II polyketide synthases (PKSs), nonribosomal peptide synthetases (NRPSs), and halogenases confirmed that all strains possessed at least 1 of these biosynthetic genes. Both PKSs and NRPSs were widely distributed, while halogenase-encoding genes were not detected. Phylogenetic comparison of type I PKS ketosynthase (KS) domain sequences between freshwater isolates and marine and terrestrial strains supported overlap between KSs from these 3 groups. Evaluation of antibiotic activity for chemical extracts from all isolates revealed that 75% produced metabolites inhibitory toward model bacteria and/or fungi. To our knowledge, this study is among the first evaluations of the genetically encoded secondary metabolic capabilities of freshwater sediment Actinobacteria. Our findings highlight the similarities and differences between freshwater and marine Actinobacteria secondary metabolism, suggesting the potential of freshwater Actinobacteria for the production of natural products that may play roles as mediators of interactions between organisms in freshwater habitats.