Phylogenomic and secondary metabolism exploration of actinobacteria isolated from sediments of Laguna Ojo de Liebre, Mexico

Abstract

The Ojo de Liebre Lagoon Complex Biosphere Reserve, is an essential habitat for migratory species such as the gray whale and various birds. This unique hypersaline environment is underexplored concerning its microbial diversity, particularly regarding actinobacteria, which are among the most prolific sources of bioactive compounds found in marine ecosystems. 12 genomes of actinobacteria isolated from marine sediments of Laguna Ojo de Liebre (LOL) in B.C.S., Mexico. were analyzed. The genomes were classified into 3 genera; Actinomadura, Nocardiopsis and Micromonospora. Genomic mining revealed the presence of 314 Biosynthetic Gene Groups (BGCs) associated with secondary metabolism. The main BGCs categories found were terpenes, type I polyketides (T1PKS), non-ribosomal peptide synthetases (NRPS) and ribosomally synthesized post-translationally modified peptides (RiPPS). In addition, the patterns of Gene Cluster Families (GCFs) were observed, obtaining common categories among the genomes. Only 4 GCFs were assigned with production to known compounds (<1%). No GCFs were assigned to pathways responsible to produce known compounds, implying that the detected clusters could be responsible to produce several novel compounds. Also, the phylogenomic analysis suggests the presence of five potential new actinobacteria species belonging to the genera Micromonospora and Nocardiopsis. Overall, the genomes of actinobacteria isolated from LOL sediments showed unknown secondary metabolites, highlighting their biotechnological potential in the production of uncharacterized compounds.