Genome‐Driven Analysis Reveals the Biotechnological Potential of a Novel Paenibacillus sp. Isolated From Crude Oil

Abstract

Microbial biotechnology plays a critical role in addressing environmental challenges and promoting sustainability. Here, we report the complete genome sequencing of Paenibacillus sp. strain 210, previously isolated from Brazilian crude oil and known for its levan metabolism and biosurfactant production. With the sequenced genome, we employed bioinformatics tools for assembly and annotation, followed by comprehensive in silico analyses, including phylogenomics, biosynthetic gene cluster (BGC) identification, carbohydrate-active enzyme (CAZyme) profiling, and metabolic pathway reconstruction. The assembled 5.7 Mb genome harbors four prophage regions and 13 antimicrobial BGCs, including those encoding fusaricidin, paenicidin A, paenilan, paeninodin, and tridecaptin. Phylogenomic analysis combined with average nucleotide identity measurements indicates that this strain does not cluster with any recognized Paenibacillus species, supporting its designation as a potential new species. Notably, the identification of 259 CAZyme genes points to a strong capacity for degrading complex polysaccharides (e.g., cellulose, xylan, and pectin), positioning this bacterium as a promising candidate for biofuel production. Furthermore, the presence of complete metabolic pathways for several B vitamins highlights predicted metabolic autonomy supporting microbial interactions, reinforcing their usefulness in soil bioremediation by enhancing nutrient availability. In contrast, incomplete pathways for vitamins B2 and K2 indicate metabolic dependencies that may facilitate syntrophic interactions with other microorganisms. In silico structural analyses of selected hydrolytic enzymes (GH1, GH5, and GH11) reveal homology to functionally validated and crystallized proteins. Collectively, these findings highlight the genetic versatility of Paenibacillus sp. strain 210 and its potential for ecosystem restoration, biofuel production, plant growth promotion, and biocontrol.