Genomic exploration of Serratia rubidaea MJ24 uncovers diverse biosynthetic capacity and agricultural relevance.

The genus Serratia encompasses metabolically versatile and ecologically significant bacteria, yet the genomic and biosynthetic potential of Serratia rubidaea remains largely unexplored compared to the well-studied S. marcescens. In this study, we present a comprehensive genomic characterization of S. rubidaea MJ24, a pigment-producing strain isolated from the Western Ghats, India. The 4.98 Mb genome (GC content: 59.22%) assembled into 25 contigs exhibits 100% completeness and minimal contamination, indicating high assembly quality. Functional annotation revealed 4,692 (4,569 Protein coding) coding sequences enriched in metabolism-related genes, stress tolerance, and secondary metabolite biosynthesis. Genome mining using AntiSMASH identified twelve biosynthetic gene clusters (BGCs), including those responsible for prodigiosin, pyrrolnitrin, aerobactin, and enterobactin biosynthesis, which were experimentally confirmed by LC-QTOF-MS, along with two of moderate similarity and six other BGCs of unassigned function. Phylogenomic and ANI analyses confirmed its placement within the S. rubidaea clade. The strain harbors an array of plant growth-promoting traits, including phytohormone biosynthesis (IAA, cytokinins), siderophore production, stress control, and heavy metal resistance genes. Together, the BGCs and plant growth-promoting traits underscore its potential as a biocontrol agent and biofertilizer. Collectively, the findings reveal S. rubidaea MJ24 as a metabolically versatile bacterium with a rich secondary metabolite repertoire and significant agricultural and biotechnological promise.

© 2026. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.