Pan-genome analysis of Morganella Morganii reveals niche-specific selection of functional traits: Friend or Foe?

Morganella morganii is a bacterium with open pangenomes, where genes move intra- and interspecies via horizontal gene transfer. Through pangenome analysis, the study maps three agriculture isolates; M. morganii with strong PGP activity, along with 78 publicly available genomes from clinical, food, wastewater, and animal sources. The analysis showed 23,829 gene clusters with only 8.52% core genes and discriminating distribution of 78.34% cloud genes across different niches. KEGG analysis showed 33, 12, and 38 genes related to nutrient solubilization in M. morganii isolates HM01, HM02, and HM04, respectively. Chemotaxis genes, crucial for stress response, were most abundant in HM04 (30), followed by HM01 (17) and HM02 (11). Additionally, numerous biosynthetic gene clusters encoding antibacterial and antifungal metabolites were identified. Clinical and wastewater isolates harboured a higher number of mobile genetic element (MGE) linked antimicrobial resistance (AMR) genes that confer resistance to 15 antibiotic classes. These AMR genes were predominantly plasmid-borne and found to transfer in M. morganii from clinical pathogens such as E. coli and A. baumannii . This study indicates that habitat pressure creates the scenario for selection of functional traits which enables the ecosystem specific survival of M. morganii . Together, the present investigation provides important insight into the genomic diversity and remarkable PGP potential of M. morganii strains for sustainable agriculture. The pangenome analysis proposes that detailed investigation is needed to confirm their efficacy as PGP bacterium and to distinguish them from pathogenic strains.