Functional Genomic Characteristics of Marine Sponge-Associated Microbulbifer spongiae MI-GT

The genus Microbulbifer comprises a group of marine, gram-negative bacteria known for their remarkable ability to adapt to a variety of environments. Therefore, this study aimed to investigate the genetic diversity and metabolic characteristics of M. spongiae MI-GT and three Microbulbifer reference strains by genomic and comparative genomic analysis. Compared to free-living reference strains, the lower GC content, higher number of strain-specific genes, pseudogenes, unique paralogs, dispensable genes, and mobile gene elements (MGEs) such as genomic islands (GIs) and insertion sequence (IS) elements, while the least number of CAZymes, indicates that M. spongiae MI-GT may be a facultative sponge-symbiont. Comparative genomic analysis indicates that M. spongiae MI-GT possesses a plasmid and a higher number of strain-specific genes than Microbulbifer reference strains, showing that M. spongiae MI-GT may have acquired unique genes to adapt sponge-host environment. Moreover, there are differences in the functional distribution of genes belonging to different COG-classes in four Microbulbifer strains. COG-functional analysis reveals a lower number of strain-specific genes associated with metabolism, energy production, and motility in M. spongiae MI-GT compared to Microbulbifer reference strains, suggesting that sponge-associated lifestyle may force this bacterium to acquire nutrients from the sponge host and loss motility genes. Finally, we found that several proteins associated with oxidative stress response (sodC, katA, catA, bcp, trmH, cspA), osmotic stress response (dsbG, ampG, amiD_2, czcA, czcB, and corA), and tolerance to biotoxic metal proteins (dsbG, ampG, amiD_2, czcA, czcB, and corA) are absent in M. spongiae MI-GT but present in Microbulbifer reference strains, indicating that M. spongiae MI-GT live in a stable and less stress environment provided by the sponge host than free-living Microbulbifer strains. Our results suggest M. spongiae MI-GT exhibits gene characteristics related to its adaptation to the sponge host habitat, meanwhile reflecting its evolution towards a sponge-associated lifestyle.