Next-generation sequencing-based comparative mapping and culture-based screening of bacterial rhizobiome in -resistant and susceptible species.

Black pepper ( L.), a highly valued spice crop, is economically significant as one of the most widely traded spices in the world. The global yield and quality of black pepper ( L.) are affected by foot rot-causing soil-borne oomycete pathogen . To gain initial insights toward developing an approach that utilizes microbial genetic resources for controlling foot rot disease in black pepper, we mapped the rhizobiome communities in susceptible Piper nigrum L. and wild-resistant . The analysis showed compositional differences in the rhizobiome of two species, which revealed higher diversity and the presence of more differentially abundant genera in . Furthermore, rhizobiome had a significantly higher abundance of known anti-oomycete genera, such as , and a higher differential abundance of , , and , indicating their probable contribution to pathogen resistance. Predictive functional profiling in rhizobiome showed highly enriched functional gene orthologs (KOs), particularly chemotaxis proteins, osmoprotectants, and other transport systems that aid in pathogen resistance. Similarly, pathways such as phenylpropanoid biosynthesis and other antimicrobial synthesis were enriched in rhizobiome. The culturable diversity of the resistant root endosphere, which harbors efficient biocontrol agents such as , strengthens the possible role of root microbiome in conferring resistance against soil-borne pathogens. Our results depicted a clear distinction in the rhizobiome architecture of resistant and susceptible spp., suggesting its influence in recruiting bacterial communities that probably contribute to pathogen resistance.