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

Black pepper (Piper nigrum 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 (Piper nigrum L.) are affected by foot rot-causing soil-borne oomycete pathogen Phytophthora capsici. 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 Piper colubrinum. The analysis showed compositional differences in the rhizobiome of two Piper species, which revealed higher diversity and the presence of more differentially abundant genera in P. colubrinum. Furthermore, P. colubrinum rhizobiome had a significantly higher abundance of known anti-oomycete genera, such as Pseudomonas, and a higher differential abundance of Janthinobacterium, Variovorax, and Comamonas, indicating their probable contribution to pathogen resistance. Predictive functional profiling in P. colubrinum 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 P. colubrinum rhizobiome. The culturable diversity of the resistant root endosphere, which harbors efficient biocontrol agents such as Pseudomonas, 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 Piper spp., suggesting its influence in recruiting bacterial communities that probably contribute to pathogen resistance.