Pomegranate Rhizosphere Microbial Diversity Revealed by Metagenomics: Toward Organic Farming, Plant Growth Promotion and Biocontrol?

Food production must undergo systems change to meet the sustainable development goals (SDGs). For example, organic farming can be empowered by soil microorganisms with plant growth promotion (PGP) and biocontrol features. In this context, there have been limited studies on pomegranate. We investigated microbial diversity in rhizosphere of the pomegranate "Bhagwa" variety and its potential role in PGP and biocontrol. Both bulk and rhizosphere soil samples were analyzed for their physicochemical properties. Whole metagenome sequencing was conducted using the Illumina NovaSeq6000 platform. Surprisingly, we found that bulk and rhizosphere soil samples had comparable microbial diversity. Metagenome sequencing revealed the abundance of Streptomyces indicus, Bradyrhizobium kalamazoonesis, and Pseudomonas cellulosum in the rhizosphere that are reported here for the first time in agricultural literature. Pathway prediction analysis using KEGG (Kyoto Encyclopedia for Genes and Genomes) and COG (clusters of orthologous genes) databases identified metabolic pathways associated with biocontrol properties against pathogens. We confirmed the metagenome data in vitro, which demonstrated their PGP potential and antimicrobial properties. For instance, S. indicus produced high concentration of indole-3-acetic acid, a PGP phytohormone, that can stimulate plant growth. In addition, an antimicrobial susceptibility assay suggested that bacterial extracts displayed activity against Xanthomonas, a primary pathogen causing the pomegranate wilt disease. In conclusion, this study suggests that S. indicus, B. kalamazoonesis, and P. cellulosum can potentially be PGP and biocontrol agents that may contribute to increased crop productivity in pomegranate cultivation. These agents and their combinations warrant future research with an eye on SDGs and so as to enable and innovate organic farming and pomegranate agricultural practices.

Integrated transcriptomic, metabolomic, and functional analyses unravel the mechanism of bagging delaying fruit cracking of pomegranate (Punica granatum L.).

The economic impact of fruit cracking in pomegranate products is substantial. In this study, we present the inaugural comprehensive analysis of transcriptome and metabolome in the outermost pericarp of pomegranate fruit in bagging conditions. Our investigation revealed a notable upregulation of differentially expressed genes (DEGs) associated with the calcium signaling pathway (76.92%) and xyloglucan endotransglucosylase/hydrolase (XTH) genes (87.50%) in the fruit peel of non-cracking fruit under bagging. Metabolomic analysis revealed that multiple phenolics, flavonoids, and tannins were identified in pomegranate. Among these, calmodulin-like 23 (PgCML23) exhibited a significant correlation with triterpenoids and demonstrated a marked upregulation under bagging treatment. The transgenic tomatoes overexpressing PgCML23 exhibited significantly higher cellulose content and xyloglucan endotransglucosylase (XET) enzyme activity in the pericarp at the red ripening stage compared to the wild type. Conversely, water-soluble pectin content, polygalacturonase (PG), and ß-galactosidase (ß-GAL) enzyme activities were significantly lower in the transgenic tomatoes. Importantly, the heterologous expression of PgCML23 led to a substantial reduction in the fruit cracking rate in tomatoes. Our findings highlight the reduction of fruit cracking in bagging conditions through the manipulation of PgCML23 expression.