Genotype-specificity in putative competitive endophytes modulated by root exudation of rice

Abstract

The putative competitive endophytic bacteria with plant-growth-promoting attributes could be potential bio inputs to enhance agricultural sustainability. These special rhizosphere colonizing bacteria possess distinct strategies to enter and colonize the host plant asymptomatically and offer several plant growth-promoting benefits. However, the molecular interaction between the endophyte and host plant remains unclear in many crop spheres. In this study, we categorize putative endophytes in rice into two groups—common endophytes and genotype-specific endophytes—based on their ability to colonize alternative hosts. The putative competitive endophytes of rice landrace Norungan and high-yielding cultivar Co51 were cross-inoculated with each other under gnotobiotic conditions and attempted to re-isolate from the inoculated plants. Two Norungan endophytes (Priestia endophytica NE14 and NE21) and one Co51-endophyte (Peribacillus endoradicis CE10) could not colonize the internal tissues of the alternate hosts, and they were considered as genotype-specific endophytes. In contrast, the rest of the strains could colonize both genotypes (common endophytes). The bait trap assay with flow cytometry revealed that the Norungan root exudate significantly enhanced the chemotactic movement of NE14 and NE21 compared to Co51-endophyte (CE10) and common endophytes (NE09 and CE07). Likewise, the Co51-root exudate triggered high levels of chemotaxis of CE10 but not the others. The root exudates did not alter the growth and biofilm-producing capability of genotype-specific and common endophytes. The cell wall degrading enzyme, pectinase of genotype-specific endophytes (NE14 and NE21), had positively enhanced due to Norungan root exudate but not with Co51 exudate. When the genotype-specific endophytes were inoculated to alternate host, a strain-level difference was observed in the induction of rice defense enzymes. NE14 inoculation in Co51 rice had high levels of peroxidase, polyphenol oxidase, phenylalanine ammonia lyase, and glutathione reductase; NE21 induced high levels of glutathione reductase and peroxidase alone in Co51. Likewise, CE10 triggered relatively high levels of catalase, glutathione reductase, peroxidase, and polyphenol oxidase in Norungan rice. No apparent difference between the two rice genotypes in defense enzymes’ levels was observed due to common endophytes (NE09 and CE07). These results authenticate the occurrence of genotype-specific putative competitive endophytes in rice, and exploring them for crop growth and yield would be a better choice for rice sustainability.