Bioactivity-driven high throughput screening of microbiomes of medicinal plants for discovering new biological control agents

In a preliminary DNA−based microbiome studies, diverse culturable and unculturable bacterial taxa were identified in the roots and rhizospheres of different medicinal plants. In this report, culturable endophytic bacteria were isolated from four economically important medicinal plants Dodonaea viscosa , Fagonia indica , Caralluma tuberculata and Calendula arvensis . On the basis of initial antimicrobial screening, nine bacterial species in seven different genera, Streptomyces , Pseudomonas , Enterobacter , Bacillus , Pantoea , Pseudarthrobacter and Delftia , were selected for further analyses. These bacteria were identified using 16S rRNA gene sequencing. Antimicrobial assays of these selected bacteria revealed that Pseudomonas taiwanensis has strong anti− Phytophthora activity. Volatiles produced by P. taiwanensis inhibited growth of P. parasitica more than 80%. Ethyl acetate extracts of S. alboniger MOSEL−RD3, P. taiwanensis MOSEL−RD23, E. hormaechei MOSEL−FLS1 and B. tequilensis MOSEL−FLS3 and D. lacustris MB322 also displayed high potency against P. parasitica . All these bacterial extracts showed strong inhibition against P. parasitica at different concentrations (4−400 μg/mL). Bacterial extracts showing higher bioactivity (>80% inhibition in vitro) were selected for detached−leaf assay against P. parasitica on tobacco. In detached−leaf assay, application of 1% ethyl acetate bacterial extract of MOSEL−RD3, MOSEL−RD23, MOSEL−FLS1, MOSEL−FLS3 and MB322 reduced lesion sizes and lesion frequencies caused by P. parasitica by 68 to 81%. Over all P. taiwenensis MOSEL−RD23 showed positive activities in all the assays. Analyzing the potential of bacterial endophytes from unexplored flora and locations as biological control agents can potentially lead to the formulation of broad-spectrum biopesticides for sustainable production of crops.