Molecular insights from integrated metabolome-transcriptome into endophyte Bacillus subtilis L1-21 surfactin against citrus Huanglongbing

Metabolites of plant and microbial origin have a great influence on plant-microbe interactions. Members from Bacillus subtilis are known to produce a plethora of metabolites that shape plant responses towards biotic and abiotic stresses. Similarly, endophyte B. subtilis L1–21 efficiently controls the Huanglongbing (HLB) causing pathogen: Candidatus Liberibacter asiaticus (CLas). However, the molecular mechanisms are highly elusive. Herein, our study highlights the critical role of endophyte L1–21 in planta-produced surfactin in its colonization in citrus plants and regulation of plant-microbe interactions by comparing three gene knockout mutants △srfAA-L1–21, △sfp-L1–21, and △pel-L1–21. All three mutants exhibited reduced pathogen control and colonization efficiency compared to wild-type (WT) L1–21, but knockout mutant deficient of surfactin △srfAA-L1–21 was significantly impaired in the abovementioned functions as compared to △sfp-L1–21 and △pel-L1–21. Further, △srfAA-L1–21 could not activate various metabolic pathways in citrus as WT-L1–21. Integrated metabolomic-transcriptomic analysis reveals that important secondary metabolites such as flavonoids, volatile organic compounds, and lignins were highly accumulated in citrus plants treated with WT-L1–21 as compared to △srfAA-L1–21, highlighting the role of surfactin as an elicitor of the defense system in citrus-HLB pathosystem. Interestingly, auxin-related metabolites and transcripts were also downregulated in △srfAA-L1–21 compared to WT-L1–21 showing that surfactin might also influence plant-microbe interactions through metabolic reprogramming. Further, higher enrichment of Bacilli with WT-L1–21 might corresponds to surfactin-mediated regulation of community-related behavior in Bacilli. To the best of our knowledge, this is the first study reporting the role of surfactin from Bacillus endophyte in metabolic reprogramming in citrus-HLB pathosystem and mounting defense response against CLas pathogen.