Background: Root-knot nematode Meloidogyne incognita infects root systems of many crops resulting in huge decrease of crop production. Nematicidal microorganisms provides a safe and effective strategy to control M. incognita infection. In order to find microorganisms with high activity and new nematicidal metabolites, we collected the M. incognita infected tobacco rhizosphere soils (RNI) and non-infected tobacco rhizosphere soils (NS), and investigated their microbial community and network via metagenomics and metabolomics analysis.
Results: Microbial networks of RNI soils were very different from the NS soils. Many nematicidal microorganisms were enriched in the NS soils, including isolates of Aspergillus , Achromobacter , Acinetobacter , Bacillus , Burkholderia , Comamonas , Enterobacter , Lysobacter , Microbacterium , Paenibacillus , Pantoea , Pseudomonas , Streptomyces and Variovorax. Enzymes analysis showed these nematicidal microorganisms can produce proteases, chitinase and lipases. The functions genes belonging to pathways of secondary metabolites biosynthesis and carbohydrate transport and metabolism were overrepresented in the rhizophere microbiota of NS soils comparing with the RNI soils. 102 metabolites contents were significantly different between the RNI and NS rhizosphere microbiota. 35 metabolites were overrepresented in the NS soils comparing the RNI samples, including acetophenone. Acetophenone showed high nematicidal (LC 50 = 0.66 μg/ml) and avoidance activity against M. incognita . Bacillus amyloliquefaciens W1 could produce acetophenone. Liquid culture of W1 could kill 98.8% of M . incognita J2 juveniles after treatment for 24 h.
Conclusions: In general, the rhizophere microbiota of NS soils could produce volatile materials, multiple enzymes and secondary metabolites against nematode. Collectively, the microbiota of NS and RNI rhizophere differed significantly in microbial network structure, community composition, function genes and metabolites. Collectively, combination of multi-omics analysis and culture-dependent technology is powerful for finding nematicidal microorganisms and metabolites from soil.