Bacterial wilt disease caused by Ralstonia solanacearum leads to decrease of crops yield. Investigation of cultivable bacteria diversity provides more microbial species for screening antagonistic bacteria. In the present study, a variety of cultivation methods were used to investigate the diversity of cultivable bacteria alive in tobacco field. A total of 441 bacterial strains were obtained that belonged to four phyla, 49 genera and 146 species. Actinobacteria and Proteobacteria were the dominant phyla. Agrobacterium, Arthrobacter, Bacillus, Klebsiella, Paenarthrobacter, Pseudomonas and Pseudarthrobacter were the dominant genera. Some rare genera were discovered including Bosea, Cedecea, Delftia and Dyella. Diversity, species and abundances of bacteria altered under different cultivation conditions. One hundred three bacterial strains showed plant growthpromoting attributes. Twenty Bacillus strains showed high antibacterial activity against R. solanacearum. In field experiments, individual strain and consortia of Bacillus subtilis, B. siamensis and B. vallismortis effectively inhibited bacterial wilt. The core genes that controlled synthesis of secondary metabolites were knocked out in B. vallismortis SSB-10. Difficidin, which was synthesized by dif operon and controlled by sfp gene, was the antibacterial substance produced by SSB-10. Difficidin destroyed cell wall and cell membrane of R. solanacearum and inhibited its motility, production of extracellular polysaccharides and cellulase activity.

BackgroundRoot-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 more 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. ResultsMicrobial networks of RNI soils were very different from the NS soils. Many nematicidal microorganisms were enriched in the NS soils, including some isolates such as 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 . A isolate of Bacillus amyloliquefaciens W1 with production of acetophenone can kill 98.8% of M . incognita . ConclusionsIn 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.

Background: Meloidogyne incognita infestation has led to huge economic loss worldwide. Nematicidal microorganisms provide an effective strategy to control M. incognita . In order to find microorganisms and new metabolites with high nematicidal activity, we collected M. incognita - infested tobacco rhizosphere soils and non-infested rhizosphere soils, and investigated functional genes, microbial community and network, and metabolites via metagenomics and metabolomics analyses. Results: Rhizosphere microbial composition, function, network and metabolites were altered accompanying with M . incognita infestation. Abundances of nematicidal microorganisms, metabolites, antibiotics and extracellular enzymes’ genes in the non-infested rhizosphere microbiota were higher than those in M. incognita -infested rhizosphere microbiota. Abundances of functions genes involved in secondary metabolites biosynthesis and carbohydrate transport and metabolism in the non-infested rhizosphere microbiota were higher than M. incognita -infested rhizosphere microbiota. Contents of 102 metabolites were different in the two rhizosphere microbiota. Contents of 35 metabolites (acetophenone, indole-3-acetic acid, etc.) in the non-infested rhizosphere microbiota were higher than those in M . incognita -infested rhizosphere microbiota. Acetophenone showed high nematicidal (LC 50 = 0.66 μg/ml) and repellent activities against M. incognita . Co-occurrence network analyses found Bacillus showed a stronger positive correlation with acetophenone. Nematicidal microorganisms were isolated from soils, and one isolate of B . amyloliquefaciens W1 produced acetophenone. Exposing J2 larvae of M. incognita to liquid culture filtrate of W1 resulted in a mortality rate of 98.8% after 24 h. Other isolates such as Aspergillus , Achromobacter , Acinetobacter , Bacillus , Burkholderia , Comamonas , Enterobacter , Lysobacter , Microbacterium , Paenibacillus , Pantoea , Pseudomonas , Streptomyces and Variovorax produced extracellular nematicidal enzymes. Conclusions: M eloidogyne incognita -infested rhizophere microbiota differed in microbial community composition, network structure, function genes and metabolites contents from the non-infested rhizosphere microbiota. Abundances of nematicidal microorganisms and metabolites, and genes involved in secondary metabolites biosynthesis and carbohydrate metabolism in the non-infested rhizosphere microbiota were higher than those in M . incognita -infested rhizosphere microbiota. Network complexity in M . incognita -infested rhizosphere microbiota was lower than that in non-infested rhizosphere microbiota. Keystone microorganisms were also different between these two networks. Acetophenone was identified as a new nematicidal compound with high activity to kill and repel M. incognita , and B. amyloliquefacens W1 isolated from non-infested soil produced acetophenone against M. incognita .

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.