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Key factors influencing rhizosphere competence, biocontrol activity of BCA and their effects on microbial communities in the rhizosphere
Project
Project code: JKI-EP-08-1116
Contract period: 01.04.2010
- 30.09.2013
Purpose of research: Experimental development
The use of antagonistic bacteria could be an environmentally friendly alternative to protect plants towards soil-borne pathogenes if the rhizosphere competence and biocontrol efficiency of the antagonists would be more predictable. In this project, we aim to test the hypothesis that the soil type, plant species, and the growing season (annual variation) influence the rhizosphere competence and bio-control efficiency of inoculant strains. Moreover, we hypothesize that the structural and functional diversity of the indigenous microbial community might be affected by the inoculation either directly of indirectly due to its interaction with the plant, which might result in changes of the root morphology and exudation patterns, with potential impact on the rhizosphere competence of the inoculants.
Key factors influencing fate and activity of bacterial inoculants and their effect on the indigenous microbial community in the rhizosphere
The use of antagonistic bacteria could be an environmentally friendly alternative to protect plants from soil-borne pathogens if the rhizosphere competence and biocontrol efficiency of the antagonists would be more predictable. In this project, we aimed to test the hypothesis that the soil type and plant species influence the rhizosphere competence and biocontrol efficiency of inoculant strains. Vice versa the structural diversity of the indigenous microbial community in the rhizosphere might be affected by the inoculation either directly or indirectly due to the interaction of the inoculant with the plant, with potential impact on the rhizosphere competence of the inoculants.
Total community DNA from the rhizosphere of the plants was extracted and analyzed by denaturing gradient gel electrophoresis (DGGE) as well as by pyrosequencing of 16S rRNA genes. DGGE revealed highly significant differences in bacterial and fungal community patterns between plant species and soil types, whereas the plant species had a more pronounced effect than the soil type. The application of the bacterial antagonist did not affect the indigenous microbial community. Amplicon pyrosequencing of 16S rRNA genes from rhizosphere samples from two plant species (lettuce and potato) revealed that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Acidobacteria were the dominant phyla. The Proteobacteria had the highest relative abundance in the three soil types. Within the Proteobacteria, the Alphaproteobacteria were the most prominent class. In the comparison between bulk soil and rhizosphere enriched taxa could be identified. The fast growing Proteobacteria were enriched in the rhizosphere compared with the bulk soil whereas the relative abundance of the other dominant groups decreased. The Firmicutes are enriched in one of the loamy, but decreased in the other soils. Significant differences between the soil types, especially the two loamy soils seem to enrich other OTUs than the sandy soil. OTUs belonging to Rhizobium, Sphingobium, Sphingomonas, Variovorax and Methylophilus significantly increased in abundance in the rhizosphere in all soils. Mesorhizobium increased only in the sandy soil, while Acidovorax and Burkholderia had increased abundance in the loamy soils at harvest. The OTU report also showed that the rhizospheres of different plant species contain several common OTUs, but also OTUs exclusively for one plant species. Whereas in the rhizosphere of potato for example Lysobacter sp., Streptomyces scabies, Sphingobium and Shinella were enriched, Acidovorax, Methylibium, Burkholderia, Azospirillum, and Massilia were enriched in the rhizosphere of lettuce. The application of the biocontrol strain did not cause a shift in the composition of the microbial community and confirmed the DGGE results. In conclusion, the plant species and the soil type had a strong influence on the bacterial community in the rhizosphere, but the application of the biocontrol strain had a minor effect. Hence, a negative ecological effect could not be detected. Biocontrol strains are promising biocontrol agents and can improve disease management.
Section overview
Subjects
- Crop Protection
- Soil science
Framework programme
Funding programme
Excutive institution
Institute for Epidemiology and Pathogen Diagnostics (JKI-EP)
