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Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants.

Schmidt R, Köberl M, Mostafa A, Ramadan EM, Monschein M, Jensen KB, Bauer R, Berg G - Front Microbiol (2014)

Bottom Line: Plant-associated bacteria fulfill important functions for plant growth and health.In contrast, a pyrosequencing analysis of the 16S rRNA gene libraries revealed significant differences in the community structure of bacteria between the treatments.This indicates a possible new function of bacterial inoculants: to interact with the plant microbiome as well as to influence the plant metabolome.

View Article: PubMed Central - PubMed

Affiliation: Institute for Environmental Biotechnology, Graz University of Technology Graz, Austria.

ABSTRACT
Plant-associated bacteria fulfill important functions for plant growth and health. However, our knowledge about the impact of bacterial treatments on the host's microbiome and physiology is limited. The present study was conducted to assess the impact of bacterial inoculants on the microbiome of chamomile plants Chamomilla recutita (L.) Rauschert grown in a field under organic management in Egypt. Chamomile seedlings were inoculated with three indigenous Gram-positive strains (Streptomyces subrutilus Wbn2-11, Bacillus subtilis Co1-6, Paenibacillus polymyxa Mc5Re-14) from Egypt and three European Gram-negative strains (Pseudomonas fluorescens L13-6-12, Stenotrophomonas rhizophila P69, Serratia plymuthica 3Re4-18) already known for their beneficial plant-microbe interaction. Molecular fingerprints of 16S rRNA gene as well as real-time PCR analyses did not show statistically significant differences for all applied bacterial antagonists compared to the control. In contrast, a pyrosequencing analysis of the 16S rRNA gene libraries revealed significant differences in the community structure of bacteria between the treatments. These differences could be clearly shown by a shift within the community structure and corresponding beta-diversity indices. Moreover, B. subtilis Co1-6 and P. polymyxa Mc5Re-14 showed an enhancement of the bioactive secondary metabolite apigenin-7-O-glucoside. This indicates a possible new function of bacterial inoculants: to interact with the plant microbiome as well as to influence the plant metabolome.

No MeSH data available.


Related in: MedlinePlus

Comparison of the microbial communities of Chamomilla recutita (L.) Rauschert rhizosphere by jackknifed principal coordinate analysis. The 2D-plot illustrates the compositional similarity between samples based on weighted UniFrac. The positions of the points are the averages for the jackknifed replicates generated by QIIME and are shown with ellipses representing the interquartile range (IQR) in each axis. Larger ellipses represent more diverse communities. Colors correspond to the different treatments.
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Figure 5: Comparison of the microbial communities of Chamomilla recutita (L.) Rauschert rhizosphere by jackknifed principal coordinate analysis. The 2D-plot illustrates the compositional similarity between samples based on weighted UniFrac. The positions of the points are the averages for the jackknifed replicates generated by QIIME and are shown with ellipses representing the interquartile range (IQR) in each axis. Larger ellipses represent more diverse communities. Colors correspond to the different treatments.

Mentions: To deeply investigate the diversity and the composition of the bacterial communities associated with C. recutita (L.) Rauschert, a pyrosequencing approach was employed. Rarefaction analysis was performed to an extent of diversity coverage (Figure S1). Assessment of richness revealed that pyrosequencing effort attained 35.8-46.5% of estimated richness at a genetic similarity of 97% (Table 1). At the genetic similarity levels of 95% and 80%, amplicon libraries covered 41.7–49.7% and 56.6–88.8% of estimated richness, respectively (Table 1). Taxonomic composition of bacterial communities was similar at phylum level, comprising Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as the most dominant phyla (Figure 4). However, the phylum Verrucomicrobia was only present in the sample from the treatment with S. rhizophila P69, considering only taxa covering more than 1% of quality sequences. Acidobacteria were observed in samples treated with B. subtilis Co1-6, S. rhizophila P69, and S. plymuthica 3Re4-18. At genus level, Rhizobium (phylum Proteobacteria), Pseudoxanthomonas (phylum Proteobacteria), Pseudomonas (phylum Proteobacteria), Flavobacterium (phylum Bacteroidetes), and Arthrobacter (phylum Actinobacteria) represented the most abundant genera, showing a different composition according to the different treatments. Alpha-diversity of the amplicon libraries was characterized by Shannon index (H') for 97, 95, and 80% similarity levels. Slight differences between treatments where revealed by the comparison of the index values (Table 1). Jackknifed weighted UniFrac two-dimensional (Figure 5) and three-dimensional (Figure 6) principal coordinates analysis (PCoA) biplots were constructed in order to visualize relationships among samples based on differences in taxonomic diversity. Weighted biplots showed that the samples were clearly separated, implying a difference in bacterial community composition according to the treatments.


Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants.

Schmidt R, Köberl M, Mostafa A, Ramadan EM, Monschein M, Jensen KB, Bauer R, Berg G - Front Microbiol (2014)

Comparison of the microbial communities of Chamomilla recutita (L.) Rauschert rhizosphere by jackknifed principal coordinate analysis. The 2D-plot illustrates the compositional similarity between samples based on weighted UniFrac. The positions of the points are the averages for the jackknifed replicates generated by QIIME and are shown with ellipses representing the interquartile range (IQR) in each axis. Larger ellipses represent more diverse communities. Colors correspond to the different treatments.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928675&req=5

Figure 5: Comparison of the microbial communities of Chamomilla recutita (L.) Rauschert rhizosphere by jackknifed principal coordinate analysis. The 2D-plot illustrates the compositional similarity between samples based on weighted UniFrac. The positions of the points are the averages for the jackknifed replicates generated by QIIME and are shown with ellipses representing the interquartile range (IQR) in each axis. Larger ellipses represent more diverse communities. Colors correspond to the different treatments.
Mentions: To deeply investigate the diversity and the composition of the bacterial communities associated with C. recutita (L.) Rauschert, a pyrosequencing approach was employed. Rarefaction analysis was performed to an extent of diversity coverage (Figure S1). Assessment of richness revealed that pyrosequencing effort attained 35.8-46.5% of estimated richness at a genetic similarity of 97% (Table 1). At the genetic similarity levels of 95% and 80%, amplicon libraries covered 41.7–49.7% and 56.6–88.8% of estimated richness, respectively (Table 1). Taxonomic composition of bacterial communities was similar at phylum level, comprising Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as the most dominant phyla (Figure 4). However, the phylum Verrucomicrobia was only present in the sample from the treatment with S. rhizophila P69, considering only taxa covering more than 1% of quality sequences. Acidobacteria were observed in samples treated with B. subtilis Co1-6, S. rhizophila P69, and S. plymuthica 3Re4-18. At genus level, Rhizobium (phylum Proteobacteria), Pseudoxanthomonas (phylum Proteobacteria), Pseudomonas (phylum Proteobacteria), Flavobacterium (phylum Bacteroidetes), and Arthrobacter (phylum Actinobacteria) represented the most abundant genera, showing a different composition according to the different treatments. Alpha-diversity of the amplicon libraries was characterized by Shannon index (H') for 97, 95, and 80% similarity levels. Slight differences between treatments where revealed by the comparison of the index values (Table 1). Jackknifed weighted UniFrac two-dimensional (Figure 5) and three-dimensional (Figure 6) principal coordinates analysis (PCoA) biplots were constructed in order to visualize relationships among samples based on differences in taxonomic diversity. Weighted biplots showed that the samples were clearly separated, implying a difference in bacterial community composition according to the treatments.

Bottom Line: Plant-associated bacteria fulfill important functions for plant growth and health.In contrast, a pyrosequencing analysis of the 16S rRNA gene libraries revealed significant differences in the community structure of bacteria between the treatments.This indicates a possible new function of bacterial inoculants: to interact with the plant microbiome as well as to influence the plant metabolome.

View Article: PubMed Central - PubMed

Affiliation: Institute for Environmental Biotechnology, Graz University of Technology Graz, Austria.

ABSTRACT
Plant-associated bacteria fulfill important functions for plant growth and health. However, our knowledge about the impact of bacterial treatments on the host's microbiome and physiology is limited. The present study was conducted to assess the impact of bacterial inoculants on the microbiome of chamomile plants Chamomilla recutita (L.) Rauschert grown in a field under organic management in Egypt. Chamomile seedlings were inoculated with three indigenous Gram-positive strains (Streptomyces subrutilus Wbn2-11, Bacillus subtilis Co1-6, Paenibacillus polymyxa Mc5Re-14) from Egypt and three European Gram-negative strains (Pseudomonas fluorescens L13-6-12, Stenotrophomonas rhizophila P69, Serratia plymuthica 3Re4-18) already known for their beneficial plant-microbe interaction. Molecular fingerprints of 16S rRNA gene as well as real-time PCR analyses did not show statistically significant differences for all applied bacterial antagonists compared to the control. In contrast, a pyrosequencing analysis of the 16S rRNA gene libraries revealed significant differences in the community structure of bacteria between the treatments. These differences could be clearly shown by a shift within the community structure and corresponding beta-diversity indices. Moreover, B. subtilis Co1-6 and P. polymyxa Mc5Re-14 showed an enhancement of the bioactive secondary metabolite apigenin-7-O-glucoside. This indicates a possible new function of bacterial inoculants: to interact with the plant microbiome as well as to influence the plant metabolome.

No MeSH data available.


Related in: MedlinePlus