Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness
Data files
May 09, 2024 version files 426.53 KB
-
all_data_08_05_2024.xlsx
422.85 KB
-
README.md
3.68 KB
Abstract
Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol, and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency, and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomatoes. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.
https://doi.org/10.5061/dryad.dz08kps40
Description of the data and file structure
Datasets included:
Figure 1
- In the row of “trt”, “0” represents no phage cocktail application, “1” represents applied once (day 2), “2” represents applied two times (days 2 and 9), “3” represents applied three times (days 2, 9 and 16) after pathogen inoculation. "trt" means treatment.
- In the row of “rep”, “1” represents the first replicate, “2” represents the second replicate, “3” represents the third replicate, “4” represents the fourth replicate.
- “index” is the mean disease incidence of 6 plants within each replicate.
- “audpc” is the area under the disease index curve, calculated as the integral.
Figure 2
- The alpha diversity metrics, Species Richness, and Simpson Index were calculated using the 'diversity' function within the R package 'vegan', considering all bacterial ASVs.
Figure 3
- We conducted correlation-based indicator analysis using the 'multipatt' function in the R package 'indispecies'. This analysis determined the point-biserial general correlation coefficient (r.g.) for ASVs positively associated with phage cocktail application frequency, with statistical significance determined after 999 permutations and a cutoff line of p < 0.05.
- For the co-occurrence network analysis, we included the most common genera with an appearance frequency of ≥50%. We calculated pairwise Spearman correlation matrices using the 'Hmisc' package and adjusted p-values using the 'fdrtool' package. Only correlations with absolute Spearman R-values > 0.90 and adjusted p-values < 0.05 were retained in the final co-occurrence network.
- To identify groups of taxa responding similarly to phage cocktail application frequency, we utilized the 'cluster_fast_greedy' function from the 'igraph' package, applying the Newman algorithm.
- “s.0” represents no phage cocktail application, “s.1” represents applied once, “s.2” represents applied two times, “s.3” represents applied three times.
- In the row of “trt”, 'I' signifies genera present in all phage cocktail treatments. 'II' signifies genera present in treatments with twice and thrice phage cocktail applications. 'III' signifies genera present in treatments with once and twice phage cocktail applications. 'IV' signifies genera present only in treatments with once phage cocktail application. 'V' signifies genera present only in treatments with twice phage cocktail application. 'VI' signifies genera present only in treatments with thrice phage cocktail application. 'O' signifies genera present only in the treatment without phage cocktail application.
Figure 4
- Displayed here are the relative abundances of the top 8 phyla and the top 8 genera belonging to the Actinobacteriota phylum. We conducted a Random Forest analysis to identify key predictor taxa for pathogen suppression.
Figure 5
- The suppressiveness of 10 Actinobacterial isolates for the growth of R. solanacearum based on the supernatant assay. “ie” represents the inhibition effect on R. solanacearum.
- “Control”: pathogen only, “P”: phage alone, “N”: Nocardioides alone, “S”: Streptomyces alone, “PN”: phage and Nocardioides, and “PS”: phage and Streptomyces.
Sharing/Access information
The raw sequencing reads were deposited into the NCBI Sequence Read Archive (SRA) database (Accession Number: PRJNA819579)
Code/Software
NA