Effects of the Denitrification Inhibitor “Procyanidins” on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Growth, Experimental Design, and Harvesting
2.2. Measurement of Environmental Variables
2.3. DNA Extraction
2.4. Amplicon Libraries and Illumina Sequencing
2.5. Bioinformatic Analysis
2.6. Statistical Analyses
2.7. Functional Inference
2.8. Microbial Networks
3. Results
3.1. Soil Type: Predominant Factor Affecting Microbiome Richness and Diversity
3.2. Microbiome Composition Among Treatments
3.3. Core Microbiome and Differential Microbial Community Composition among Amended and Unamended Treatments
3.4. Relationship between Microbiome Diversity and Edaphic Variables
3.5. Prediction of Fungal and Prokaryotic Ecological Functions
3.6. Microbial Network Description
4. Discussion
4.1. Soil Type and Edaphic Variables as Driver of Bacterial and Fungal Diversity
4.2. Procyanidin Amendment Does Not Affect the Diversity and Potential Activity of the Plant Microbiome
4.3. Procyanidin Amendment Modifies Microbial Network
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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(A) | ||||||||||||
BSM | L0M | LPM | BSS | L0S | LPS | |||||||
Mean | SD | Mean | SD | Mean | SD | Mean | SD | Mean | SD | Mean | SD | |
Taxa Number | 1138.7 | 89.0 | 1162.3 | 38.0 | 1162.7 | 34.2 | 1066.3 | 80.7 | 1172.0 | 36.5 | 1183.7 | 24.1 |
Simpson | 1.0 | 0.0 | 1.0 | 0.0 | 1.0 | 0.0 | 1.0 | 0.0 | 1.0 | 0.0 | 1.0 | 0.0 |
Shannon | 6.2 | 0.2 | 6.3 | 0.0 | 6.2 | 0.0 | 5.5 | 0.8 | 6.2 | 0.0 | 6.2 | 0.1 |
Evenness | 0.4 | 0.1 | 0.5 | 0.0 | 0.4 | 0.0 | 0.3 | 0.2 | 0.4 | 0.0 | 0.4 | 0.1 |
Chao-1 | 1350.0 | 74.1 | 1374.7 | 28.7 | 1380.0 | 46.5 | 1357.7 | 25.8 | 1353.3 | 33.2 | 1371.3 | 29.6 |
(B) | ||||||||||||
BSM | L0M | LPM | BSS | L0S | LPS | |||||||
Mean | SD | Mean | SD | Mean | SD | Mean | SD | Mean | SD | Mean | SD | |
Taxa Number | 193.7 | 5.1 | 202.3 | 3.5 | 186.3 | 16.8 | 245.7 | 11.9 | 249.7 | 4.9 | 242.0 | 24.9 |
Simpson | 0.9 | 0.0 | 0.9 | 0.0 | 0.9 | 0.0 | 0.9 | 0.0 | 0.9 | 0.0 | 0.9 | 0.0 |
Shannon | 3.4 | 0.3 | 3.4 | 0.1 | 3.2 | 0.1 | 3.6 | 0.2 | 3.6 | 0.1 | 3.6 | 0.4 |
Evenness | 0.2 | 0.0 | 0.1 | 0.0 | 0.1 | 0.0 | 0.2 | 0.0 | 0.2 | 0.0 | 0.2 | 0.1 |
Chao-1 | 205.2 | 7.7 | 216.9 | 6.6 | 195.7 | 18.0 | 261.9 | 13.8 | 283.4 | 14.4 | 260.7 | 10.7 |
(A) Abundance of OTUs | ||||||||
Prokaryotic 16S rRNA Gene | Fungal ITS | |||||||
Df | F | p value | R2 | Df | F | p value | R2 | |
Effect | ||||||||
Plant | 1 | 1.40 | 0.184 | 0.048 | 1 | 1.41 | 0.138 | 0.039 |
Treatment | 1 | 0.52 | 0.875 | 0.018 | 1 | 0.96 | 0.357 | 0.027 |
Soil | 1 | 13.31 | 0.001 | 0.457 | 1 | 19.28 | 0.001 | 0.541 |
Effect Interactions | ||||||||
Plant*Soil | 1 | 1.32 | 0.231 | 0.045 | 1 | 1.15 | 0.294 | 0.032 |
Treatment*Soil | 1 | 0.54 | 0.853 | 0.019 | 1 | 0.84 | 0.460 | 0.235 |
Residuals | 12 | 0.412 | 12 | 0.337 | ||||
(B) Richness of OTUs | ||||||||
Prokaryotic 16S rRNA Gene | Fungal ITS | |||||||
Df | F | p value | R2 | Df | F | p value | R2 | |
Effect | ||||||||
Plant | 1 | 1.33 | 0.156 | 0.033 | 1 | 1.88 | 0.154 | 0.024 |
Treatment | 1 | 0.72 | 0.447 | 0.018 | 1 | 1.24 | 0.280 | 0.016 |
Soil | 1 | 24.56 | 0.001 | 0.609 | 1 | 62.60 | 0.001 | 0.790 |
Effect Interactions | ||||||||
Plant*Treatment*Soil | 1 | 0.87 | 0.445 | 0.043 | 1 | 0.78 | 0.506 | 0.020 |
Residuals | 12 | 0.198 | 12 | 0.151 |
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Hugoni, M.; Galland, W.; Lecomte, S.; Bruto, M.; Barakat, M.; Piola, F.; Achouak, W.; Haichar, F.e.Z. Effects of the Denitrification Inhibitor “Procyanidins” on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome. Microorganisms 2021, 9, 1406. https://doi.org/10.3390/microorganisms9071406
Hugoni M, Galland W, Lecomte S, Bruto M, Barakat M, Piola F, Achouak W, Haichar FeZ. Effects of the Denitrification Inhibitor “Procyanidins” on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome. Microorganisms. 2021; 9(7):1406. https://doi.org/10.3390/microorganisms9071406
Chicago/Turabian StyleHugoni, Mylène, William Galland, Solène Lecomte, Maxime Bruto, Mohamed Barakat, Florence Piola, Wafa Achouak, and Feth el Zahar Haichar. 2021. "Effects of the Denitrification Inhibitor “Procyanidins” on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome" Microorganisms 9, no. 7: 1406. https://doi.org/10.3390/microorganisms9071406