Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Design and Sample Collection
2.2. DNA Extraction, Amplification, and Sequencing
2.3. Bioinformatic Processing
2.4. Statistical Analyses
3. Results
3.1. Bacterial and Fungal Community Composition and Richness Strongly Associate with Plant Compartment
3.2. Rootstock Genotype and Irrigation have Subtle Effects on Community Patterns
3.3. Rootstock and Irrigation Influence Microbiota of Winemaking Relevance
3.4. Machine Learning and Differential Abundance Analyses
4. Discussion
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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Bacterial Unweighted UniFrac | Fungal Bray–Curtis | |||||
---|---|---|---|---|---|---|
Factor | Pseudo-F | p-Value | R2 | Pseudo-F | p-Value | R2 |
Rootstock (R) | F3176 = 1.124 | 0.252 | 0.011 | F3173 = 2.178 | 0.013 | 0.016 |
Compartment (C) | F3176 = 40.720 | <0.001 | 0.407 | F3173 = 74.320 | <0.001 | 0.550 |
Irrigation (I) | F2177 = 1.107 | 0.273 | 0.007 | F2174 = 1.203 | 0.247 | 0.006 |
Block | F2177 = 1.304 | 0.147 | 0.009 | F2174 = 1.402 | 0.151 | 0.007 |
R × C | F9170 = 1.057 | 0.326 | 0.032 | F9167 = 1.459 | 0.040 | 0.032 |
R × I | F6173 = 1.058 | 0.324 | 0.021 | F6170 = 1.146 | 0.261 | 0.017 |
C × I | F6163 = 1.009 | 0.417 | 0.020 | F6170 = 0.936 | 0.526 | 0.014 |
C × R × I | F18,161 = 0.989 | 0.501 | 0.059 | F18,158 = 0.998 | 0.473 | 0.044 |
Residual | 0.433 | 0.313 |
Acetobacterales | Saccharomycetes | |||
---|---|---|---|---|
Factor | F Value | p-Value | F Value | p-Value |
Rootstock (R) | F3128 = 8.329 | <0.001 | F3124 = 4.337 | 0.006 |
Compartment (C) | F3128 = 0.002 | 1.000 | F3124 = 0.003 | 1.000 |
Irrigation (I) | F2129 = 0.169 | 0.844 | F2125 = 0.458 | 0.633 |
Block | F2129 = 0.347 | 0.708 | F2125 = 0.311 | 0.733 |
R × C | F9122 = 2.111 | 0.033 | F9118 = 0.969 | 0.469 |
R × I | F6125 = 9.855 | <0.001 | F6121 = 3.139 | 0.007 |
C × I | F6125 = 0.046 | 1.000 | F6121 = 0.114 | 0.995 |
C × R × I | F18,113 = 2.454 | 0.002 | F18,109 = 0.787 | 0.713 |
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Swift, J.F.; Hall, M.E.; Harris, Z.N.; Kwasniewski, M.T.; Miller, A.J. Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems. Microorganisms 2021, 9, 92. https://doi.org/10.3390/microorganisms9010092
Swift JF, Hall ME, Harris ZN, Kwasniewski MT, Miller AJ. Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems. Microorganisms. 2021; 9(1):92. https://doi.org/10.3390/microorganisms9010092
Chicago/Turabian StyleSwift, Joel F., Megan E. Hall, Zachary N. Harris, Misha T. Kwasniewski, and Allison J. Miller. 2021. "Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems" Microorganisms 9, no. 1: 92. https://doi.org/10.3390/microorganisms9010092