A Comparative Analysis of Microbial Communities in the Rhizosphere Soil and Plant Roots of Healthy and Diseased Yuanyang Nanqi (Panax vietnamensis) with Root Rot
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling Location and Sample Collection
2.2. Genome DNA Extraction
2.3. PCR Amplification
2.4. Illumina MiSeq Sequencing
2.5. Statistical Analysis
2.6. Isolation Microorganisms in the Roots of Diseased Plants
2.7. Molecular Biological Identification of Fungi Strains
2.8. Pathogenicity Determination and Reisolation of Pathogens
2.9. Construction of Phylogenetic Trees
3. Results
3.1. Quality Analysis of Sequencing Results
3.2. Microbial Diversity of Rhizosphere Soil and Roots in Yuanyang Nanqi OTU Levels
3.3. Bacterial and Fungal α-Diversity
3.4. Relative Abundance of Bacterial and Fungal Genera
3.5. β-Diversity Analysis
3.6. Functional Prediction of Fungal Communities
3.7. Molecular Identification Results of Microorganisms Separated via the Culture Method
3.8. Anti-Inoculation Test Results and Phylogenetic Tree of Pathogenic Fungi
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Sample Type | Plant Status | Latitude | Longitude | Number | Group |
---|---|---|---|---|---|
Rhizosphere soil | Healthy | 23°18′04″ N | 102°71′94″ E | HHTJ-1 | HHTJ |
Rhizosphere soil | Healthy | 23°18′04″ N | 102°71′94″ E | HHTJ-2 | HHTJ |
Rhizosphere soil | Healthy | 23°18′04″ N | 102°71′94″ E | HHTJ-3 | HHTJ |
Rhizosphere soil | Disease | 23°18′04″ N | 102°71′94″ E | HHTB-1 | HHTB |
Rhizosphere soil | Disease | 23°18′04″ N | 102°71′94″ E | HHTB-2 | HHTB |
Rhizosphere soil | Disease | 23°18′04″ N | 102°71′94″ E | HHTB-3 | HHTB |
Rhizosphere soil | Healthy | 23°12′72″ N | 102°73′25″ E | YYTJ-1 | YYTJ |
Rhizosphere soil | Healthy | 23°12′72″ N | 102°73′25″ E | YYTJ-2 | YYTJ |
Rhizosphere soil | Healthy | 23°12′72″ N | 102°73′25″ E | YYTJ-3 | YYTJ |
Rhizosphere soil | Disease | 23°12′72″ N | 102°73′25″ E | YYTB-1 | YYTB |
Rhizosphere soil | Disease | 23°12′72″ N | 102°73′25″ E | YYTB-2 | YYTB |
Rhizosphere soil | Disease | 23°12′72″ N | 102°73′25″ E | YYTB-3 | YYTB |
Rhizosphere soil | Healthy | 23°41′43″ N | 103°14′58″ E | GJTJ-1 | GJTJ |
Rhizosphere soil | Healthy | 23°41′43″ N | 103°14′58″ E | GJTJ-2 | GJTJ |
Rhizosphere soil | Healthy | 23°41′43″ N | 103°14′58″ E | GJTJ-3 | GJTJ |
Rhizosphere soil | Disease | 23°41′43″ N | 103°14′58″ E | GJTB-1 | GJTB |
Rhizosphere soil | Disease | 23°41′43″ N | 103°14′58″ E | GJTB-2 | GJTB |
Rhizosphere soil | Disease | 23°41′43″ N | 103°14′58″ E | GJTB-3 | GJTB |
Plant Root | Healthy | 23°18′04″ N | 102°71′94″ E | HHGJ-1 | HHGJ |
Plant Root | Healthy | 23°18′04″ N | 102°71′94″ E | HHGJ-2 | HHGJ |
Plant Root | Healthy | 23°18′04″ N | 102°71′94″ E | HHGJ-3 | HHGJ |
Plant Root | Disease | 23°18′04″ N | 102°71′94″ E | HHGB-1 | HHGB |
Plant Root | Disease | 23°18′04″ N | 102°71′94″ E | HHGB-2 | HHGB |
Plant Root | Disease | 23°18′04″ N | 102°71′94″ E | HHGB-3 | HHGB |
Plant Root | Healthy | 23°12′72″ N | 102°73′25″ E | YYGJ-1 | YYGJ |
Plant Root | Healthy | 23°12′72″ N | 102°73′25″ E | YYGJ-2 | YYGJ |
Plant Root | Healthy | 23°12′72″ N | 102°73′25″ E | YYGJ-3 | YYGJ |
Plant Root | Disease | 23°12′72″ N | 102°73′25″ E | YYGB-1 | YYGB |
Plant Root | Disease | 23°12′72″ N | 102°73′25″ E | YYGB-2 | YYGB |
Plant Root | Disease | 23°12′72″ N | 102°73′25″ E | YYGB-3 | YYGB |
Plant Root | Healthy | 23°41′43″ N | 103°14′58″ E | GJGJ-1 | GJGJ |
Plant Root | Healthy | 23°41′43″ N | 103°14′58″ E | GJGJ-2 | GJGJ |
Plant Root | Healthy | 23°41′43″ N | 103°14′58″ E | GJGJ-3 | GJGJ |
Plant Root | Disease | 23°41′43″ N | 103°14′58″ E | GJGB-1 | GJGB |
Plant Root | Disease | 23°41′43″ N | 103°14′58″ E | GJGB-2 | GJGB |
Plant Root | Disease | 23°41′43″ N | 103°14′58″ E | GJGB-3 | GJGB |
Bacteria | Fungi | ||||||||
---|---|---|---|---|---|---|---|---|---|
OTUs | ACE | Chao1 | Shannon | OTUs | ACE | Chao1 | Shannon | ||
Soil | GJTB | 3462 | 2564.333 | 2521.612 | 9.527 | 1374 | 899.728 | 854.927 | 5.446 |
GJTJ | 3462 | 2206.305 | 2142.524 | 8.145 | 1051 | 694.534 | 659.495 | 4.305 | |
HHTB | 3131 | 2756.736 | 2677.472 | 8.566 | 1861 | 1088.916 | 1044.913 | 5.706 | |
HHTJ | 2907 | 2215.109 | 2170.085 | 8.387 | 1641 | 963.598 | 944.412 | 5.941 | |
YYTB | 3157 | 2492.986 | 2495.198 | 8.988 | 1175 | 821.936 | 768.858 | 3.893 | |
YYTJ | 3963 | 2763.247 | 2697.771 | 9.476 | 1399 | 920.027 | 862.295 | 4.353 | |
Root | GJGB | 559 | 420.871 | 409.548 | 1.374 | 669 | 453.300 | 437.215 | 4.137 |
GJGJ | 249 | 207.837 | 185.174 | 0.447 | 646 | 435.469 | 422.407 | 4.009 | |
HHGB | 167 | 127.812 | 113.063 | 0.383 | 413 | 240.323 | 236.925 | 3.774 | |
HHGJ | 541 | 406.055 | 385.912 | 1.487 | 752 | 491.033 | 505.245 | 4.094 | |
YYGB | 208 | 153.551 | 132.562 | 1.110 | 878 | 525.474 | 518.450 | 4.003 | |
YYGJ | 258 | 196.795 | 177.253 | 0.452 | 1436 | 691.628 | 675.902 | 5.183 |
Number | Type Strain | Reference Strain | Homology |
---|---|---|---|
GJGB ZHEN2 | MT561402.1 | Chaetomium cochliodes | 99.81% |
GJGB ZHEN3 | MT561402.1 | Chaetomium cochliodes | 99.45% |
GJGB ZHEN5 | MT561402.1 | Chaetomium cochliodes | 100% |
GJGB ZHEN11 | MN689717.1 | Fusarium solani | 97.01% |
GJGB ZHEN12 | MN689717.1 | Fusarium solani | 94.82% |
GJGB ZHEN13 | MH856055.1 | Fusarium tonkinense | 96.94% |
GJGB ZHEN14 | MN689717.1 | Fusarium solani | 99.63% |
HHGB ZHEN1 | MN816432.1 | Diaporthe fusicola | 99.82% |
HHGB ZHEN2 | MN816432.1 | Diaporthe fusicola | 98.40% |
HHGB ZHEN3 | OP090371.1 | Fusarium oxysporum | 99.23% |
HHGB ZHEN4 | NR_152889.1 | Ilyonectria leucospermi | 99.42% |
HHGB ZHEN6 | KR364584.1 | Fusarium oxysporum | 97.90% |
HHGB ZHEN7 | MG564294.1 | Fusarium oxysporum | 99.79% |
HHGB ZHEN9 | MT606194.1 | Colletotrichum sp. | 97.44% |
HHGB ZHEN11 | MT476912.1 | Trametes hirsuta | 99.33% |
HHGB ZHEN15 | MG543786.1 | Galactomyces pseudocandidus | 99.64% |
HHGB ZHEN16 | MW221103.1 | Galactomyces pseudocandidus | 98.30% |
YYGB ZHEN2 | OP237439.1 | Fusarium solani | 94.40% |
YYGB ZHEN3 | MH397492.1 | Fusarium sp. | 99.81% |
YYGB ZHEN4 | MF467275.1 | Fusarium oxysporum | 99.81% |
YYGB ZHEN5 | MT251175.1 | Fusarium falciforme | 99.63% |
YYGB ZHEN6 | MT605584.1 | Fusarium solani | 100% |
YYGB ZHEN7 | MT605584.1 | Fusarium solani | 97.25% |
YYGB ZHEN8 | MG650069.1 | Fusarium sp. | 96.58% |
YYGB ZHEN9 | MT032635.1 | Fusarium oxysporum | 99.81% |
YYGB ZHEN10 | MK372218.1 | Penicillium sp. | 99.81% |
GJGJ ZHEN3 | MN341788.1 | Nemania diffusa | 99.45% |
GJGJ ZHEN4 | MK372218.1 | Penicillium sp. | 99.81% |
HHGJ ZHEN1 | OK030894.1 | Colletotrichum sp. | 100% |
HHGJ ZHEN2 | MT322235.1 | Colletotrichum gigasporum | 100% |
HHGJ ZHEN3 | MT588864.1 | Chaetomium globosum | 99.63% |
HHGJ ZHEN4 | OK030894.1 | Colletotrichum sp. | 99.24% |
GJGB XI2 | KY689942.1 | Pseudomonas sp. | 99.71% |
GJGB XI3 | MT568560.1 | Raoultella ornithinolytica | 99.93% |
GJGB XI4 | MK834812.1 | Pseudomonas sp. | 99.61% |
GJGB XI5 | MT568560.1 | Raoultella ornithinolytica | 99.93% |
HHGB XI1 | MT341797.1 | Pseudomonas sp. | 100% |
HHGB XI4 | CP027561.1 | Pseudomonas fluorescens | 99.78% |
HHGB XI6 | MN826151.1 | Burkholderia contaminans | 99.62% |
HHGB XI7 | MG593863.1 | Burkholderia sp. | 99.70% |
HHGB XI8 | MG571655.1 | Pseudomonas batumici | 99.77% |
HHGB XI9 | MG571655.1 | Pseudomonas batumici | 99.70% |
HHGB XI10 | MT895634.1 | Paraburkholderia sp. | 99.55% |
HHGB XI11 | MT341797.1 | Pseudomonas sp. | 99.85% |
YYGB XI1 | KU950364.1 | Serratia liquefaciens | 99.86% |
GJGJ XI1 | KT695823.1 | Pseudomonas fluorescens | 99.85% |
GJGJ XI2 | KC790251.1 | Pseudomonas reinekei | 99.93% |
GJGJ XI3 | CP024646.1 | Pseudomonas syringae | 99.85% |
HHGJ XI1 | MW959056.1 | Pseudomonas sp. | 99.34% |
HHGJ XI3 | GQ306158.1 | Burkholderia sp. | 99.12% |
HHGJ XI4 | KJ781942.1 | Rahnella aquatilis | 99.03% |
HHGJ XI5 | EU275360.1 | Rahnella sp. | 99.77% |
HHGJ XI7 | MF948895.1 | Paraburkholderia ginsengiterrae | 99.46% |
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Chen, C.; Cheng, Y.; Zhang, F.; Yu, S.; Cui, X.; Wu, Y. A Comparative Analysis of Microbial Communities in the Rhizosphere Soil and Plant Roots of Healthy and Diseased Yuanyang Nanqi (Panax vietnamensis) with Root Rot. Agriculture 2024, 14, 719. https://doi.org/10.3390/agriculture14050719
Chen C, Cheng Y, Zhang F, Yu S, Cui X, Wu Y. A Comparative Analysis of Microbial Communities in the Rhizosphere Soil and Plant Roots of Healthy and Diseased Yuanyang Nanqi (Panax vietnamensis) with Root Rot. Agriculture. 2024; 14(5):719. https://doi.org/10.3390/agriculture14050719
Chicago/Turabian StyleChen, Changyuan, Yifan Cheng, Fangli Zhang, Saiying Yu, Xiuming Cui, and Yuanshuang Wu. 2024. "A Comparative Analysis of Microbial Communities in the Rhizosphere Soil and Plant Roots of Healthy and Diseased Yuanyang Nanqi (Panax vietnamensis) with Root Rot" Agriculture 14, no. 5: 719. https://doi.org/10.3390/agriculture14050719