Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome
Abstract
1. Introduction
2. Results
2.1. Pseudomonas oryzihabitans GDW1 Enhances Tomato Plant Growth and Biomass Accumulation
2.2. Transcriptome Profiling and Differentially Expressed Gene Analysis
2.3. Different Pathway Enrichment Analyses
2.4. Analysis of the Protein–Protein Interaction (PPI) Network and Hub Gene Screening
2.5. Pseudomonas oryzihabitans GDW1 Influences the Assembly, Diversity, and Composition of Tomato Root Bacteriome
2.6. Application of Pseudomonas oryzihabitans GDW1 Increases Bacterial Network Complexity
2.7. Functional Prediction Analysis
2.8. Integration Analysis of Bacteriome and Transcriptome Data
3. Discussion
4. Materials and Methods
4.1. Bacterial Strain and Growth Conditions
4.2. Plant Material and Nursery Raising
4.3. Greenhouse Pot Experiment
4.4. Assessment of Plant-Growth-Promoting Traits
4.5. Plant Samples Collection and Processing
4.6. Transcriptome Analysis
4.6.1. Total RNA Extraction and Library Preparation
4.6.2. Data Processing and Analysis of Differentially Expressed Genes
4.7. Analysis of the Tomato Plant Root Bacteriome Using 16S Amplicon Sequencing
4.7.1. Total Genomic DNA Extraction and Library Construction
4.7.2. Sequencing Data Processing and Bioinformatics Analyses
4.8. Different Joint Analyses
4.9. Validation of RNA-Seq Data by RT-qPCR and Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Total Reads | Clean Reads | Total Mapped Reads | Mapped Reads (%) | Q20 (%) | Q30 (%) | GC Content (%) | Clean Data Ratio (%) |
---|---|---|---|---|---|---|---|---|
CK.1 | 52,713,686 | 44,499,896 | 43,203,060 | 97.09 | 98.49 | 94.4 | 44.58 | 90.7 |
CK.2 | 53,326,478 | 46,835,834 | 45,637,248 | 97.44 | 98.53 | 94.47 | 44.12 | 91.42 |
CK.3 | 46,567,128 | 41,096,730 | 40,138,662 | 97.67 | 98.59 | 94.65 | 44.38 | 91.77 |
T.1 | 49,919,330 | 44,373,886 | 43,353,271 | 97.7 | 98.73 | 95.04 | 44.26 | 92.36 |
T.2 | 47,267,046 | 38,240,942 | 37,364,930 | 97.71 | 98.69 | 94.95 | 45.37 | 92.4 |
T.3 | 54,946,518 | 42,801,358 | 41,649,310 | 97.31 | 98.57 | 94.61 | 45.43 | 90.91 |
Total | 304,740,186 | 257,848,646 | 251,346,481 | 97.49 | 98.6 | 94.69 | 44.69 | 91.59 |
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Ahmed, W.; Wang, Y.; Ji, W.; Liu, S.; Zhou, S.; Pan, J.; Li, Z.; Wang, F.; Wang, X. Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome. Int. J. Mol. Sci. 2025, 26, 1922. https://doi.org/10.3390/ijms26051922
Ahmed W, Wang Y, Ji W, Liu S, Zhou S, Pan J, Li Z, Wang F, Wang X. Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome. International Journal of Molecular Sciences. 2025; 26(5):1922. https://doi.org/10.3390/ijms26051922
Chicago/Turabian StyleAhmed, Waqar, Yan Wang, Wenxia Ji, Songsong Liu, Shun Zhou, Jidong Pan, Zhiguang Li, Fusheng Wang, and Xinrong Wang. 2025. "Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome" International Journal of Molecular Sciences 26, no. 5: 1922. https://doi.org/10.3390/ijms26051922
APA StyleAhmed, W., Wang, Y., Ji, W., Liu, S., Zhou, S., Pan, J., Li, Z., Wang, F., & Wang, X. (2025). Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome. International Journal of Molecular Sciences, 26(5), 1922. https://doi.org/10.3390/ijms26051922