Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance
Abstract
1. Introduction
2. Material and Methods
2.1. Microbial Community DNA Extraction
2.2. Metagenomics Amplicon Sequencing
2.2.1. 16S rRNA Gene Amplification
2.2.2. Library Preparation and Next-Generation Sequencing
2.3. Sequence Analysis
Data Filtering and Normalization
2.4. Visual Exploration Profiling
2.5. Community Profiling
Alpha, Beta Diversity, and Core Microbiome
2.6. Interactions Through Spearman Rank Correlation Analysis
2.7. Differential Abundance Analysis
3. Results
3.1. Microbial Abundance Data
3.2. Visual Exploration
3.3. Microbial Community Profiling
3.3.1. Alpha Diversity Assessment
3.3.2. Beta Diversity Assessment
3.3.3. Core Microbiome Analysis
3.4. Correlation Analysis
3.5. Differential Abundance Profiling (DAP)
- a.
- Microbial recruiting:
- 1
- Wheat microbial recruitment under normal conditions: BC vs. RC:
- 2
- Wheat microbial recruitment under saline conditions: BS vs. RS:
- b.
- Salinity-Induced Microbial Shifts:
- c.
- Microbial signature:
4. Discussion
4.1. Assessment of Abundance Count Data
4.2. Alpha and Beta Diversity Analysis
4.3. Consistent Core Microbiome Communities
4.4. Stability of Microbial Communities
4.5. Variation in Bacterial Abundance Across Treatments
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Type | Counts |
---|---|
OTU annotation: | GreengenesID |
OTU number: | 1110 |
OTUs with ≥2 counts: | 752 |
Number of experimental factors with replicates: | 3 [discrete: 3 continuous: 0] |
Total read counts: | 4,526,902 |
Average counts per sample: | 377,241 |
Maximum counts per sample: | 796,235 |
Minimum counts per sample: | 141,355 |
Number of sample names matched (metadata vs. OTU table): | 12 |
Plant–Microbial Interaction (Microbial Recruitment) | ||||||
---|---|---|---|---|---|---|
No. | Phylum (Class) | Taxa | Log2FC | Estimated BS | Fold Change | Percentage Increase (%) |
1 | Proteobacteria (DeltaProteobacteria) | Sandaracinaceae | 3.37 | 0.097 | 10.34 | 933.88 |
2 | Proteobacteria (GammaProteobacteria) | Halomonas_xianhensis | 3.83 | 0.07 | 14.22 | 1322.15 |
3 | Legionella | 3.64 | 0.08 | 12.47 | 1146.66 | |
4 | Thermomonas | 3.58 | 0.084 | 11.96 | 1095.88 | |
5 | Azotobacter_armeniacus | 3.28 | 0.103 | 9.71 | 871.36 | |
6 | Rhizobacter | 3.14 | 0.113 | 8.82 | 781.52 | |
7 | Pseudomonas_sagittaria | 2.87 | 0.137 | 7.31 | 631.06 | |
8 | Rhizobacter_fulvus | 2.78 | 0.145 | 6.87 | 586.85 | |
9 | Halomonas_daqiaonensis | 2.43 | 0.185 | 5.39 | 438.89 | |
10 | Rheinheimera | 2.35 | 0.196 | 5.1 | 409.82 | |
11 | Pseudomonas_azotifigens | 2.34 | 0.198 | 5.06 | 405.88 | |
12 | Proteobacteria (AlphaProteobacteria) | Devosia_terrae | 2.77 | 0.147 | 6.82 | 582.11 |
13 | Altererythrobacter_sp_ | 2.22 | 0.215 | 4.66 | 366.24 | |
14 | Novosphingobium | 2.11 | 0.231 | 4.32 | 331.69 | |
15 | Altererythrobacter | 2.09 | 0.234 | 4.26 | 326.27 | |
16 | Actinobacteria | Saccharothrix_hoggarensis | 3.46 | 0.091 | 11 | 1000.43 |
17 | Saccharothrix | 4.03 | 0.061 | 16.34 | 1533.62 | |
18 | Firmicutes (Bacilli) | Gracilibacillus_ureilyticus | 3.26 | 0.104 | 9.58 | 858.35 |
19 | Fibrobacteres (Fibrobacteria) | Fibrobacteraceae | 2.29 | 0.205 | 4.89 | 388.93 |
20 | Bacteroidetes (Flavobacteriia) | Ulvibacter | 2.81 | 0.143 | 7.01 | 601.28 |
21 | Verrucomicrobia (Opitutae) | Opitutaceae | 2.11 | 0.231 | 4.32 | 331.69 |
22 | Puniceicoccaceae | 2.24 | 0.212 | 4.72 | 372.43 |
Salinity-Induced Microbial Shifts | ||||||
---|---|---|---|---|---|---|
No. | Phylum (Class) | Taxa | Log2FC | RC | Fold Change (FC) | Percentage Increase of RS over RC (%) |
1 | Proteobacteria (GammaProteobacteria) | Idiomarinaceae | 6.11 | 0.014477938 | 69.07060714 | 6807.060714 |
2 | Microbulbifer | 3.61 | 0.081899588 | 12.21007367 | 1121.007367 | |
3 | Rheinheimera | 3.43 | 0.092782723 | 10.77786861 | 977.7868615 | |
4 | Halomonadaceae | 3.13 | 0.114228931 | 8.75434961 | 775.434961 | |
5 | Marinobacter_sp_ | 3.11 | 0.115823508 | 8.633825892 | 763.3825892 | |
6 | Halomonas | 2.98 | 0.126744935 | 7.889861636 | 688.9861636 | |
7 | Marinobacter | 2.8 | 0.143587294 | 6.964404506 | 596.4404506 | |
8 | Pseudomonas_sp_ | 2.29 | 0.204475515 | 4.890561111 | 389.0561111 | |
9 | Pseudomonas_sagittaria | 2.17 | 0.22221067 | 4.500233939 | 350.0233939 | |
10 | Firmicutes (Bacilli) | Gracilibacillus | 4.45 | 0.045752678 | 21.85664411 | 2085.664411 |
11 | Gracilibacillus_kekensis | 3.73 | 0.075362989 | 13.26911273 | 1226.911273 | |
12 | Bacillaceae | 2.04 | 0.243163737 | 4.112455307 | 311.2455307 | |
13 | Bacteroidetes (Cytophagia) | Nafulsella | 3.72 | 0.07588718 | 13.17745628 | 1217.745628 |
14 | Bacteroidetes (Flavobacteriia) | Salegentibacter | 3.71 | 0.076415017 | 13.08643294 | 1208.643294 |
15 | Salinimicrobium_marinum | 3.45 | 0.091505356 | 10.92832205 | 992.8322054 | |
16 | Psychroflexus | 2.86 | 0.137738139 | 7.260153243 | 626.0153243 |
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Fouad, N.; El-Zayat, E.M.; Amr, D.; El-Khishin, D.A.; Abd-Elhalim, H.M.; Hafez, A.; Radwan, K.H.; Hamwieh, A.; Tadesse, W. Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance. Plants 2025, 14, 1033. https://doi.org/10.3390/plants14071033
Fouad N, El-Zayat EM, Amr D, El-Khishin DA, Abd-Elhalim HM, Hafez A, Radwan KH, Hamwieh A, Tadesse W. Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance. Plants. 2025; 14(7):1033. https://doi.org/10.3390/plants14071033
Chicago/Turabian StyleFouad, Nourhan, Emad M. El-Zayat, Dina Amr, Dina A. El-Khishin, Haytham M. Abd-Elhalim, Amr Hafez, Khaled H. Radwan, Aladdin Hamwieh, and Wuletaw Tadesse. 2025. "Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance" Plants 14, no. 7: 1033. https://doi.org/10.3390/plants14071033
APA StyleFouad, N., El-Zayat, E. M., Amr, D., El-Khishin, D. A., Abd-Elhalim, H. M., Hafez, A., Radwan, K. H., Hamwieh, A., & Tadesse, W. (2025). Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance. Plants, 14(7), 1033. https://doi.org/10.3390/plants14071033