Functional Characterization of a Synthetic Bacterial Community (SynCom) and Its Impact on Gene Expression and Growth Promotion in Tomato
Abstract
1. Introduction
2. Materials and Methods
2.1. Isolation and Construction of the Rhizosphere Consortium and Growth Conditions
2.2. Extraction of DNA, Shotgun Metagenome Sequencing, and Genomes Reconstruction
2.3. Bacterial Soil Community Analysis
2.4. Plant RNA Isolation and Transcriptomic Analysis
2.5. Statistical Analyses
3. Results
3.1. SynCom Design and Construction
3.2. Genomes Reconstruction (MAGs) and Functional Analysis
3.3. Effect of SynCom on Soil and Rhizosphere Bacterial Communities’ Composition and Diversity
3.4. Differential Gene Expression in Tomato Plants After Application of the SynCom
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Abbreviations
PGP | Plant growth promoting |
PGPR | Plant growth promoting rhizobacteria |
SynCom | Synthetic bacterial communities |
SA | Sucrose-Asparagine |
PCA | Plate Count Agar |
YMA | Yeast Mannitol Agar |
MM | Minimal Salt Medium |
PAS | Phosphate-buffered mineral medium salts |
TYGS | Type-Strain Genome Server |
DEGs | Differentially expressed genes |
MAGs | Metagenome-assembled genomes |
DAPG | 2,4-diacetylphloroglucinol |
P | Phosphate |
N | Nitrogen |
IAA | Auxin indole-3-acetic acid |
IAM | Indole-3-acetamide |
PAA | Degradation of auxin phenylacetic acid |
ACC | 1-aminocyclopropane-1-carboxylicacid |
HCN | Hydrogen cyanide |
PQQ | Pyrroloquinoline quinone |
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Assembly | Closest Relative Genome | % dDDH | Length (bp) | Contigs | Completeness |
---|---|---|---|---|---|
Rhizobium | Rhizobium metallidurans | 31.9 | 5,818,479 | 5 | 99.00 |
Pseudomonas | Pseudomonas monsensis | 94.8 | 6,443,679 | 16 | 98.40 |
Agromyces | Agromyces mediolanus | 72.8 | 4,695,114 | 26 | 97.11 |
Pseudomonas | Pseudomonas ogarae | 87.3 | 7,066,282 | 29 | 95.30 |
Chryseobacterium | Chryseobacterium taeanense | 74.4 | 4,333,431 | 18 | 79.94 |
Ensifer | Ensifer morelensis | 21.0 | 8,190,650 | 460 | 72.33 |
Microbacterium | Microbacteium oxydans | 91.9 | 4,028,011 | 3 | 99.50 |
Possible Specie | Genes/Clusters | Function | PGP Category |
---|---|---|---|
Pseudomonas monsensis | fecAR | Transport of iron dicitrate (III) | Siderophore |
fitD | Insect toxin | Toxin | |
hasDEF | Hemophore biosynthesis | Siderophore | |
hcnABC | Hydrocyanic acid biosynthesis | Biocontrol | |
hcp (T6SS) | Type VI secretion system | Biocontrol | |
iaaHM | Auxin biosynthesis | Phytohormone modulation | |
paaFIKY | Phenylacetic acid degradation | Phytohormone modulation | |
phnBCDENWXZ | Phosphate transport | Nutrient mobilization (P) | |
phoBDHH2LPQRU | Phosphate transport | Nutrient mobilization (P) | |
pqqABCDE | Pyrroloquinoline quinone | Plant–bacteria interaction, antioxidant | |
pstABCS | Phosphate transport | Nutrient mobilization (P) | |
pvdAELMNOPRSY | Pyoverdine | Nutrient mobilization (Fe) | |
ubiA | Production of 4-hydroxibenzoate | Antibiotic | |
Cluster 1 | Type NRPS/lokisin | Antifungal | |
Chryseobacterium taeanense | paaABCDEGHIKYZ | Phenylacetic acid degradation | Phytohormone modulation |
phnABP | Phosphate transport | Nutrient mobilization (P) | |
phoABB1DHLPR | Phosphate transport | Nutrient mobilization (P) | |
ubiA | Production of 4-hydroxibenzoate | Antibiotic | |
Cluster 1 | Type lantipeptide class I | Antimicrobial | |
Cluster 2 | Type Aryl polyene, resorcinol | Biocontrol | |
Rhizobium spp. | acsA | Achromobactin biosynthesis | Siderophore |
napABCD | Nitrate reductase | Denitrification/nutrient mobilization(N) | |
nirBCDFS | Nitrite reductase | Denitrification/nutrient mobilization(N) | |
norBCDEGQR | Nitric oxide reductase | Denitrification | |
nosDFLYZ | Nitrous oxide reductase | Denitrification/nutrient mobilization(N) | |
paaABCDEFGHIKXYZ | Phenylacetic acid degradation | Phytohormone modulation | |
pchR | Enantio-pyochelin biosynthesis | Siderophore | |
phnABCDEFGHIJKLMNOPW | Phosphate transport | Nutrient mobilization (P) | |
phoABB1PDHLQRU | Phosphate transport | Nutrient mobilization (P) | |
pstABCS | Phosphate transport | Nutrient mobilization (P) | |
speE | Spermidine biosynthesis | Plant–bacteria interaction | |
ubiA | Production of 4-hydroxibenzoate | Antibiotic | |
Agromyces mediolanus | hcnABC | Hydrocyanic acid biosynthesis | Biocontrol |
paaABCDEFGHIKYZ | Phenylacetic acid degradation | Phytohormone modulation | |
phnBCDEF | Phosphate transport | Nutrient mobilization (P) | |
phoABB1HPLH2UPR | Phosphate transport | Nutrient mobilization (P) | |
pstABCS | Phosphate transport | Nutrient mobilization (P) | |
speE | Spermidine biosynthesis | Plant–bacteria interaction | |
Microbacterium oxydans | paaDFH | Phenylacetic acid degradation | Phytohormone modulation |
phnBCDEO | Phosphate transport | Nutrient mobilization (P) | |
phoBHLRU | Phosphate transport | Nutrient mobilization (P) | |
Cluster 1 | Type NRP-metallophore/parabactin | Siderophore | |
Pseudomonas ogarae | acdS | ACC deaminase | Phytohormone modulation |
fecAR | Transport of iron dicitrate (III) | Siderophore | |
fitD | Insect toxin | Toxin | |
hasDEF | Hemophore biosynthesis | Siderophore | |
hcnABC | Hydrocyanic acid biosynthesis | Biocontrol | |
hcp (T6SS) | Type VI secretion system | Biocontrol | |
narGHIJ | Nitrate reductase | Denitrification/nutrient mobilization (N) | |
nirBCDFS | Nitrite reductase | Denitrification/nutrient mobilization (N) | |
norBCDEGQR | Nitric oxide reductase | Denitrification | |
nosDFLYZ | Nitrous oxide reductase | Denitrification/phytohormone modulation | |
paaFGIKY | Phenylacetic acid degradation | Phytohormone modulation | |
pchR | Enantio-pyochelin biosynthesis | Siderophore | |
phnABCDEXZ | Phosphate transport | Nutrient mobilization (P) | |
phoBDHH2LPQRU | Phosphate transport | Nutrient mobilization (Fe) | |
pqqBCDE | Pyrroloquinoline quinone | Plant–bacteria interaction, antioxidant | |
pstABCS | Phosphate transport | Nutrient mobilization (P) | |
pvdAELMNOPRSY | Pyoverdine | Nutrient mobilization (Fe) | |
speE | Spermidine biosynthesis | Plant–bacteria interaction | |
ubiA | Production of 4-hydroxibenzoate | Antibiotic | |
Cluster 1 | Type 2,4-diacetylphloroglucinol (DAPG) | Antifungal | |
Cluster 2 | Type lantipeptide class II | Antimicrobial | |
Ensifer spp. | paaFG | Phenylacetic acid degradation | Phytohormone modulation |
phnAB | Phosphate transport | Nutrient mobilization (P) | |
phoABQR | Phosphate transport | Nutrient mobilization (P) | |
ubiA | Production of 4-hydroxibenzoate | Antibiotic | |
Cluster 1 | Type β-lactone | Antimicrobial | |
Cluster 2 | Type β-lactone/mycosubtilin | Antifungal | |
Cluster 3 | Type Resorcinol | Biocontrol |
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Montoya, M.; Durán-Wendt, D.; Garrido-Sanz, D.; Carrera-Ruiz, L.; Vázquez-Arias, D.; Redondo-Nieto, M.; Martín, M.; Rivilla, R. Functional Characterization of a Synthetic Bacterial Community (SynCom) and Its Impact on Gene Expression and Growth Promotion in Tomato. Agronomy 2025, 15, 1794. https://doi.org/10.3390/agronomy15081794
Montoya M, Durán-Wendt D, Garrido-Sanz D, Carrera-Ruiz L, Vázquez-Arias D, Redondo-Nieto M, Martín M, Rivilla R. Functional Characterization of a Synthetic Bacterial Community (SynCom) and Its Impact on Gene Expression and Growth Promotion in Tomato. Agronomy. 2025; 15(8):1794. https://doi.org/10.3390/agronomy15081794
Chicago/Turabian StyleMontoya, Mónica, David Durán-Wendt, Daniel Garrido-Sanz, Laura Carrera-Ruiz, David Vázquez-Arias, Miguel Redondo-Nieto, Marta Martín, and Rafael Rivilla. 2025. "Functional Characterization of a Synthetic Bacterial Community (SynCom) and Its Impact on Gene Expression and Growth Promotion in Tomato" Agronomy 15, no. 8: 1794. https://doi.org/10.3390/agronomy15081794
APA StyleMontoya, M., Durán-Wendt, D., Garrido-Sanz, D., Carrera-Ruiz, L., Vázquez-Arias, D., Redondo-Nieto, M., Martín, M., & Rivilla, R. (2025). Functional Characterization of a Synthetic Bacterial Community (SynCom) and Its Impact on Gene Expression and Growth Promotion in Tomato. Agronomy, 15(8), 1794. https://doi.org/10.3390/agronomy15081794