Genomic Insights into Two Endophytic Strains: Stenotrophomonas geniculata NWUBe21 and Pseudomonas carnis NWUBe30 from Cowpea with Plant Growth-Stimulating Attributes
Abstract
:1. Introduction
2. Materials and Methods
- The isolation, morphogenomic authentication, and plant growth-stimulating screening of cowpea endophytic bacterial isolates.
- Isolation protocol.
- In vitro PGP screening assay.
- Genomic DNA extraction, whole-genome sequencing, and annotation.
3. Results
3.1. Genomic Features of the Endophytic Pseudomonas carnis Strain NWUBe30 and Stenotrophomonas geniculata Strain NWUBe21
3.2. Abundance of Plant Growth-Improving Genes in the Genomes of the Endophytic Bacteria Strains
4. Discussion
- Authentication of the endophytic bacteria strains as plant growth enhancers.
- Genetic components that are involved in plant growth enhancement.
- Iron acquisition and metabolism.
- Motility and Chemotaxis
- Nitrogen Metabolism
- Phosphorus Metabolism.
- Plant hormone-auxin biosynthesis.
- Stress Response.
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Endophytic Bacteria | P. carnis NWUBe30 | S. geniculata NWUBe21 | ||
---|---|---|---|---|
Plant growth-promoting assay | Qualitative screening output | Quantitative screening output | Qualitative screening output | Quantitative screening output |
Exopolysaccharide production | ++ | ++ | ||
Ammonia production | +++ | ++ | ||
Indole acetic acid (IAA) production | +++ | 17.46 ± 0.08 | +++ | 15.67 ± 0.05 |
Phosphate solubilization | ++ | 35.85 ± 0.12 | ++ | 32.15 ± 0.05 |
Siderophore production | ++ | 89.25 ± 0.23 | ++ | 89.60 ± 0.42 |
Biofilm formation | + | 10.46 ± 0.11 | + | 11.29 ± 0.03 |
Acds production | + | + | ||
Hydrogen cyanide production Biochemical traits | ++ | + | ||
Gram reaction | _ | - | ||
Shape | R | R | ||
Citrate utilization | - | - | ||
Starch | + | + | ||
Nitrate reduction | - | - | ||
Fructose | - | - | ||
Glucose | - | + | ||
Catalase | + | + | ||
Oxidase | + | - | ||
Maltose | + | + |
Genome | S. geniculata Strain NWUBe21 | P. carnis Strain NWUBe30 |
---|---|---|
Size | 512,0194 | 5,901,107 |
GC value | 64.79 | 60.2 |
N50 | 113,089 | 401,656 |
L50 | 105 | 6 |
Number of contigs | 410 | 23 |
Number of subsystems | 427 | 377 |
Number of coding sequences | 4986 | 5300 |
Number of tRNA | 63 | 52 |
Number of rRNA | 5 | 3 |
Noncoding repeat | 169 | 189 |
Genes with SEED annotation | 3934 | 2117 |
Clusters | Regions | Size (bp) | Most Similar Known Cluster | Percentage Similarity |
---|---|---|---|---|
Pseudomonas carnis NWUBe30 | ||||
RIPP-like | 1.1 | 10,845 | - | - |
Redox-cofactor | 1.2 | 22,147 | Lankacidin C NRP + Polyketide | 13% |
Arylpolyene | 2.1 | 43,575 | APE Vf Other | 40% |
NRPS-like | 2.2 | 25,880 | Fragin NRP | 25% |
Siderophore | 3.1 | 11,925 | - | - |
NRPS | 3.2 | 52,896 | Pyoverdin NRP | 10% |
NAGGN | 3.3 | 14,863 | - | - |
Hserlactone | 3.4 | 20,575 | - | - |
NRPS-like betalactone | 4.1 | 43,476 | Pyoverdin NRP | 1% |
NRPS | 5.1 | 65,892 | Pyoverdin NRP | 11% |
Terpene | 7.1 | 22,225 | - | - |
NRPS | 10.1 | 64,235 | Viscosin NRP | 43% |
RIPP-like | 12.1 | 10,878 | - | - |
NRPS | 13.1 | 46,269 | Tolaasin I/Tolaasin F NRP: Lipopeptide | 50% |
Betalactone | 15.1 | 23,174 | Fengycin NRP | 13% |
Stenotrophomonas geniculata NWUBe21 | ||||
Lassopeptide | 1.1 | 15,117 | - | - |
NRPS | 36.1 | 22,883 | Bacillibactin NRP: NRP Siderophore | 80% |
Arylpolyene | 146.1 | 10,332 | APE Vf Other | 20% |
RIPP-like | 166.1 | 5818 | - | - |
RIPP-like | 171.1 | 7325 | - | - |
Arylpolyene | 358.1 | 3655 | APE Vf Other | 10% |
Contigs Tag | Product Role | Gene | Pathway |
---|---|---|---|
S geniculata NWUBe21 Node_255 | Biofilm PGA outer membrane secretin | PgaA | Biofilm Adhesin biosynthesis |
Node_21 | Indole-3-Pyruvate decarboxylase | IPDC | Pyruvate metabolism |
Node_17 | Intermediate for the synthesis of Tryptophan | Indole-3-glycerol phosphate synthase | Tryptophan biosynthesis |
Node_1 | Glucose-6-phosphate 1-dehydrogenase | GCD | Phosphate pentose |
Node_120 | Ferri-Bacillibactin esterase (iron transport and uptake) | BesA | Iron metabolism |
Node_67 | Ammonia/Ammonium transporter | amtB | Ammonia metabolism |
Node_39 | Phosphoribosylanthranilate isomerase | trpC | Tryptophan biosynthesis |
Node_89 | Exopolyphosphatase monomer | Ppx | Phosphorus metabolism |
Node_20 | Alkaline phosphatase | phoA2 | Organic phosphorus metabolism |
Node_5 | Nitrate reductase | narG | Nitrate metabolism |
P. carnis NWUBe30 Node_2 | Biofilm PGA synthesis auxiliary protein | PgaD | Biofilm Adhesin biosynthesis |
Node_5 | Pellicle/biofilm biosynthesis protein | PslA | Biofilm Adhesin biosynthesis |
Node_5 | Iron siderophore receptor protein | FecA | Iron metabolism |
Node_2 | Nitrogen regulation protein | NtrC | Nitrogen metabolism |
Node_10 | Exopolysaccharide protein | ExoZ | Polysaccharide degradation |
Node_8 | Auxin efflux carrier family protein | Auxin biosynthesis | |
Node_8 | Tryptophan synthase | trpA | IAA production |
Node_6 | Nitrogen-fixing | NifU | Nitrogen fixation |
Node_6 | Ammonia monooxygenase | Ammonia metabolism | |
Node_1 | Indole-3-glycerol phosphate synthase | Tryptophan biosynthesis |
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Omomowo, O.I.; Babalola, O.O. Genomic Insights into Two Endophytic Strains: Stenotrophomonas geniculata NWUBe21 and Pseudomonas carnis NWUBe30 from Cowpea with Plant Growth-Stimulating Attributes. Appl. Sci. 2022, 12, 12953. https://doi.org/10.3390/app122412953
Omomowo OI, Babalola OO. Genomic Insights into Two Endophytic Strains: Stenotrophomonas geniculata NWUBe21 and Pseudomonas carnis NWUBe30 from Cowpea with Plant Growth-Stimulating Attributes. Applied Sciences. 2022; 12(24):12953. https://doi.org/10.3390/app122412953
Chicago/Turabian StyleOmomowo, Olawale Israel, and Olubukola Oluranti Babalola. 2022. "Genomic Insights into Two Endophytic Strains: Stenotrophomonas geniculata NWUBe21 and Pseudomonas carnis NWUBe30 from Cowpea with Plant Growth-Stimulating Attributes" Applied Sciences 12, no. 24: 12953. https://doi.org/10.3390/app122412953
APA StyleOmomowo, O. I., & Babalola, O. O. (2022). Genomic Insights into Two Endophytic Strains: Stenotrophomonas geniculata NWUBe21 and Pseudomonas carnis NWUBe30 from Cowpea with Plant Growth-Stimulating Attributes. Applied Sciences, 12(24), 12953. https://doi.org/10.3390/app122412953