RNA-TGGE, a Tool for Assessing the Potential for Bioremediation in Impacted Marine Ecosystems
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Nucleic Acid Extraction
2.3. DNase Treatment of RNA Samples
2.4. cDNA Synthesis
2.5. Bacterial cDNA Amplification
2.6. TGGE (Temperature Gradient Gel Electrophoresis)
2.7. Identification of Bacterial Species from TGGE Gel
2.8. Statistical Analyses
3. Results and Discussion
3.1. Microbial Community Dynamics
3.2. Shannon Weaver Diversity
3.3. Pareto-Lorenz Curve
3.4. RNA-TGGE Bands
Identified Species | Treatment | Accession No. | Similarity (%) |
---|---|---|---|
Pseudomonas sp. (Gammaproteobacteria) | C | JF778683.1 | 96 |
Uncultured marine bacterium | C | FM211075.1 | 93 |
Uncultured Alcanivorax sp. (Gammaproteobacteria) | C | JF979266.1 | 84 |
Uncultured bacterium clone | C | HQ827507.1 | 100 |
Uncultured organism clone | C | JN528201.1 | 88 |
Uncultured bacterium clone | C | HM580751.1 | 99 |
Uncultured bacterium clone | C | JN178389.1 | 100 |
Alcanivoraxborkuumensis (Gammaproteobacteria) | C | FJ218422.1 | 94 |
Alcanivorax sp. (Gammaproteobacteria) | C | AB681673.1 | 91 |
Alcanivoracaceae bacterium (Gammaproteobacteria) | O | HQ537302.1 | 97 |
Uncultured betaproteobacteruim | O | GQ274246.1 | 88 |
Alcanivorax sp. (Gammaproteobacteria) | O | HE586882.1 | 96 |
Uncultured bacterium | O | EU255846.1 | 81 |
Uncultured bacterium | S | DQ861039.1 | 91 |
Alcanivorax sp. (Gammaproteobacteria) | S | HM171217.1 | 95 |
Alcanivorax sp. (Gammaproteobacteria) | S | HM171217.1 | 98 |
Marinobactermobilis strain (Gammaproteobacteria) | S | NR_044456.1 | 95 |
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Kadali, K.K.; Shahsavari, E.; Simons, K.L.; Sheppard, P.J.; Ball, A.S. RNA-TGGE, a Tool for Assessing the Potential for Bioremediation in Impacted Marine Ecosystems. J. Mar. Sci. Eng. 2015, 3, 968-980. https://doi.org/10.3390/jmse3030968
Kadali KK, Shahsavari E, Simons KL, Sheppard PJ, Ball AS. RNA-TGGE, a Tool for Assessing the Potential for Bioremediation in Impacted Marine Ecosystems. Journal of Marine Science and Engineering. 2015; 3(3):968-980. https://doi.org/10.3390/jmse3030968
Chicago/Turabian StyleKadali, Krishna K., Esmaeil Shahsavari, Keryn L. Simons, Petra J. Sheppard, and Andrew S. Ball. 2015. "RNA-TGGE, a Tool for Assessing the Potential for Bioremediation in Impacted Marine Ecosystems" Journal of Marine Science and Engineering 3, no. 3: 968-980. https://doi.org/10.3390/jmse3030968
APA StyleKadali, K. K., Shahsavari, E., Simons, K. L., Sheppard, P. J., & Ball, A. S. (2015). RNA-TGGE, a Tool for Assessing the Potential for Bioremediation in Impacted Marine Ecosystems. Journal of Marine Science and Engineering, 3(3), 968-980. https://doi.org/10.3390/jmse3030968