Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling, Enrichment Assays, and DNA-SIP Experiments
2.2. Identification of Active Isoprene-Degrading Bacteria from Oil Palm Soils and Leaves
2.3. Enrichment and Isolation of Isoprene-Degrading Bacteria from Oil Palm Samples
2.4. Genome Sequencing and Analysis
2.5. Genome Analysis
2.6. Isoprene Oxidation Assays
3. Results and Discussion
3.1. Testing Methods to Recover Leaf Epiphytes
3.2. Active Isoprene-Degrading Bacteria Associated with an Oil Palm Tree
3.3. Bacterial Community Composition in SIP Enrichments
3.4. 13C—Labelling of Putative Isoprene Degraders in Leaf Washings
3.5. 13C—Labelling of Putative Isoprene Degraders in Soil
3.6. Targeted Isolation of Isoprene Degraders from Oil Palm
3.7. Genome Sequencing and Characterization of Isoprene Gene Clusters
3.8. Sphingopyxis Strain OPL5 Growth and Affinity for Isoprene
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gordonia OPL2 | Sphingopyxis OPL5 | |
---|---|---|
NCBI Tax ID | 2486274 | 2486273 |
Length (bp) | 5,759,526 | 4,676,975 |
GC (%) | 67.3 | 65.89 |
Contigs | 132 | 1 |
N50 | 80,039 | 4,676,975 |
CDS (total) | 5313 | 4403 |
Genes (coding) | 5200 | 4392 |
Genes (RNA) | 55 | 51 |
rRNAs (5S, 16S, 23S) | 3, 3, 1 | 1, 1, 1 |
tRNAs | 45 | 55 |
Pseudogenes (total) | 113 | 69 |
Coding Density (%) | 91.2 | 91.9 |
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Larke-Mejía, N.L.; Carrión, O.; Crombie, A.T.; McGenity, T.J.; Murrell, J.C. Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves. Microorganisms 2020, 8, 1557. https://doi.org/10.3390/microorganisms8101557
Larke-Mejía NL, Carrión O, Crombie AT, McGenity TJ, Murrell JC. Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves. Microorganisms. 2020; 8(10):1557. https://doi.org/10.3390/microorganisms8101557
Chicago/Turabian StyleLarke-Mejía, Nasmille L., Ornella Carrión, Andrew T. Crombie, Terry J. McGenity, and J. Colin Murrell. 2020. "Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves" Microorganisms 8, no. 10: 1557. https://doi.org/10.3390/microorganisms8101557
APA StyleLarke-Mejía, N. L., Carrión, O., Crombie, A. T., McGenity, T. J., & Murrell, J. C. (2020). Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves. Microorganisms, 8(10), 1557. https://doi.org/10.3390/microorganisms8101557