Pseudomonas sp., Strain L5B5: A Genomic and Transcriptomic Insight into an Airborne Mine Bacterium
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling, Isolation, and Identification of the Bacterium
2.2. Bacterial Inhibition Assays
2.3. Fungal Inhibition Assays
2.4. DNA Extraction
2.5. RNA Extraction
2.6. rRNA 16S Analysis
2.7. Genomic Analysis
2.8. Transcriptomic Analysis
3. Results
3.1. Inhibition Assays
3.2. 16S rRNA Analysis
3.3. Genomics Analyses
3.4. Functional Annotations
3.5. Transcriptomic Analysis—Pre-Treatment and Statistics
3.6. Overexpression in Secondary Metabolism
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Pseudomonas sp., strain L5B5 | 1 | 2 | 3 | 4 | |
---|---|---|---|---|---|
Metabolite-Region (R) | UniProtKb Similarity (Core Biosynthetic Genes) | ||||
Other-R1 (Pyrrolnitrin) | 95% Pseudomonas sp. CMR5c (prnB) | + | + | + | + |
NRPS-R2 (Enantio/Iso-pyochelin) | 90%–95% Pseudomonas sp. CMR5c (pchEF) | − | + | + | + |
Phenazine-R3 | 84.7%–85.3%–98.2% P. piscis-P. yamanorum-Pseudomonas sp. FW507-12TSA (phzI-phzAB) | + | − | − | − |
T1PKS-R4 (Pyoluteorin) | 84.1%–77% Pseudomonas sp. MSSRFD41 (PltBC-like PKSynthase) | − | + | + | + |
NRPS-R5 (Orfamides) | 89.3%–90.3%–90% Pseudomonas sp. CMR5c (ofaABC) | + | + | + | + |
CDPS-R6 | 97.6% P. protegens CHA0 (Cyclodipeptide synthase) | + | + | + | + |
RiPP-like-R7 | 86.3% Pseudomonas sp. FW507-12TSA (Uncharacterized protein) | + | + | + | + |
Arylpolyene-R8 | 89.7%–97.3% P. protegens CHA0-Pseudomonas sp. CMR5c (Beta-ketoacyl-ACP synthases) | + | + | + | + |
RiPP-like-R9 | 93.2% Pseudomonas sp. CMR12a (Uncharacterized protein) | + | + | + | + |
T3PKS-R10 (2,4-diacetylphloroglucinol) | 94.6% P. protegens Pf-5 (phlD) | + | + | + | + |
Siderophore-R11 | 80.7% Pseudomonas sp. CMR12a (Uncharacterized protein) | − | − | − | − |
Redox-cofactor-R12 (Lankacidin C) | 98.8%–96.7%–97.2% Pseudomonas sp. CMR12a-P. protegens Pf-5 (pqqABCDEF) | + | + | + | + |
NRPS-R13 (Putative NRPS) | 88.7% P. juntendi/P. putida (Thioesterase) | − | − | − | − |
Hserlactone-R14 | 80.5% Pseudomonas sp. FW507-12TSA (psyL) | + | − | − | − |
Arylpolyene-R15 | 90.6% Pseudomonas sp. CMR5c (Thiolase) | − | − | − | − |
NAGGN-R16 | 98.7%–96%–97.6% Pseudomonas sp. BIOMIG1BAC (M42 family peptidase- N-acetylglutaminylglutamine synthetase | + | + | + | + |
NRPS-R17-18 (Pyoverdine) | 96.4%–96%–94.3%–95.2% P. protegens CHA0 (pvdLIJD) | + | + | + | + |
NRPS-R19 | 85.4% Pseudomonas sp. CMR5c (Thioester reductase-like domain) | − | − | − | − |
Betalactone-R20 | 94.8%–95% P. piscis-Pseudomonas sp. CMR12a (Acyl-CoA synthase-pyruvate carboxylase) | + | + | + | + |
RNA-Sample | Raw Reads | Reads after rRNA Removing | Filtered Reads | Passed Reads | Mapped Reads |
---|---|---|---|---|---|
SGE | 40,589,012 | 40,333,005 | 38,932,275 | 95.92% | 94.46% |
SGS | 31,304,717 | 31,221,230 | 30,076,663 | 96.08% | 94.17% |
GYS | 31,931,209 | 31,583,884 | 30,443,705 | 95.34% | 90.74% |
GLY | 35,637,786 | 35,492,545 | 34,789,606 | 97.62% | 94.06% |
GLU | 33,422,936 | 32,805,879 | 32,587,198 | 97.50% | 93.38% |
MAN | 32,739,745 | 32,624,884 | 31,908,361 | 97.46% | 94.83% |
FRU | 33,195,686 | 33,098,880 | 32,344,406 | 97.44% | 93.90% |
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Gonzalez-Pimentel, J.L.; Dominguez-Moñino, I.; Jurado, V.; Caldeira, A.T.; Saiz-Jimenez, C. Pseudomonas sp., Strain L5B5: A Genomic and Transcriptomic Insight into an Airborne Mine Bacterium. Appl. Sci. 2022, 12, 10854. https://doi.org/10.3390/app122110854
Gonzalez-Pimentel JL, Dominguez-Moñino I, Jurado V, Caldeira AT, Saiz-Jimenez C. Pseudomonas sp., Strain L5B5: A Genomic and Transcriptomic Insight into an Airborne Mine Bacterium. Applied Sciences. 2022; 12(21):10854. https://doi.org/10.3390/app122110854
Chicago/Turabian StyleGonzalez-Pimentel, Jose Luis, Irene Dominguez-Moñino, Valme Jurado, Ana Teresa Caldeira, and Cesareo Saiz-Jimenez. 2022. "Pseudomonas sp., Strain L5B5: A Genomic and Transcriptomic Insight into an Airborne Mine Bacterium" Applied Sciences 12, no. 21: 10854. https://doi.org/10.3390/app122110854
APA StyleGonzalez-Pimentel, J. L., Dominguez-Moñino, I., Jurado, V., Caldeira, A. T., & Saiz-Jimenez, C. (2022). Pseudomonas sp., Strain L5B5: A Genomic and Transcriptomic Insight into an Airborne Mine Bacterium. Applied Sciences, 12(21), 10854. https://doi.org/10.3390/app122110854