Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland
Abstract Microbial communities of wetlands play key roles in the earth’s ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W...
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Nature Portfolio
2023-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-41323-x |
| _version_ | 1827711243602886656 |
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| author | Lingling Xiong Yanmei Li Hang Yu Yunlin Wei Haiyan Li Xiuling Ji |
| author_facet | Lingling Xiong Yanmei Li Hang Yu Yunlin Wei Haiyan Li Xiuling Ji |
| author_sort | Lingling Xiong |
| collection | DOAJ |
| description | Abstract Microbial communities of wetlands play key roles in the earth’s ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution. |
| first_indexed | 2024-03-10T17:51:00Z |
| format | Article |
| id | doaj.art-89a87d051b2a4ba4bcfdf2fff642f026 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T17:51:00Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
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| spelling | doaj.art-89a87d051b2a4ba4bcfdf2fff642f0262023-11-20T09:20:58ZengNature PortfolioScientific Reports2045-23222023-08-0113111210.1038/s41598-023-41323-xWhole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetlandLingling Xiong0Yanmei Li1Hang Yu2Yunlin Wei3Haiyan Li4Xiuling Ji5Faculty of Life Science and Technology, Kunming University of Science and TechnologyFaculty of Life Science and Technology, Kunming University of Science and TechnologyFaculty of Life Science and Technology, Kunming University of Science and TechnologyFaculty of Life Science and Technology, Kunming University of Science and TechnologyMedical School, Kunming University of Science and TechnologyMedical School, Kunming University of Science and TechnologyAbstract Microbial communities of wetlands play key roles in the earth’s ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.https://doi.org/10.1038/s41598-023-41323-x |
| spellingShingle | Lingling Xiong Yanmei Li Hang Yu Yunlin Wei Haiyan Li Xiuling Ji Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland Scientific Reports |
| title | Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland |
| title_full | Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland |
| title_fullStr | Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland |
| title_full_unstemmed | Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland |
| title_short | Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland |
| title_sort | whole genome analysis and cold adaptation strategies of pseudomonas sivasensis w 6 isolated from the napahai plateau wetland |
| url | https://doi.org/10.1038/s41598-023-41323-x |
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