Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland

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 col...

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Bibliographic Details
Published in:Scientific reports 2023-08, Vol.13 (1), p.14190-14190, Article 14190
Main Authors: Xiong, Lingling, Li, Yanmei, Yu, Hang, Wei, Yunlin, Li, Haiyan, Ji, Xiuling
Format: Article
Language:English
Subjects:
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Adaptation
Coevolution
Cold
CRISPR
Fluidity
Gene transfer
Genomes
Genomic analysis
Genomic islands
Glycogen
Horizontal transfer
Humanities and Social Sciences
Low temperature
Membrane fluidity
Microbial activity
multidisciplinary
Prophages
Pseudomonas
Science
Science (multidisciplinary)
Trehalose
Wetlands
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-023-41323-x