Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments
Abstract Background Cold-adapted archaea have diverse ecological roles in a wide range of low-temperature environments. Improving our knowledge of the genomic features that enable psychrophiles to grow in cold environments helps us to understand their adaptive responses. However, samples from typica...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09597-7 |
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| author | Liangzhong Chen Tao Hong Zirui Wu Weizhi Song Shaoxing X. Chen Yongqin Liu Liang Shen |
| author_facet | Liangzhong Chen Tao Hong Zirui Wu Weizhi Song Shaoxing X. Chen Yongqin Liu Liang Shen |
| author_sort | Liangzhong Chen |
| collection | DOAJ |
| description | Abstract Background Cold-adapted archaea have diverse ecological roles in a wide range of low-temperature environments. Improving our knowledge of the genomic features that enable psychrophiles to grow in cold environments helps us to understand their adaptive responses. However, samples from typical cold regions such as the remote Arctic and Antarctic are rare, and the limited number of high-quality genomes available leaves us with little data on genomic traits that are statistically associated with cold environmental conditions. Results In this study, we examined the haloarchaeal genus Halorubrum and defined a new clade that represents six isolates from polar and deep earth environments (‘PD group’ hereafter). The genomic G + C content and amino acid composition of this group distinguishes it from other Halorubrum and the trends are consistent with the established genomic optimization of psychrophiles. The cold adaptation of the PD group was further supported by observations of increased flexibility of proteins encoded across the genome and the findings of a growth test. Conclusions The PD group Halorubrum exhibited denser genome packing, which confers higher metabolic potential with constant genome size, relative to the reference group, resulting in significant differences in carbon, nitrogen and sulfur metabolic patterns. The most marked feature was the enrichment of genes involved in sulfur cycling, especially the production of sulfite from organic sulfur-containing compounds. Our study provides an updated view of the genomic traits and metabolic potential of Halorubrum and expands the range of sources of cold-adapted haloarchaea. |
| first_indexed | 2024-03-10T22:15:15Z |
| format | Article |
| id | doaj.art-449ffd3583e244cf9fef41d102978d89 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:15Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-449ffd3583e244cf9fef41d102978d892023-11-19T12:28:04ZengBMCBMC Genomics1471-21642023-08-0124111310.1186/s12864-023-09597-7Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environmentsLiangzhong Chen0Tao Hong1Zirui Wu2Weizhi Song3Shaoxing X. Chen4Yongqin Liu5Liang Shen6College of Life Sciences, Anhui Normal UniversityCollege of Life Sciences, Anhui Normal UniversityCollege of Life Sciences, Anhui Normal UniversityCentre for Marine Bio-Innovation, University of New South WalesCollege of Life Sciences, Anhui Normal UniversityCenter for the Pan-third Pole Environment, Lanzhou UniversityCollege of Life Sciences, Anhui Normal UniversityAbstract Background Cold-adapted archaea have diverse ecological roles in a wide range of low-temperature environments. Improving our knowledge of the genomic features that enable psychrophiles to grow in cold environments helps us to understand their adaptive responses. However, samples from typical cold regions such as the remote Arctic and Antarctic are rare, and the limited number of high-quality genomes available leaves us with little data on genomic traits that are statistically associated with cold environmental conditions. Results In this study, we examined the haloarchaeal genus Halorubrum and defined a new clade that represents six isolates from polar and deep earth environments (‘PD group’ hereafter). The genomic G + C content and amino acid composition of this group distinguishes it from other Halorubrum and the trends are consistent with the established genomic optimization of psychrophiles. The cold adaptation of the PD group was further supported by observations of increased flexibility of proteins encoded across the genome and the findings of a growth test. Conclusions The PD group Halorubrum exhibited denser genome packing, which confers higher metabolic potential with constant genome size, relative to the reference group, resulting in significant differences in carbon, nitrogen and sulfur metabolic patterns. The most marked feature was the enrichment of genes involved in sulfur cycling, especially the production of sulfite from organic sulfur-containing compounds. Our study provides an updated view of the genomic traits and metabolic potential of Halorubrum and expands the range of sources of cold-adapted haloarchaea.https://doi.org/10.1186/s12864-023-09597-7GenomicsCold adaptationPolar and deep Earth environmentsMicrobial adaptationHypersaline environments |
| spellingShingle | Liangzhong Chen Tao Hong Zirui Wu Weizhi Song Shaoxing X. Chen Yongqin Liu Liang Shen Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments BMC Genomics Genomics Cold adaptation Polar and deep Earth environments Microbial adaptation Hypersaline environments |
| title | Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments |
| title_full | Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments |
| title_fullStr | Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments |
| title_full_unstemmed | Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments |
| title_short | Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments |
| title_sort | genomic analyses reveal a low temperature adapted clade in halorubrum a widespread haloarchaeon across global hypersaline environments |
| topic | Genomics Cold adaptation Polar and deep Earth environments Microbial adaptation Hypersaline environments |
| url | https://doi.org/10.1186/s12864-023-09597-7 |
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