Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment
Glaciers have been recognized as biomes, dominated by microbial life. Many novel species have been isolated from glacier ecosystems, and their physiological features are well characterized. However, genomic features of bacteria isolated from the deep ice core are poorly understood. In this study, we...
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ftmdpi:oai:mdpi.com:/2076-2607/7/7/211/ 2023-08-20T04:07:11+02:00 Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment Liang Shen Yongqin Liu Ninglian Wang Namita Paudel Adhikari agris 2019-07-22 application/pdf https://doi.org/10.3390/microorganisms7070211 EN eng Multidisciplinary Digital Publishing Institute Environmental Microbiology https://dx.doi.org/10.3390/microorganisms7070211 https://creativecommons.org/licenses/by/4.0/ Microorganisms; Volume 7; Issue 7; Pages: 211 glacier ice core genomics Dyadobacter Text 2019 ftmdpi https://doi.org/10.3390/microorganisms7070211 2023-07-31T22:27:22Z Glaciers have been recognized as biomes, dominated by microbial life. Many novel species have been isolated from glacier ecosystems, and their physiological features are well characterized. However, genomic features of bacteria isolated from the deep ice core are poorly understood. In this study, we performed a comparative genomic analysis to uncover the genomic features of strain Dyadobacter tibetensis Y620-1 isolated from a 59 m depth of the ice core drilled from a Tibetan Plateau glacier. Strain D. tibetensis Y620-1 had the smallest genome among the 12 cultured Dyadobacter strains, relatively low GC content, and was placed at the root position of the phylogenomic tree. The gene family based on a nonmetric multidimensional scaling (NMDS) plot revealed a clear separation of strain D. tibetensis Y620-1 from the reference strains. The genome of the deep ice core isolated strain contained the highest percentage of new genes. The definitive difference is that all genes required for the serine-glyoxylate cycle in one-carbon metabolism were only found in strain D. tibetensis Y620-1, but not in any of the reference strains. The placement of strain D. tibetensis Y620-1 in the root of the phylogenomic tree suggests that these new genes and functions are of ancient origin. All of these genomic features may contribute to the survival of D. tibetensis Y620-1 in the glacier. Text ice core MDPI Open Access Publishing Microorganisms 7 7 211 |
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Open Polar |
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MDPI Open Access Publishing |
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English |
topic |
glacier ice core genomics Dyadobacter |
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glacier ice core genomics Dyadobacter Liang Shen Yongqin Liu Ninglian Wang Namita Paudel Adhikari Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment |
topic_facet |
glacier ice core genomics Dyadobacter |
description |
Glaciers have been recognized as biomes, dominated by microbial life. Many novel species have been isolated from glacier ecosystems, and their physiological features are well characterized. However, genomic features of bacteria isolated from the deep ice core are poorly understood. In this study, we performed a comparative genomic analysis to uncover the genomic features of strain Dyadobacter tibetensis Y620-1 isolated from a 59 m depth of the ice core drilled from a Tibetan Plateau glacier. Strain D. tibetensis Y620-1 had the smallest genome among the 12 cultured Dyadobacter strains, relatively low GC content, and was placed at the root position of the phylogenomic tree. The gene family based on a nonmetric multidimensional scaling (NMDS) plot revealed a clear separation of strain D. tibetensis Y620-1 from the reference strains. The genome of the deep ice core isolated strain contained the highest percentage of new genes. The definitive difference is that all genes required for the serine-glyoxylate cycle in one-carbon metabolism were only found in strain D. tibetensis Y620-1, but not in any of the reference strains. The placement of strain D. tibetensis Y620-1 in the root of the phylogenomic tree suggests that these new genes and functions are of ancient origin. All of these genomic features may contribute to the survival of D. tibetensis Y620-1 in the glacier. |
format |
Text |
author |
Liang Shen Yongqin Liu Ninglian Wang Namita Paudel Adhikari |
author_facet |
Liang Shen Yongqin Liu Ninglian Wang Namita Paudel Adhikari |
author_sort |
Liang Shen |
title |
Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment |
title_short |
Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment |
title_full |
Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment |
title_fullStr |
Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment |
title_full_unstemmed |
Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment |
title_sort |
genomic insights of dyadobacter tibetensis y620-1 isolated from ice core reveal genomic features for succession in glacier environment |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2019 |
url |
https://doi.org/10.3390/microorganisms7070211 |
op_coverage |
agris |
genre |
ice core |
genre_facet |
ice core |
op_source |
Microorganisms; Volume 7; Issue 7; Pages: 211 |
op_relation |
Environmental Microbiology https://dx.doi.org/10.3390/microorganisms7070211 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/microorganisms7070211 |
container_title |
Microorganisms |
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7 |
container_issue |
7 |
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211 |
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1774718645181612032 |