Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment
BACKGROUND: Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated...
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ftpubmed:oai:pubmedcentral.nih.gov:9580203 2023-05-15T13:32:47+02:00 Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment Liu, Wenqi Cong, Bailin Lin, Jing Zhao, Linlin Liu, Shenghao 2022-10-19 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580203/ https://doi.org/10.1186/s12864-022-08942-6 en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580203/ http://dx.doi.org/10.1186/s12864-022-08942-6 © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. CC0 PDM CC-BY BMC Genomics Research Text 2022 ftpubmed https://doi.org/10.1186/s12864-022-08942-6 2022-10-23T01:13:11Z BACKGROUND: Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated in order to understand nitrogen cycling involved in the deep-sea environment. RESULTS: In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 and Halomonas profundus 13 genome sizes are 4,160,095 bp with a GC content of 62.5% and 5,251,450 bp with a GC content of 54.84%. Through a comparison of functional analyses, we predicted the possible C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 could use more carbon sources than Cobetia amphilecti N-80. The main genes associated with N metabolism in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, nosZ, and nirD. On the contrast, nirD, using NH(4)(+) for energy, plays a main role in Cobetia amphilecti N-80. Both of them have the same genes for fixing inorganic carbon: icd, ppc, fdhA, accC, accB, accD, and accA. CONCLUSION: In this study, the whole genomes of two strains were sequenced to clarify the basic characteristics of their genomes, laying the foundation for further studying nitrogen-metabolizing bacteria. Halomonas profundus 13 can utilize more carbon sources than Cobetia amphilecti N-80, as indicated by API as well as COG and KEGG prediction results. Finally, through the analysis of the nitrification and denitrification abilities as well as the inorganic carbon fixation ability of the two strains, the related genes were identified, and the possible metabolic pathways were predicted. Together, these results provide molecular markers and theoretical support for the mechanisms of inorganic carbon fixation by deep-sea microorganisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at ... Text Antarc* Antarctic PubMed Central (PMC) Antarctic BMC Genomics 23 1 |
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Research Liu, Wenqi Cong, Bailin Lin, Jing Zhao, Linlin Liu, Shenghao Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment |
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Research |
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BACKGROUND: Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated in order to understand nitrogen cycling involved in the deep-sea environment. RESULTS: In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 and Halomonas profundus 13 genome sizes are 4,160,095 bp with a GC content of 62.5% and 5,251,450 bp with a GC content of 54.84%. Through a comparison of functional analyses, we predicted the possible C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 could use more carbon sources than Cobetia amphilecti N-80. The main genes associated with N metabolism in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, nosZ, and nirD. On the contrast, nirD, using NH(4)(+) for energy, plays a main role in Cobetia amphilecti N-80. Both of them have the same genes for fixing inorganic carbon: icd, ppc, fdhA, accC, accB, accD, and accA. CONCLUSION: In this study, the whole genomes of two strains were sequenced to clarify the basic characteristics of their genomes, laying the foundation for further studying nitrogen-metabolizing bacteria. Halomonas profundus 13 can utilize more carbon sources than Cobetia amphilecti N-80, as indicated by API as well as COG and KEGG prediction results. Finally, through the analysis of the nitrification and denitrification abilities as well as the inorganic carbon fixation ability of the two strains, the related genes were identified, and the possible metabolic pathways were predicted. Together, these results provide molecular markers and theoretical support for the mechanisms of inorganic carbon fixation by deep-sea microorganisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at ... |
format |
Text |
author |
Liu, Wenqi Cong, Bailin Lin, Jing Zhao, Linlin Liu, Shenghao |
author_facet |
Liu, Wenqi Cong, Bailin Lin, Jing Zhao, Linlin Liu, Shenghao |
author_sort |
Liu, Wenqi |
title |
Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment |
title_short |
Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment |
title_full |
Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment |
title_fullStr |
Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment |
title_full_unstemmed |
Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment |
title_sort |
complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from antarctic deep-sea sediment |
publisher |
BioMed Central |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580203/ https://doi.org/10.1186/s12864-022-08942-6 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
BMC Genomics |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580203/ http://dx.doi.org/10.1186/s12864-022-08942-6 |
op_rights |
© The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
op_rightsnorm |
CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s12864-022-08942-6 |
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BMC Genomics |
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23 |
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