Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres
Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic an...
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ftpubmed:oai:pubmedcentral.nih.gov:3990693 2023-05-15T18:21:08+02:00 Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres Swan, Brandon K. Chaffin, Mark D. Martinez-Garcia, Manuel Morrison, Hilary G. Field, Erin K. Poulton, Nicole J. Masland, E. Dashiell P. Harris, Christopher C. Sczyrba, Alexander Chain, Patrick S. G. Koren, Sergey Woyke, Tanja Stepanauskas, Ramunas 2014-04-17 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990693 http://www.ncbi.nlm.nih.gov/pubmed/24743558 https://doi.org/10.1371/journal.pone.0095380 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990693 http://www.ncbi.nlm.nih.gov/pubmed/24743558 http://dx.doi.org/10.1371/journal.pone.0095380 This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. PDM CC0 Research Article Text 2014 ftpubmed https://doi.org/10.1371/journal.pone.0095380 2014-04-27T00:43:50Z Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures. Text South Atlantic Ocean PubMed Central (PMC) Pacific PLoS ONE 9 4 e95380 |
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Research Article Swan, Brandon K. Chaffin, Mark D. Martinez-Garcia, Manuel Morrison, Hilary G. Field, Erin K. Poulton, Nicole J. Masland, E. Dashiell P. Harris, Christopher C. Sczyrba, Alexander Chain, Patrick S. G. Koren, Sergey Woyke, Tanja Stepanauskas, Ramunas Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres |
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Research Article |
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Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures. |
format |
Text |
author |
Swan, Brandon K. Chaffin, Mark D. Martinez-Garcia, Manuel Morrison, Hilary G. Field, Erin K. Poulton, Nicole J. Masland, E. Dashiell P. Harris, Christopher C. Sczyrba, Alexander Chain, Patrick S. G. Koren, Sergey Woyke, Tanja Stepanauskas, Ramunas |
author_facet |
Swan, Brandon K. Chaffin, Mark D. Martinez-Garcia, Manuel Morrison, Hilary G. Field, Erin K. Poulton, Nicole J. Masland, E. Dashiell P. Harris, Christopher C. Sczyrba, Alexander Chain, Patrick S. G. Koren, Sergey Woyke, Tanja Stepanauskas, Ramunas |
author_sort |
Swan, Brandon K. |
title |
Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres |
title_short |
Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres |
title_full |
Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres |
title_fullStr |
Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres |
title_full_unstemmed |
Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres |
title_sort |
genomic and metabolic diversity of marine group i thaumarchaeota in the mesopelagic of two subtropical gyres |
publisher |
Public Library of Science |
publishDate |
2014 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990693 http://www.ncbi.nlm.nih.gov/pubmed/24743558 https://doi.org/10.1371/journal.pone.0095380 |
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Pacific |
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Pacific |
genre |
South Atlantic Ocean |
genre_facet |
South Atlantic Ocean |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990693 http://www.ncbi.nlm.nih.gov/pubmed/24743558 http://dx.doi.org/10.1371/journal.pone.0095380 |
op_rights |
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. |
op_rightsnorm |
PDM CC0 |
op_doi |
https://doi.org/10.1371/journal.pone.0095380 |
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PLoS ONE |
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9 |
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4 |
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e95380 |
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