Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres
The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e95380, doi:10.1371/journal.pone.0095380. Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global...
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ftwhoas:oai:darchive.mblwhoilibrary.org:1912/6692 2023-05-15T18:21:17+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 image/tiff application/pdf https://hdl.handle.net/1912/6692 en_US eng Public Library of Science https://doi.org/10.1371/journal.pone.0095380 PLoS One 9 (2014): e95380 https://hdl.handle.net/1912/6692 doi:10.1371/journal.pone.0095380 Public Domain Dedication http://creativecommons.org/publicdomain/zero/1.0/ PDM CC0 PLoS One 9 (2014): e95380 doi:10.1371/journal.pone.0095380 Article 2014 ftwhoas https://doi.org/10.1371/journal.pone.0095380 2022-05-28T22:59:07Z The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e95380, doi:10.1371/journal.pone.0095380. 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. This work was supported by NSF grants EF-826924 (R.S.), OCE-821374 (R.S.) and OCE-1232982 (R.S. and B.K.S.); the DOE JGI 2010 Microbes Program grant CSP77 (R.S. and M.E.S.); National Institutes of Health grant 1UH2DK083993 (H.G.M.). Work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of ... Article in Journal/Newspaper South Atlantic Ocean Woods Hole Scientific Community: WHOAS (Woods Hole Open Access Server) Pacific PLoS ONE 9 4 e95380 |
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Woods Hole Scientific Community: WHOAS (Woods Hole Open Access Server) |
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English |
description |
The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e95380, doi:10.1371/journal.pone.0095380. 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. This work was supported by NSF grants EF-826924 (R.S.), OCE-821374 (R.S.) and OCE-1232982 (R.S. and B.K.S.); the DOE JGI 2010 Microbes Program grant CSP77 (R.S. and M.E.S.); National Institutes of Health grant 1UH2DK083993 (H.G.M.). Work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of ... |
format |
Article in Journal/Newspaper |
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 |
spellingShingle |
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 |
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 |
https://hdl.handle.net/1912/6692 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
South Atlantic Ocean |
genre_facet |
South Atlantic Ocean |
op_source |
PLoS One 9 (2014): e95380 doi:10.1371/journal.pone.0095380 |
op_relation |
https://doi.org/10.1371/journal.pone.0095380 PLoS One 9 (2014): e95380 https://hdl.handle.net/1912/6692 doi:10.1371/journal.pone.0095380 |
op_rights |
Public Domain Dedication http://creativecommons.org/publicdomain/zero/1.0/ |
op_rightsnorm |
PDM CC0 |
op_doi |
https://doi.org/10.1371/journal.pone.0095380 |
container_title |
PLoS ONE |
container_volume |
9 |
container_issue |
4 |
container_start_page |
e95380 |
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1766200463025242112 |