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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Online Access: | https://escholarship.org/uc/item/7jt0j6fp https://escholarship.org/content/qt7jt0j6fp/qt7jt0j6fp.pdf https://doi.org/10.1371/journal.pone.0095380 |
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ftcdlib:oai:escholarship.org:ark:/13030/qt7jt0j6fp 2024-09-15T18:36:28+00:00 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 SG Koren, Sergey Woyke, Tanja Stepanauskas, Ramunas Randau, Lennart e95380 2014-01-01 application/pdf https://escholarship.org/uc/item/7jt0j6fp https://escholarship.org/content/qt7jt0j6fp/qt7jt0j6fp.pdf https://doi.org/10.1371/journal.pone.0095380 unknown eScholarship, University of California qt7jt0j6fp https://escholarship.org/uc/item/7jt0j6fp https://escholarship.org/content/qt7jt0j6fp/qt7jt0j6fp.pdf doi:10.1371/journal.pone.0095380 public PLOS ONE, vol 9, iss 4 Microbiology Oceanography Biological Sciences Earth Sciences Biotechnology Human Genome Genetics Life Below Water Archaea DNA Archaeal Phylogeny General Science & Technology article 2014 ftcdlib https://doi.org/10.1371/journal.pone.0095380 2024-08-15T23:46:56Z 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. Article in Journal/Newspaper South Atlantic Ocean University of California: eScholarship PLoS ONE 9 4 e95380 |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Microbiology Oceanography Biological Sciences Earth Sciences Biotechnology Human Genome Genetics Life Below Water Archaea DNA Archaeal Phylogeny General Science & Technology |
spellingShingle |
Microbiology Oceanography Biological Sciences Earth Sciences Biotechnology Human Genome Genetics Life Below Water Archaea DNA Archaeal Phylogeny General Science & Technology 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 SG Koren, Sergey Woyke, Tanja Stepanauskas, Ramunas Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres |
topic_facet |
Microbiology Oceanography Biological Sciences Earth Sciences Biotechnology Human Genome Genetics Life Below Water Archaea DNA Archaeal Phylogeny General Science & Technology |
description |
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. |
author2 |
Randau, Lennart |
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 SG 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 SG 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 |
eScholarship, University of California |
publishDate |
2014 |
url |
https://escholarship.org/uc/item/7jt0j6fp https://escholarship.org/content/qt7jt0j6fp/qt7jt0j6fp.pdf https://doi.org/10.1371/journal.pone.0095380 |
op_coverage |
e95380 |
genre |
South Atlantic Ocean |
genre_facet |
South Atlantic Ocean |
op_source |
PLOS ONE, vol 9, iss 4 |
op_relation |
qt7jt0j6fp https://escholarship.org/uc/item/7jt0j6fp https://escholarship.org/content/qt7jt0j6fp/qt7jt0j6fp.pdf doi:10.1371/journal.pone.0095380 |
op_rights |
public |
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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1810480128765984768 |