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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ftdoajarticles:oai:doaj.org/article:22d11cdb2c0046d198b3a81281db26eb 2023-05-15T18:21:08+02:00 Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. Brandon K Swan Mark D Chaffin Manuel Martinez-Garcia Hilary G Morrison Erin K Field Nicole J Poulton E Dashiell P Masland Christopher C Harris Alexander Sczyrba Patrick S G Chain Sergey Koren Tanja Woyke Ramunas Stepanauskas 2014-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0095380 https://doaj.org/article/22d11cdb2c0046d198b3a81281db26eb EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC3990693?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0095380 https://doaj.org/article/22d11cdb2c0046d198b3a81281db26eb PLoS ONE, Vol 9, Iss 4, p e95380 (2014) Medicine R Science Q article 2014 ftdoajarticles https://doi.org/10.1371/journal.pone.0095380 2022-12-31T16:26:48Z 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 Directory of Open Access Journals: DOAJ Articles Pacific PLoS ONE 9 4 e95380 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Brandon K Swan Mark D Chaffin Manuel Martinez-Garcia Hilary G Morrison Erin K Field Nicole J Poulton E Dashiell P Masland Christopher C Harris Alexander Sczyrba Patrick S G Chain Sergey Koren Tanja Woyke Ramunas Stepanauskas Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. |
topic_facet |
Medicine R Science Q |
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. |
format |
Article in Journal/Newspaper |
author |
Brandon K Swan Mark D Chaffin Manuel Martinez-Garcia Hilary G Morrison Erin K Field Nicole J Poulton E Dashiell P Masland Christopher C Harris Alexander Sczyrba Patrick S G Chain Sergey Koren Tanja Woyke Ramunas Stepanauskas |
author_facet |
Brandon K Swan Mark D Chaffin Manuel Martinez-Garcia Hilary G Morrison Erin K Field Nicole J Poulton E Dashiell P Masland Christopher C Harris Alexander Sczyrba Patrick S G Chain Sergey Koren Tanja Woyke Ramunas Stepanauskas |
author_sort |
Brandon K Swan |
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 (PLoS) |
publishDate |
2014 |
url |
https://doi.org/10.1371/journal.pone.0095380 https://doaj.org/article/22d11cdb2c0046d198b3a81281db26eb |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
South Atlantic Ocean |
genre_facet |
South Atlantic Ocean |
op_source |
PLoS ONE, Vol 9, Iss 4, p e95380 (2014) |
op_relation |
http://europepmc.org/articles/PMC3990693?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0095380 https://doaj.org/article/22d11cdb2c0046d198b3a81281db26eb |
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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1766200252550873088 |