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PLoS One. 2014 Apr 17;9(4):e95380. doi: 10.1371/journal.pone.0095380. eCollection 2014.

Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres.

Author information

1
Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America.
2
Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America; Department of Biology, Colby College, Waterville, Maine, United States of America.
3
Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain.
4
Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Massachusetts, United States of America.
5
Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
6
Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America; Joint Genome Institute, Walnut Creek, California, United States of America.
7
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America; National Biodefense Analysis and Countermeasures Center, Frederick, Maryland, United States of America.
8
Joint Genome Institute, Walnut Creek, California, United States of America.

Abstract

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.

PMID:
24743558
PMCID:
PMC3990693
DOI:
10.1371/journal.pone.0095380
[Indexed for MEDLINE]
Free PMC Article
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