Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans
BackgroundPhytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genome...
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ftcdlib:oai:escholarship.org:ark:/13030/qt67v1k0x0 2023-10-01T03:52:58+02:00 Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans Duncan, Anthony Barry, Kerrie Daum, Chris Eloe-Fadrosh, Emiley Roux, Simon Schmidt, Katrin Tringe, Susannah G Valentin, Klaus U Varghese, Neha Salamov, Asaf Grigoriev, Igor V Leggett, Richard M Moulton, Vincent Mock, Thomas 67 2022-01-01 https://escholarship.org/uc/item/67v1k0x0 unknown eScholarship, University of California qt67v1k0x0 https://escholarship.org/uc/item/67v1k0x0 public Microbiome, vol 10, iss 1 Genetics Human Genome Life Below Water Atlantic Ocean Chlorophyll A Eukaryota Metagenome Microbiota Phylogeny Phytoplankton Ecology Microbiology Medical Microbiology article 2022 ftcdlib 2023-09-04T18:04:30Z BackgroundPhytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes.ResultsHere, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51-88% MAGs in common with most species associations between Prasinophytes and Proteobacteria. Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic.ConclusionOur study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean. Video Abstract. Article in Journal/Newspaper Arctic Phytoplankton University of California: eScholarship Arctic |
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Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Genetics Human Genome Life Below Water Atlantic Ocean Chlorophyll A Eukaryota Metagenome Microbiota Phylogeny Phytoplankton Ecology Microbiology Medical Microbiology |
spellingShingle |
Genetics Human Genome Life Below Water Atlantic Ocean Chlorophyll A Eukaryota Metagenome Microbiota Phylogeny Phytoplankton Ecology Microbiology Medical Microbiology Duncan, Anthony Barry, Kerrie Daum, Chris Eloe-Fadrosh, Emiley Roux, Simon Schmidt, Katrin Tringe, Susannah G Valentin, Klaus U Varghese, Neha Salamov, Asaf Grigoriev, Igor V Leggett, Richard M Moulton, Vincent Mock, Thomas Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans |
topic_facet |
Genetics Human Genome Life Below Water Atlantic Ocean Chlorophyll A Eukaryota Metagenome Microbiota Phylogeny Phytoplankton Ecology Microbiology Medical Microbiology |
description |
BackgroundPhytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes.ResultsHere, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51-88% MAGs in common with most species associations between Prasinophytes and Proteobacteria. Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic.ConclusionOur study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean. Video Abstract. |
format |
Article in Journal/Newspaper |
author |
Duncan, Anthony Barry, Kerrie Daum, Chris Eloe-Fadrosh, Emiley Roux, Simon Schmidt, Katrin Tringe, Susannah G Valentin, Klaus U Varghese, Neha Salamov, Asaf Grigoriev, Igor V Leggett, Richard M Moulton, Vincent Mock, Thomas |
author_facet |
Duncan, Anthony Barry, Kerrie Daum, Chris Eloe-Fadrosh, Emiley Roux, Simon Schmidt, Katrin Tringe, Susannah G Valentin, Klaus U Varghese, Neha Salamov, Asaf Grigoriev, Igor V Leggett, Richard M Moulton, Vincent Mock, Thomas |
author_sort |
Duncan, Anthony |
title |
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans |
title_short |
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans |
title_full |
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans |
title_fullStr |
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans |
title_full_unstemmed |
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans |
title_sort |
metagenome-assembled genomes of phytoplankton microbiomes from the arctic and atlantic oceans |
publisher |
eScholarship, University of California |
publishDate |
2022 |
url |
https://escholarship.org/uc/item/67v1k0x0 |
op_coverage |
67 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Phytoplankton |
genre_facet |
Arctic Phytoplankton |
op_source |
Microbiome, vol 10, iss 1 |
op_relation |
qt67v1k0x0 https://escholarship.org/uc/item/67v1k0x0 |
op_rights |
public |
_version_ |
1778519244232720384 |